# DRAGEN Publications The following list of selected publications summarizes the extensive applications of Illumina DRAGEN Secondary Analysis Software. Expand each section to view publications by year.
2025 | Title | Publisher / Link | Application area | | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------- | | Evaluation of false positive and false negative errors in targeted next generation sequencing | Genome Biology / [link](https://pmc.ncbi.nlm.nih.gov/articles/PMC12670792/) | Oncology | | Genomics of Acute Myeloid Leukemia at Diagnosis and Remission | medRxiv / [link](https://www.medrxiv.org/content/10.64898/2025.12.04.25340141v1) | Oncology | | Whole-genome sequencing of 490,640 UK Biobank participants | Nature / [link](https://www.nature.com/articles/s41586-025-09272-9) | Population Genomics | | Characterization of subclonal variants in HG002 Genome in a Bottle reference material as a resource for benchmarking variant callers | Cell Genomics / [link](https://github.com/illumina-swi/dragen-docs/blob/release/4.5-prod/reference/\[https:/www.nature.com/articles/s41586-025-09272-9]\(https:/doi.org/10.1016/j.xgen.2025.101104\)) | Benchmarking | | Comprehensive investigation of gene mutations in canine large cell gastrointestinal lymphoma | Frontiers in Veterinary Science / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11880205/) | Oncology | |

Comparisons of performances of structural variants detection algorithms in solitary or combination strategy

| PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0314982#pone-0314982-t004) | Population Genomics | |

Comparative genomics reveals phylogenetic intermixing of Stomoxys fly, manure, and bovine mastitis-associated bacteria in dairy settings

| biorxiv / [link](https://www.biorxiv.org/content/10.1101/2025.01.31.635862v1) | Population Genomics | |

Comparative analysis of the Mexico City Prospective Study and the UK Biobank identifies ancestry-specific effects on clonal hematopoiesis

| nature genetics / [link](https://www.nature.com/articles/s41588-025-02085-6) | Population Genomics | |

Clinical characteristics of the Ala21Val variant in the myelin proteolipid protein 1 (PLP1) gene associated with Pelizaeus-Merzbacher disease in a Brazilian male patient

| Human Genome Variation / [link](https://www.nature.com/articles/s41439-024-00306-8) | Genetic Disease | |

Classification of acute myeloid leukemia based on multi-omics and prognosis prediction value

| Molecular Oncology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/1878-0261.70000) | Oncology | |

CIROZ is dispensable in ancestral vertebrates but essential for left-right patterning in humans

| The American Journal of Human Genetics / [link](https://www.cell.com/ajhg/abstract/S0002-9297\(24\)00448-8) | Genetic Disease | |

Case Report: Importance of high-throughput genetic investigations in the differential diagnosis of unexplained erythrocytosis

| National Library of Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11930660/) | Genetic Disease | |

Building a growing genomic repository for maternal and fetal health through the PING Consortium

| Nature / [link](https://www.nature.com/articles/s41390-024-03793-1) | Genetic Disease | |

Blood DNA virome associates with autoimmune diseases and COVID-19

| nature genetics / [link](https://www.nature.com/articles/s41588-024-02022-z) | Population Genomics | |

Bi-Allelic MARVELD2 Variant Identified with Exome Sequencing in a Consanguineous Multiplex Ghanaian Family Segregating Non-Syndromic Hearing Loss

| MDPI / [link](https://www.mdpi.com/1422-0067/26/7/3337) | Genetic Disease | |

Beyond the BRCA1/2 genes in ovarian cancer: the
clinical and prognostic role of germline pathogenic
variants in the ATM gene

| Research Square / [link](https://www.researchsquare.com/article/rs-5769485/v1) | Genetic Disease | |

Beneficial mutualistic fungus Suillus luteus provided excellent buffering insurance in Scots pine defense responses under pathogen challenge at transcriptome level

| BMC Plant Biology / [link](https://doi.org/10.1186/s12870-024-06026-z) | Genomic Factory | | Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications | Bioinformatics Advances / [link](https://doi.org/10.1093/bioadv/vbaf071) | Genomic Factory | |

Bacteriophage Treatment Induces Phenotype Switching and Alters Antibiotic Resistance of ESBL Escherichia coli

| MDPI / [link](https://www.mdpi.com/2079-6382/14/1/76) | Genomic Factory | | BACH2 regulates T cell lineage states to overcome dysfunction driven by tonic CAR signaling | Research Square / [link](https://www.researchsquare.com/article/rs-5845875/v1) | Oncology | | Assessment of candidate high-grade serous ovarian carcinoma predisposition genes through integrated germline and tumour sequencing | npj Genomic Medicine / [link](https://www.nature.com/articles/s41525-024-00447-3) | Genetic Disease | | Assessing the Impact of Cell Isolation Method on B cell Gene Expression using Next-Generation Sequencing | Experimental Hematology / [link](https://www.sciencedirect.com/science/article/pii/S0301472X25000578) | Genomic Factory | | Assessing the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases | Nature Communications / [link](https://www.nature.com/articles/s41467-025-56944-1) | Genetic Disease | | Asian diversity in human immune cells | Cell / [link](https://www.cell.com/cell/abstract/S0092-8674\(25\)00202-8) | Population Genomics | |

APOBEC3A drives ovarian cancer metastasis by altering epithelial-mesenchymal transition

| JCI Insight / [link](https://insight.jci.org/articles/view/186409) | Oncology | |

Analysis of Population-Level Avirulence and Virulence Genetic Frequencies Provides Insight Into Resistance Gene Rotation and Plant Disease Epidemiology

| Plant Pathology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/ppa.14072) | Population Genomics | | An orally available P1′-5-fluorinated Mpro inhibitor blocks SARS-CoV-2 replication without booster and exhibits high genetic barrier | PNAS Nexus / [link](https://academic.oup.com/pnasnexus/article/doi/10.1093/pnasnexus/pgae578/7944109) | Genomic Factory | |

An Exploratory Genomic and Transcriptomic Analysis Between Choloepus didactylus and Homo sapiens

| Genes / [link](https://www.mdpi.com/2073-4425/16/3/272) | Genomic Factory | | AMPed up immunity: 418 whole genomes reveal intraspecific diversity of koala antimicrobial peptides | Immunogenetics / [link](https://link.springer.com/article/10.1007/s00251-024-01368-2) | Population Genomics | |

Adrenal mixed corticomedullary tumors: report of a case with molecular characterization and systematic review

| Virchows Archiv / [link](https://doi.org/10.1007/s00428-025-04091-9) | Oncology | | Activated cardiac fibroblasts are a primary source of high-molecular-weight hyaluronan production | American Journal of Physiology-Cell Physiology / [link](https://journals.physiology.org/doi/10.1152/ajpcell.00786.2024) | Genetic Disease | |

Acquired sperm hypomethylation by gestational arsenic exposure is re-established in both the paternal and maternal genomes of post-epigenetic reprogramming embryos

| Epigenetics & Chromatin / [link](https://doi.org/10.1186/s13072-025-00569-7) | Genetic Disease | |

A triad of somatic mutagenesis converges in self-reactive B cells to cause a virus-induced autoimmune disease

| Immunity / [link](https://www.cell.com/immunity/fulltext/S1074-7613\(24\)00575-2) | Genetic Disease | | A phase II trial of mTORC1/2 inhibition in STK11 deficient non small cell lung cancer | npj Precision Oncology / [link](https://www.nature.com/articles/s41698-025-00838-4) | Oncology | | A nationwide comprehensive genomic profiling and molecular tumor board platform for patients with advanced cancer | npj Precision Oncology / [link](https://www.nature.com/articles/s41698-025-00858-0) | Oncology | | A comparative template-switching cDNA approach for HTS-based multiplex detection of three viruses and one viroid commonly found in apple trees | Nature / [link](https://www.nature.com/articles/s41598-025-86065-0) | Genomic Factory | | Effect of DNA input on analytical and clinical parameters of a circulating tumor DNA assay for comprehensive genomic profiling | Journal of Laboratory Medicine / [link](https://www.degruyterbrill.com/document/doi/10.1515/labmed-2024-0110/html) | | | P260: Enhancing copy number variant analysis in exome sequencing with backbone probe optimization | -- / [link](https://www.sciencedirect.com/science/article/pii/S294977442500264X) | | | Identification of technically challenging variants: Whole-genome sequencing improves diagnostic yield in patients with high clinical suspicion of rare diseases | HGG Advances / [link](https://www.cell.com/hgg-advances/fulltext/S2666-2477\(25\)00072-7) | Genetic Disease | | Benchmarking of variant calling software for whole-exome sequencing using gold standard datasets | Nature / [link](https://www.nature.com/articles/s41598-025-97047-7) | | | Evaluating Discordant Somatic Calls Across Mutation Discovery Approaches to Minimize False-Negative Drug-Resistant Findings | The Journals of Molecular Diagnostics / [link](https://doi.org/10.1016/j.jmoldx.2025.04.012) | |
2024 | Title | Publisher / Link | Tags | | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------- | | Analysis of tumor mutational burden and mutational landscape comparing whole-exome sequencing and comprehensive genomic profiling in patients with resectable early-stage non-small-cell lung cancer | Therapeutic Advances in Medical Oncology / [link](https://journals.sagepub.com/doi/10.1177/17588359241240657) | v3.10; TMB | | Whole genome sequencing in paediatric channelopathy and cardiomyopathy | Frontiers in Cardiovascular Medicine / [link](https://www.frontiersin.org/articles/10.3389/fcvm.2024.1335527/full) | BSSH; Germline Pipeline; Joint genotyping; v3.9.5 | | Somatic CAG repeat instability in intermediate alleles of the HTT gene and its potential association with a clinical phenotype | European Journal of Human Genetics / [link](https://www.nature.com/articles/s41431-024-01546-6) | ExpansionHunter; Germline Pipeline | | Spectrum of genetic variants in bilateral sensorineural hearing loss | Frontiers in Genetics / [link](https://www.frontiersin.org/articles/10.3389/fgene.2024.1314535/full) | | | High fusion and cytopathy of SARS-CoV-2 variant B.1.640.1 | Journal of Virology / [link](https://journals.asm.org/doi/10.1128/jvi.01351-23) | COVIDSeq Test pipeline; DRAGEN server | | Interleukin‐4 induced 1 ‐mediated resistance to an immune checkpoint inhibitor through suppression of CD8 + T cell infiltration in melanoma | Cancer Science / [link](https://onlinelibrary.wiley.com/doi/10.1111/cas.16073) | BSSH; Differential Expression; RNA pipeline; v3.6.3 | | Oxytocin-induced birth causes sex-specific behavioral and brain connectivity changes in developing rat offspring | Iscience / [link](https://www.cell.com/iscience/pdf/S2589-0042\(24\)00181-0.pdf) | v3.9.3 | | Prevalence and impact of sarcopenia in individuals with heart failure with reduced ejection fraction (the SARC-HF study): A prospective observational study protocol | Plos one / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0300918) | BSSH; Enrichment pipeline | | PKHD1L1, a gene involved in the stereocilia coat, causes autosomal recessive nonsyndromic hearing loss | Human Genetics / [link](https://link.springer.com/10.1007/s00439-024-02649-2) | CNV pipeline | | LncRNAs expression profile in a family household cluster of COVID ‐19 patients | Journal of Cellular and Molecular Medicine / [link](https://onlinelibrary.wiley.com/doi/10.1111/jcmm.18226) | COVID Lineage App; v3.5.7; BSSH | | A protective role for type I interferon signaling following infection with Mycobacterium tuberculosis carrying the rifampicin drug resistance-conferring RpoB mutation H445Y | PLoS pathogens / [link](https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1012137) | RNA seq; v3.9.3 | | Successful skipping of abnormal pseudoexon by antisense oligonucleotides in vitro for a patient with beta-propeller protein-associated neurodegeneration | Scientific reports / [link](https://www.nature.com/articles/s41598-024-56704-z) | v3.5 | | A novel framework for human leukocyte antigen (HLA) genotyping using probe capture-based targeted next-generation sequencing and computational analysis | Computational and Structural Biotechnology Journal / [link](https://www.sciencedirect.com/science/article/pii/S2001037024000837) | v4.2.4 | | Genetics of psycho-emotional well-being: genome-wide association study and polygenic risk score analysis | Frontiers in Psychiatry / [link](https://www.frontiersin.org/articles/10.3389/fpsyt.2023.1188427/full) | | | Claudin-10 Expression and the Gene Expression Pattern of Thick Ascending Limb Cells | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/25/7/4008) | v3.10.11 | | Insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme | Nature Medicine / [link](https://www.nature.com/articles/s41591-023-02682-0) | alignment | | A Case of Maturity-Onset Diabetes of the Young With Complex Mutations | JCEM Case Reports / [link](https://academic.oup.com/jcemcr/article-abstract/2/3/luae031/7630301) | | | Whole-genome sequencing of tetraploid potato varieties reveals different strategies for drought tolerance | Scientific Reports / [link](https://www.nature.com/articles/s41598-024-55669-3) | DRAGEN-GATK | | Prospective cohort study of genomic newborn screening: BabyScreen+ pilot study protocol | BMJ open / [link](https://bmjopen.bmj.com/content/14/4/e081426.abstract) | | | SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation? | Frontiers in Microbiology / [link](https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1358258/full) | COVID Lineage App; v3.5.4 | | Detection of SARS-CoV-2 in Wastewater Associated with Scientific Stations in Antarctica and Possible Risk for Wildlife | Microorganisms / [link](https://www.mdpi.com/2076-2607/12/4/743) | COVID Lineage App | | Generation of murine tumor models refractory to αPD-1/-L1 therapies due to defects in antigen processing/presentation or IFNγ signaling using CRISPR/Cas9 | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0287733) | Somatic variant calling | | Chronic stress alters hepatic metabolism and thermodynamic respiratory efficiency affecting epigenetics in C57BL/6 mice | iScience / [link](https://linkinghub.elsevier.com/retrieve/pii/S2589004224004978) | Germline Pipeline; v3.9.5 | | Synchronous Epidermodysplasia Verruciformis and Intraepithelial Lesion of the Vulva Is Caused by Coinfection With Alpha-Human Papillomavirus and Beta-Human Papillomavirus Genotypes and Facilitated by Mutations in Cell-Mediated Immunity Genes | Archives of Pathology & Laboratory Medicine / [link](https://doi.org/10.5858/arpa.2023-0193-OA) | | | Immune infiltration, aggressive pathology, and poor survival outcomes in RECQL helicase deficient breast cancers | Neoplasia / [link](https://www.sciencedirect.com/science/article/pii/S1476558623000805) | Somatic pipeline; v4.0.3 | | Extending DeepTrio for sensitive detection of complex de novo mutation patterns | NAR Genomics and Bioinformatics / [link](https://doi.org/10.1093/nargab/lqae013) | v3.6 | | Spatial Mapping of Hematopoietic Clones in Human Bone Marrow | Blood Cancer Discovery / [link](https://doi.org/10.1158/2643-3230.BCD-23-0110) | alignment; v3.10.4 | | The contributions of deleterious rare alleles in NLRP12 and inflammasome-related genes to polymyalgia rheumatica | Scientific Reports / [link](https://www.nature.com/articles/s41598-024-51320-3) | | | Myxoid liposarcoma with nuclear pleomorphism: a clinicopathological and molecular study | Virchows Archiv / [link](https://doi.org/10.1007/s00428-023-03631-5) | RNA app | | Targeting cell-type-specific, choroid-peripheral immune signaling to treat age-related macular degeneration | Cell Reports Medicine / [link](https://linkinghub.elsevier.com/retrieve/pii/S2666379123005700) | alignment; DRAGEN server; v3.9.3 | | Two novel non-coding single nucleotide variants in the DNase1 hypersensitivity site of PRDM13 causing North Carolina macular dystrophy in Korea | Molecular Vision / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11006008/) | DRAGEN-GATK | | A Mutational Hotspot in The LAMP2 Gene: Unravelling Intrafamilial Phenotypic Variation and Global Distribution of The c.877C>T Variant: A Descriptive Study | Cell Journal (Yakhteh) / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10864773/) | | | iPSC-Derived Endothelial Cells Reveal LDLR Dysfunction and Dysregulated Gene Expression Profiles in Familial Hypercholesterolemia | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/25/2/689) | v3.9.5 | | Divergent HLA variations and heterogeneous expression but recurrent HLA loss-of- heterozygosity and common HLA-B and TAP transcriptional silencing across advanced pediatric solid cancers | Frontiers in Immunology / [link](https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1265469/full) | v3.10; HLA | | Secondary bone marrow graft loss after third-party virus-specific T cell infusion: Case report of a rare complication | Nature Communications / [link](https://www.nature.com/articles/s41467-024-47056-3) | BSSH; Germline Pipeline; v3.4.5 | | Changes in DNA methylation associated with a specific mode of delivery: a pilot study | Frontiers in Medicine / [link](https://www.frontiersin.org/articles/10.3389/fmed.2024.1291429/full) | Methylation pipeline | | Directing the migration of serum-free, ex vivo-expanded Vγ9Vδ2 T cells | Frontiers in Immunology / [link](https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1331322/full) | AWS; v3.10.4a | | Targeting TRIP13 in favorable histology Wilms tumor with nuclear export inhibitors synergizes with doxorubicin | Communications Biology / [link](https://www.nature.com/articles/s42003-024-06140-6) | v3.5.7 | | Immune evasion, infectivity, and fusogenicity of SARS-CoV-2 BA.2.86 and FLip variants | Cell / [link](https://linkinghub.elsevier.com/retrieve/pii/S0092867423014009) | COVID Lineage App | | Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state | Nature Communications / [link](https://www.nature.com/articles/s41467-023-42762-w) | DRAGEN server; v3.10 | | Mapping breast and prostate cancer in the Brazilian public health system: study protocol of the Onco-Genomas Brasil | Frontiers in Oncology / [link](https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2024.1350162/full) | alignment; v3.10.4 | | Disease-associated AIOLOS variants lead to immune deficiency/dysregulation by haploinsufficiency and redefine AIOLOS functional domains | The Journal of Clinical Investigation / [link](https://www.jci.org/articles/view/172573) | DNA pipeline | | A de novo nonsense variant in the DMD gene associated with X-linked dystrophin-deficient muscular dystrophy in a cat | Journal of Veterinary Internal Medicine / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/jvim.17078) | v4.0.3; joint genotyper | | Utility of polygenic scores across diverse diseases in a hospital cohort for predictive modeling | Nature Communications / [link](https://www.nature.com/articles/s41467-024-47472-5) | Genome pipeline | | Pediatric Chordoma: A Tale of Two Genomes | Molecular cancer research: MCR / [link](https://aacrjournals.org/mcr/article/doi/10.1158/1541-7786.MCR-23-0741/745133/Pediatric-Chordoma-A-Tale-of-Two-GenomesARID1B) | | | SALL4 deletion and kidney and cardiac defects associated with VACTERL association | Pediatric Nephrology / [link](https://link.springer.com/10.1007/s00467-024-06306-8) | v3.5 | | Functional variants in a TTTG microsatellite on 15q26.1 cause familial nonautoimmune thyroid abnormalities | Nature Genetics / [link](https://www.nature.com/articles/s41588-024-01735-5) | v3.9.5 | | Utility of long-read sequencing for All of Us | Nature Communications / [link](https://www.nature.com/articles/s41467-024-44804-3) | v3.4.12 | | Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort | Genetics in Medicine / [link](https://www.sciencedirect.com/science/article/pii/S1098360024000091) | | | DNA identification of monozygotic twins | Forensic Science International: Genetics / [link](https://www.sciencedirect.com/science/article/pii/S1872497323001734) | Somatic pipeline v4.0.3 | | Sequencing technologies and hardware-accelerated parallel computing transform computational genomics research | Frontiers in Bioinformatics / [link](https://www.frontiersin.org/articles/10.3389/fbinf.2024.1384497) | review | | Genome sequencing as a generic diagnostic strategy for rare disease | Genome Medicine / [link](https://doi.org/10.1186/s13073-024-01301-y) | v3.5.7; ExpansionHunter; Germline pipeline; SMA caller; CYP21A2 caller | | SARS-CoV-2 among liver transplant recipients: clinical course and mutational analysis | Journal of Clinical Virology Plus / [link](https://www.sciencedirect.com/science/article/pii/S2667038024000061) | | | COVID-19 associated pulmonary aspergillosis in critically-ill patients: a prospective multicenter study in the era of Delta and Omicron variants | Annals of Intensive Care / [link](https://doi.org/10.1186/s13613-024-01296-0) | COVIDSeq Test pipeline; DRAGEN server | | Phenotypic and transcriptional changes in lens epithelial cells following acute and fractionated ionizing radiation exposure | International Journal of Radiation Biology / [link](https://doi.org/10.1080/09553002.2023.2295965) | | | Novel hemizygous single-nucleotide duplication in RPGR in a patient with retinal dystrophy and sensorineural hearing loss | Molecular Genetics & Genomic Medicine / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/mgg3.2404) | CNV caller; Haplotype variant calling | | Simultaneous detection and characterization of common respiratory pathogens in wastewater through genomic sequencing | Water Research / [link](https://www.sciencedirect.com/science/article/pii/S004313542400513X) | RNA pathogen detection pipeline | | Germline mutations of homologous recombination genes and clinical outcomes in pancreatic cancer: a multicenter study in Taiwan | Journal of Biomedical Science / [link](https://doi.org/10.1186/s12929-024-01008-7) | BSSH; Enrichment app | | Inherited defects of piRNA biogenesis cause transposon de-repression, impaired spermatogenesis, and human male infertility | -- / [link](https://www.researchsquare.com/article/rs-3710476/latest) | v4.2 | | CpG methylation changes associated with hyperglycemia in type 1 diabetes occur at angiogenic glomerular and retinal gene loci | -- / [link](https://www.researchsquare.com/article/rs-3845834/latest) | Epigenome pipeline | | Mpox Viral Lineage Analysis and Technique Development Using Next-generation Sequencing Approach | The Journal of Infectious Diseases / [link](https://academic.oup.com/jid/article-abstract/229/Supplement_2/S163/7424306) | | | Large-scale DNA sequencing identifies rare variants associated with Systemic Lupus Erythematosus susceptibility in known risk genes | Gene / [link](https://www.sciencedirect.com/science/article/pii/S0378111924001604) | alignment; Variant calling | | Characterisation of a LINE-1 Insertion in the *RP1* Gene by Targeted Adaptive Nanopore Sequencing in a Family with Retinitis Pigmentosa | Human Mutation / [link](https://www.hindawi.com/journals/humu/2024/6580561/) | v3.9 | | Rare De Novo and Inherited Genes in Familial and Nonfamilial Pediatric Attention-Deficit/Hyperactivity Disorder | JAMA pediatrics / [link](https://jamanetwork.com/journals/jamapediatrics/article-abstract/2812165) | | | Treatment and prognostic implications of strong PD-L1 expression in primary hepatic sarcomatoid carcinoma | Immunotherapy / [link](https://www.futuremedicine.com/doi/abs/10.2217/imt-2023-0243) | | | Cellular and molecular alterations in a human hepatocellular in vitro model of nonalcoholic fatty liver disease development and stratification | Journal of Environmental Science and Health, Part C / [link](https://doi.org/10.1080/26896583.2023.2293493) | | | Cost-effectiveness of genetic testing of endocrine tumor patients using a comprehensive hereditary cancer gene panel | The Journal of Clinical Endocrinology & Metabolism / [link](https://doi.org/10.1210/clinem/dgae300) | v4.0.3; Germline pipeline | | Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives | Cells / [link](https://www.mdpi.com/2073-4409/13/6/504) | review | | The Application of Knowledge Engineering via the Use of a Biomimetic Digital Twin Ecosystem, Phenotype-Driven Variant Analysis, and Exome Sequencing to Understand the Molecular Mechanisms of Disease | The Journal of Molecular Diagnostics / [link](https://www.sciencedirect.com/science/article/pii/S152515782400062X) | Germline | | Photoperiod associated late flowering reaction norm: Dissecting loci and genomic-enviromic associated prediction in maize | Field Crops Research / [link](https://www.sciencedirect.com/science/article/pii/S0378429024001333) | Germline small variant caller | | Characterization of carboxylated cellulose nanofibrils and oligosaccharides from Kraft pulp fibers and their potential elicitor effect on the gene expression of *Capsicum annuum* | International Journal of Biological Macromolecules / [link](https://www.sciencedirect.com/science/article/pii/S0141813024020348) | RNA pipeline; Differential expression pipeline | | An Exome Capture-Based RNA-Sequencing Assay for Genome-Wide Identification and Prioritization of Clinically Important Fusions in Pediatric Tumors | The Journal of Molecular Diagnostics / [link](https://www.sciencedirect.com/science/article/pii/S152515782300274X) | v3.9.3 | | Validation of low-pass genome sequencing for prenatal diagnosis | Prenatal Diagnosis / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/pd.6525) | | | Analytical Performance Evaluation of a 523-Gene Circulating Tumor DNA Assay for Next-Generation Sequencing–Based Comprehensive Tumor Profiling in Liquid Biopsy Samples | The Journal of Molecular Diagnostics / [link](https://www.sciencedirect.com/science/article/pii/S1525157823002441) | TSO500 ctDNA v1.1; DRAGEN server v3 | | Whole genome sequencing followed by functional analysis of genomic deletion encompassing *ERCC8* and *NDUFAF2* genes in a non-consanguineous Indian family reveals dysfunctional mitochondrial bioenergetics leading to infant mortality | Mitochondrion / [link](https://www.sciencedirect.com/science/article/pii/S1567724924000023) | v3.3.1 | | *DPF2*-related Coffin-Siris syndrome type 7 in two generations | European Journal of Medical Genetics / [link](https://www.sciencedirect.com/science/article/pii/S1769721224000375) | v3.9 | | Beyond Single Diagnosis: Exploring Multidiagnostic Realities in Pediatric Patients through Genome Sequencing | Human Mutation / [link](https://www.hindawi.com/journals/humu/2024/9115364/) | Variant calling; alignment | | Whole-genome sequencing of Chromobacterium subtsugae strains exhibiting toxicity to Drosophila melanogaster | Microbiology Resource Announcements / [link](https://journals.asm.org/doi/full/10.1128/mra.00127-24) | v3.10.12 | | Gut microbiome composition: link between sports performance and protein absorption? | Journal of the International Society of Sports Nutrition / [link](https://www.tandfonline.com/doi/abs/10.1080/15502783.2023.2297992) | Metagenomics pipeline | | Performance of amplicon and capture based next-generation sequencing approaches for the epidemiological surveillance of Omicron SARS-CoV-2 and other variants of concern | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0289188) | | | PRKD1-related telangiectasia-ectodermal dysplasia-brachydactyly-cardiac anomaly syndrome: Case report and review of the literature | European Journal of Medical Genetics / [link](https://www.sciencedirect.com/science/article/pii/S176972122400034X) | | | Good Manufacturing Practice–compliant human induced pluripotent stem cells: from bench to putative clinical products | Cytotherapy / [link](https://www.sciencedirect.com/science/article/pii/S1465324924000707) | | | *PPP2R5D* heterozygous pathogenic variant causes early-onset parkinsonism and treatment implications: A case report | Parkinsonism & Related Disorders / [link](https://www.sciencedirect.com/science/article/pii/S135380202400988X) | DRAGEN-GATK | | Oncogenic cell tagging and single-cell transcriptomics reveal cell type-specific and time-resolved responses to Vhl inactivation in the kidney | Cancer Research / [link](https://doi.org/10.1158/0008-5472.CAN-23-3248) | BCL convert | | Strategies for diagnosis and management of CMMRD in low-resource countries: report of a Tunisian family | Familial Cancer / [link](https://doi.org/10.1007/s10689-024-00386-z) | Enrichment tool | | Sudden unexpected postnatal collapse and BUB1B mutation: first forensic case report | International Journal of Legal Medicine / [link](https://doi.org/10.1007/s00414-024-03231-1) | Germline | | Novel mutation of *COG5* in a Taiwanese girl with congenital disorders of glycosylation manifesting as developmental delay | Molecular Genetics and Metabolism Reports / [link](https://www.sciencedirect.com/science/article/pii/S2214426924000259) | alignment | | Intraarticular Nodular Fasciitis of the Elbow Confirmed by USP6-MYH9 Gene Fusion. | -- / [link](https://www.researchsquare.com/article/rs-4165855/latest) | fusion detection; RNA app | | Phase I/II study of the WEE1 inhibitor adavosertib (AZD1775) in combination with carboplatin in children with advanced malignancies: Arm C of the AcSé-ESMART trial | Clinical Cancer Research / [link](https://aacrjournals.org/clincancerres/article-abstract/30/4/741/734204) | | | Identification of a novel GNAS mutation in a family with pseudohypoparathyroidism type 1A | BMC Pediatrics / [link](https://doi.org/10.1186/s12887-024-04761-8) | Germline pipeline | | Biallelic NDUFA4 Deletion Causes Mitochondrial Complex IV Deficiency in a Patient with Leigh Syndrome | Genes / [link](https://www.mdpi.com/2073-4425/15/4/500) | DNA pipeline v3.9.3 | | Virus sequencing performance during the SARS-CoV-2 pandemic: a retrospective analysis of data from multiple rounds of external quality assessment in Austria | Frontiers in Molecular Biosciences / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10875003/) | | | Introducing Exome Sequencing as Part of the Diagnostic Algorithm for Pediatric Nephrology Patients in Bulgaria: A Single-Center Experience | Nephron / [link](https://doi.org/10.1159/000538172) | | | Leveraging Off-Target Reads in Panel Sequencing for Homologous Recombination Repair Deficiency Screening in Tumor | The Journal of Molecular Diagnostics / [link](https://www.sciencedirect.com/science/article/pii/S1525157824000606) | v3.10.9 | | Development and validation of a pharmacogenomics reporting workflow based on the illumina global screening array chip | Frontiers in Pharmacology / [link](https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2024.1349203/full) | v3.7.6 | | Management of SARS-CoV-2 and Persistent Viral Detection in Solid Organ Transplant Recipients | Current Pulmonology Reports / [link](https://doi.org/10.1007/s13665-024-00338-z) | COVID Lineage App | | Evolution of a Distinct SARS-CoV-2 Lineage Identified during an Investigation of a Hospital Outbreak | Viruses / [link](https://www.mdpi.com/1999-4915/16/3/337) | COVID Lineage App; BSSH | | Expanding the phenotypic spectrum of LHCGR signal peptide insertion variant: novel clinical and allelic findings causing Leydig cell hypoplasia type II | Hormones / [link](https://doi.org/10.1007/s42000-024-00546-x) | BSSH; Germline pipeline | | Colonic tubular adenoma with clear cell change–case report with whole exome sequencing and updated review of the literature | Pathobiology: Journal of Immunopathology, Molecular and Cellular Biology / [link](https://karger.com/pat/article-pdf/doi/10.1159/000538705/4190059/000538705.pdf) | | | Mapping Whole Exome Sequencing to In Vivo Imaging with Stereotactic Localization and Deep Learning | -- / [link](http://arxiv.org/abs/2401.04231) | | | The Scalable Variant Call Representation: Enabling Genetic Analysis Beyond One Million Genomes | -- / [link](https://www.biorxiv.org/content/10.1101/2024.01.09.574205v1) | | | Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithms | -- / [link](https://www.biorxiv.org/content/10.1101/2024.01.02.573821v2) | | | A deep intronic variant in MME causes autosomal recessive Charcot-Marie-Tooth neuropathy through aberrant splicing | -- / [link](https://www.medrxiv.org/content/10.1101/2024.04.22.24306048v1) | DRAGEN-GATK; GATK HaplotypeCaller | | AutScore – An integrative scoring approach for prioritization of ultra-rare autism spectrum disorder candidate variants from whole exome sequencing data | -- / [link](https://www.medrxiv.org/content/10.1101/2024.01.24.24301544v2) | | | Clinical application of Complete Long Read genome sequencing identifies a 16kb intragenic duplication in EHMT1 in a patient with suspected Kleefstra syndrome | -- / [link](https://www.medrxiv.org/content/10.1101/2024.03.28.24304304v1) | BSSH; ICLR WGS pipeline app v2.0.6 | | Comprehensive analysis of the genetic variation in the LPA gene from short-read sequencing | -- / [link](https://www.medrxiv.org/content/10.1101/2024.03.21.24304527v1) | LPA caller | | Functional Analysis of G6PD Variants Associated With Low G6PD Activity in the All of Us Research Program | -- / [link](https://www.medrxiv.org/content/10.1101/2024.04.12.24305393v1) | | | Genome-wide study of gene-by-sex interactions identifies risks for cleft palate | -- / [link](https://www.medrxiv.org/content/10.1101/2024.05.01.24306701v1) | Germline pipeline v3.7.5 | | Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease | -- / [link](https://www.medrxiv.org/content/10.1101/2024.03.22.24304565v1) | | | Pan-Cancer Interrogation of B7-H3 (CD276) as an Actionable Therapeutic Target across Human Malignancies | Cancer Research Communications / [link](https://doi.org/10.1158/2767-9764.CRC-23-0546) | | | COSAP: Comparative Sequencing Analysis Platform | BMC Bioinformatics / [link](https://doi.org/10.1186/s12859-024-05756-z) | | | A 39 kb structural variant causing Lynch Syndrome detected by optical genome mapping and nanopore sequencing | European Journal of Human Genetics / [link](https://www.nature.com/articles/s41431-023-01494-7) | SV caller | | The Genetic Landscape of Pediatric Postural Orthostatic Tachycardia Syndrome | -- / [link](https://www.medrxiv.org/content/10.1101/2024.05.03.24306814v1) | v3.3.7 | | A framework for the evaluation and reporting of incidental findings in clinical genomic testing | European Journal of Human Genetics / [link](https://www.nature.com/articles/s41431-024-01575-1) | | | Natural Killer Cell Infiltration in Prostate Cancers Predict Improved Patient Outcomes | Prostate Cancer and Prostatic Diseases / [link](https://www.nature.com/articles/s41391-024-00797-0) | demultiplexing | | Antimicrobial susceptibility and resistome of Actinobacillus pleuropneumoniae in Taiwan: a next-generation sequencing analysis | Veterinary Quarterly / [link](https://doi.org/10.1080/01652176.2024.2335947) | | | Clinical exome sequencing by general pediatricians: high clinical utility and no evidence of inappropriate testing | Frontiers in Pediatrics / [link](https://www.frontiersin.org/articles/10.3389/fped.2024.1392444) | DRAGEN server v3 | | Integrated analysis of transcriptome and genome variations in pediatric T cell acute lymphoblastic leukemia: data from north Indian tertiary care center | BMC Cancer / [link](https://doi.org/10.1186/s12885-024-12063-6) | | | Unveiling the impact of temperature shift on microbial community dynamics and metabolic pathways in anaerobic digestion | Process Safety and Environmental Protection / [link](https://www.sciencedirect.com/science/article/pii/S0957582024004804) | Metagenomics pipeline | | Two Cases of Sporadic Amyotrophic Lateral Sclerosis With Contrasting Clinical Phenotypes: Genetic Insights | Cureus / [link](https://www.cureus.com/articles/231357-two-cases-of-sporadic-amyotrophic-lateral-sclerosis-with-contrasting-clinical-phenotypes-genetic-insights.pdf) | Variant calling | | Molecular profiling and the impact of treatment on outcomes in adenoid cystic carcinoma (ACC) type-I and II | Clinical Cancer Research / [link](https://aacrjournals.org/clincancerres/article/doi/10.1158/1078-0432.CCR-23-3182/734973) | | | COVID-19 in hematopoietic stem cell transplant recipients during three years of the pandemic: a multicenter study in Brazil | Revista do Instituto de Medicina Tropical de São Paulo / [link](https://www.scielo.br/j/rimtsp/a/LkqNq7DZkvnCLQxrfbXR4Vz/) | v3.5.13 | | Repair of leukemia-associated single nucleotide variants via interallelic gene conversion | -- / [link](https://www.biorxiv.org/content/10.1101/2024.04.16.587991v1) | Somatic pipeline | | Expanding the Phenotype of the CACNA1C-Associated Neurological Disorders in Children: Systematic Literature Review and Description of a Novel Mutation | Children / [link](https://www.mdpi.com/2227-9067/11/5/541) | | | Symptomatology and IgG Levels Before and After SARS-CoV-2 Omicron Breakthrough Infections in Vaccinated Individuals | -- / [link](https://www.preprints.org/manuscript/202404.1728/v1) | | | CCR5 and CCL5 gene expression in colorectal cancer: comprehensive profiling and clinical value | Journal for Immunotherapy of Cancer / [link](https://jitc.bmj.com/content/12/1/e007939) | | | Nuclear Factor κB Signaling Deficiency in CD11c-Expressing Phagocytes Mediates Early Inflammatory Responses and Enhances Mycobacterium tuberculosis Control | The Journal of Infectious Diseases / [link](https://doi.org/10.1093/infdis/jiae060) | | | ELMO2 biallelic pathogenic variants in a patient with gingival hypertrophy and cherubism phenotype: Case report and molecular review | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.63602) | | | High Comorbidity of Pediatric Cancers in Patients with Birth Defects: Insights from Whole Genome Sequencing Analysis of Copy Number Variations | Translational Research / [link](https://www.sciencedirect.com/science/article/pii/S1931524423001846) | | | Another case of nuclear speckleopathy due to a novel NKAP pathogenic variant | Clinical Dysmorphology / [link](https://journals.lww.com/clindysmorphol/citation/2024/04000/another_case_of_nuclear_speckleopathy_due_to_a.5.aspx) | | | Multiomics Analysis of PCB126’s Effect on a Mouse Chronic-Binge Alcohol Feeding Model | Environmental Health Perspectives / [link](https://ehp.niehs.nih.gov/doi/full/10.1289/EHP14132) | v1.2.1 | | Genetic Analysis of a Mosaic Fra(16)(q22)/Del(16)(q22) Karyotype in a Primary Infertile Woman | International Journal of Women's Health / [link](https://www.tandfonline.com/doi/abs/10.2147/IJWH.S450272) | | | Unveiling New Insights: Reinterpreting DES Mutation, p.Arg383His, through a Study of an Iranian Family with Isolated Hypertrophic Cardiomyopathy, Implication for Phenotype‒Genotype Correlation Analysis | -- / [link](https://www.researchsquare.com/article/rs-3835607/v1) | | | Evidence from 2100 index cases supports genome sequencing as a first-tier genetic test | Genetics in Medicine / [link](https://www.sciencedirect.com/science/article/pii/S1098360023010110) | | | Natural Killer Cells Do Not Attenuate a Mouse-Adapted SARS-CoV-2-Induced Disease in Rag2−/− Mice | Viruses / [link](https://www.mdpi.com/1999-4915/16/4/611) | BSSH | | Predominance of the recombinant SARS-CoV-2 lineages XBB in Rio Grande do Sul State, Brazil: a genomic surveillance study and impact on vaccine response | -- / [link](https://www.researchsquare.com/article/rs-3917937/v1) | | | Identification of SARS-CoV-2 variants in indoor dust | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0297172) | COVID Lineage App v3.5.1 | | Exome Sequencing Reveals Biallelic Mutations in MBTPS1 Gene in a Girl with a Very Rare Skeletal Dysplasia | Diagnostics / [link](https://www.mdpi.com/2075-4418/14/3/313) | | | The clinical value of optical genome mapping in the rapid characterization of RB1 duplication and 15q23q24.2 triplication, for more appropriate prenatal genetic counselling | Molecular Genetics & Genomic Medicine / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/mgg3.2437) | BCL convert | | Spectrum of PHEX Mutations and FGF23 Profiles in a Taiwanese Cohort With X-Linked Hypophosphatemia Including 102 Patients | In Vivo / [link](https://iv.iiarjournals.org/content/38/1/341) | v3.7.5 | | Case report: Novel genotype of ALG2-CDG and confirmation of the heptasaccharide glycan (NeuAc-Gal-GlcNAc-Man2-GlcNAc2) as a specific diagnostic biomarker | Frontiers in Genetics / [link](https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2024.1363558/full) | CNV pipeline | | Establishing mesothelioma patient-derived organoid models from malignant pleural effusions | Lung Cancer / [link](https://www.sciencedirect.com/science/article/pii/S0169500224000758) | TSO 500 v2.1.0 | | A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population | Frontiers in Immunology / [link](https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1357731/full) | COVIDSeq Test pipeline; BSSH | | Whole genome sequencing in clinical practice | BMC Medical Genomics / [link](https://doi.org/10.1186/s12920-024-01795-w) | review | | Whole genome sequencing of a family with autosomal dominant features within the oculoauriculovertebral spectrum | -- / [link](https://www.medrxiv.org/content/10.1101/2024.02.07.24301824v2) | | | Systematic molecular analyses for 115 karyotypically normal men with isolated non-obstructive azoospermia | Human Reproduction / [link](https://doi.org/10.1093/humrep/deae057) | | | Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses | -- / [link](https://www.medrxiv.org/content/10.1101/2024.03.28.24304905v2) | Metagenomics pipeline | | Molecular basis of DEL phenotype in the Indian population: Insights from next-generation sequencing analysis of two cases | Transfusion and Apheresis Science / [link](https://www.sciencedirect.com/science/article/pii/S1473050224000041) | v3.4 | | Acquired NF2 mutation confers resistance to TRK inhibition in an ex vivo LMNA::NTRK1-rearranged soft-tissue sarcoma cell model | The Journal of Pathology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/path.6282) | alignment; RNA pipeline | | The complement regulator CD55 modulates TLR9 signaling and supports survival in marginal zone B cells | -- / [link](https://www.biorxiv.org/content/10.1101/2024.03.01.582833v1) | DRAGEN server; v3.9.3 | | Impact of Omicron variant sublineage BA.2.75 on the OnSite COVID-19 Ag Rapid Test: the applicability of rapid antigen test with universal transport media | Infectious Diseases / [link](https://doi.org/10.1080/23744235.2023.2280025) | | | Surveillance Outcome and Genetic Findings in Individuals at High Risk of Pancreatic Cancer | Clinical and Translational Gastroenterology / [link](https://journals.lww.com/ctg/fulltext/2024/02000/surveillance_outcome_and_genetic_findings_in.9.aspx?context=featuredarticles\&collectionid=6) | SV caller | | Functional evaluation of a novel nonsense variant of the calcium-sensing receptor gene leading to hypocalcemia | European Journal of Endocrinology / [link](https://doi.org/10.1093/ejendo/lvae035) | | | Influence of TP53 Comutation on the Tumor Immune Microenvironment and Clinical Outcomes With Immune Checkpoint Inhibitors in STK11-Mutant Non–Small-Cell Lung Cancer | JCO Precision Oncology / [link](https://ascopubs.org/doi/full/10.1200/PO.23.00371) | | | Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania | Genes / [link](https://www.mdpi.com/2073-4425/15/3/361) | BCL convert | | *Ex vivo* modeling of acquired drug resistance in *BRAF* - mutated pancreatic cancer organoids uncovers individual therapeutic vulnerabilities | Cancer Letters / [link](https://www.sciencedirect.com/science/article/pii/S0304383524000442) | RNA pipeline | | Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru | Tropical Medicine and Infectious Disease / [link](https://www.mdpi.com/2414-6366/9/2/46) | BSSH | | Consanguineous marriages increase the incidence of recurrent tuberculosis: Evidence from whole exome sequencing | Infection, Genetics and Evolution / [link](https://www.sciencedirect.com/science/article/pii/S1567134824000108) | alignment | | Brain injury drives optic glioma formation through neuron-glia signaling | Acta Neuropathologica Communications / [link](https://doi.org/10.1186/s40478-024-01735-w) | | | Antiviral response and HIV-1 inhibition in sickle cell disease | Iscience / [link](https://www.cell.com/iscience/pdf/S2589-0042\(24\)00034-8.pdf) | Differential expression pipeline v3.6.3; RNA pipeline v3.8.4 | | Analysis of partial Y chromosome microdeletions and NGS data in Lithuanian infertile men | -- / [link](https://www.researchsquare.com/article/rs-3941579/v1) | v3.6.4 | | Chapter 6 - Assessing microbiota composition in the context of aging | Methods in Cell Biology / [link](https://www.sciencedirect.com/science/article/pii/S0091679X22001959) | BSSH; Metagenomics pipeline | | Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics | Frontiers in Microbiology / [link](https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2024.1346762/full) | | | Intellectual disability syndrome associated with a homozygous founder variant in SGSM3 in Ashkenazi Jews | Journal of Medical Genetics / [link](https://jmg.bmj.com/content/61/3/289) | | | Molecular analysis and transfusion management in a rare case of *cis*-AB blood group: A report from India | Transfusion Clinique et Biologique / [link](https://www.sciencedirect.com/science/article/pii/S1246782023004925) | v3.4 | | Immune transcriptomic profile in adult female pigs: dominance status has more influence than environmental enrichment | -- / [link](https://www.researchsquare.com/article/rs-4016210/v1) | v3.8.4; RNA | | Differential Responses to Immune Checkpoint Inhibitors are Governed by Diverse Mismatch Repair Gene Alterations | Clinical Cancer Research / [link](https://doi.org/10.1158/1078-0432.CCR-23-3004) | | | Comparative molecular profiling of pancreatic ductal adenocarcinoma of the head versus body and tail | npj Precision Oncology / [link](https://www.nature.com/articles/s41698-024-00571-4) | BCL convert | | Beyond the kidney biopsy: genomic approach to undetermined kidney diseases | Clinical Kidney Journal / [link](https://doi.org/10.1093/ckj/sfad099) | BCL convert | | Myocardial Matrix Hydrogels Mitigate Negative Remodeling and Improve Function in Right Heart Failure Model | JACC: Basic to Translational Science / [link](https://www.jacc.org/doi/full/10.1016/j.jacbts.2024.01.006) | RNA pipeline; v3.10.12 | | Despite Recovery from Necrotizing Enterocolitis Infants Retain a Hyperinflammatory Response to Injury | Journal of Inflammation Research / [link](https://www.tandfonline.com/doi/abs/10.2147/JIR.S436125) | BSSH; Differential Expression App v4.0.3 | | Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories | PLOS Neglected Tropical Diseases / [link](https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0011672) | v1.3 | | ACBD5-related retinal dystrophy with leukodystrophy due to novel mutations in ACBD5 and with additional features including ovarian insufficiency | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.63433) | BSSH | | Genomic heterogeneity at baseline is associated with T790M resistance mutations in EGFR-mutated lung cancer treated with the first-/second-generation tyrosine kinase inhibitors | The Journal of Pathology: Clinical Research / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/cjp2.354) | alignment; v4.0.3 | | Genetic Markers Among the Israeli Druze Minority Population With End-Stage Kidney Disease | American Journal of Kidney Diseases / [link](https://www.sciencedirect.com/science/article/pii/S0272638623007989) | CNV | | Preclinical Evidence for the Glucocorticoid-Sparing Potential of a Dual Toll-Like Receptor 7/8 Inhibitor in Autoimmune Diseases | Journal of Pharmacology and Experimental Therapeutics / [link](https://jpet.aspetjournals.org/content/388/3/751) | | | High Frequencies of Genetic Variants in Patients with Atypical Femoral Fractures | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/25/4/2321) | | | Loss of function in *NSD2* causes DNA methylation signature similar to that in Wolf-Hirschhorn syndrome | Genetics in Medicine Open / [link](https://www.sciencedirect.com/science/article/pii/S2949774424009841) | | | Concordance between an FDA-approved companion diagnostic and an alternative assay kit for assessing homologous recombination deficiency in ovarian cancer | Gynecologic Oncology / [link](https://www.sciencedirect.com/science/article/pii/S0090825824000234) | | | A Cataract-Causing Mutation in the TRPM3 Cation Channel Disrupts Calcium Dynamics in the Lens | Cells / [link](https://www.mdpi.com/2073-4409/13/3/257) | v3.9 | | Homozygous variant in TKFC abolishing triokinase activities is associated with isolated immunodeficiency | Journal of Medical Genetics / [link](https://jmg.bmj.com/content/early/2024/05/02/jmg-2024-109853) | | | Renal transcriptome analysis of uninephrectomized db/db mice identified a mechanism for the transition to severe diabetic nephropathy | Experimental Animals / [link](https://www.jstage.jst.go.jp/article/expanim/73/1/73_22-0168/_article) | | | The diversity and clinical implications of genetic variants influencing clopidogrel bioactivation and response in the Emirati population | Human Genomics / [link](https://doi.org/10.1186/s40246-023-00568-3) | v4 | | A new potential therapeutic approach for ALS: A case report with NGS analysis | Medicine / [link](https://journals.lww.com/md-journal/fulltext/2024/03010/a_new_potential_therapeutic_approach_for_als__a.39.aspx?context=latestarticles) | Germline app v3.9.5 | | Conditionally replicative adenovirus as a therapy for malignant peripheral nerve sheath tumors | Molecular Therapy Oncology / [link](https://www.cell.com/molecular-therapy-family/oncology/abstract/S2950-3299\(24\)00025-0) | Somatic mode | | Embigin Is Highly Expressed on CD4+ and CD8+ T Cells but Is Dispensable for Several T Cell Effector Responses | ImmunoHorizons / [link](https://doi.org/10.4049/immunohorizons.2300083) | BSSH; v1.2.1 | | Comorbid neurotrauma increases neurodegenerative-relevant cognitive, motor, and autonomic dysfunction in patients with rapid eye movement sleep behavior disorder: a substudy of the North American Prodromal Synucleinopathy Consortium | Sleep / [link](https://doi.org/10.1093/sleep/zsae007) | Joint genotyping pipeline | | Independent activation of CREB3L2 by glucose fills a regulatory gap in mouse β-cells by co-ordinating insulin biosynthesis with secretory granule formation | Molecular Metabolism / [link](https://www.sciencedirect.com/science/article/pii/S2212877823001795) | RNA-Seq pipeline | | Molecular Epidemiology of SARS-CoV-2 Genome Sentinel Surveillance in Commercial COVID-19 Testing Sites Targeting Asymptomatic Individuals During Japan’s Seventh Epidemic Wave | -- / [link](https://www.researchsquare.com/article/rs-3968947/v1) | | | In ovo delivery of oregano essential oil activated xenobiotic detoxification and lipid metabolism at hatch in broiler chickens | Poultry Science / [link](https://www.sciencedirect.com/science/article/pii/S0032579123008404) | | | Interrogating Pharmacogenetics Using Next-Generation Sequencing | The Journal of Applied Laboratory Medicine / [link](https://doi.org/10.1093/jalm/jfad097) | | | An adult patient with Tatton–Brown–Rahman syndrome caused by a novel DNMT3A variant and axonal polyneuropathy | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.63484) | alignment | | Seasonality of respiratory, enteric, and urinary viruses revealed by wastewater genomic surveillance | mSphere / [link](https://journals.asm.org/doi/full/10.1128/msphere.00105-24) | BCL convert | | Microglial-specific knockdown of iron import gene, *Slc11a2*, blunts LPS-induced neuroinflammatory responses in a sex-specific manner | Brain, Behavior, and Immunity / [link](https://www.sciencedirect.com/science/article/pii/S0889159123004026) | v3.6.3; RNA Seq pipeline; BSSH | | Developing a genetic testing panel for evaluation of morbidities in kidney transplant recipients | Kidney International / [link](https://www.sciencedirect.com/science/article/pii/S0085253824001881) | | | Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater | Environmental Science & Technology / [link](https://doi.org/10.1021/acs.est.4c02638) | Microbial Enrichment pipeline | | Synthetic Lethality between Cohesin and WNT Signaling Pathways in Diverse Cancer Contexts | Cells / [link](https://www.mdpi.com/2073-4409/13/7/608) | Somatic pipeline | | Skin Cancer Risk Is Increased by Somatic Mutations Detected Noninvasively in Healthy-Appearing Sun-Exposed Skin | Journal of Investigative Dermatology / [link](https://www.sciencedirect.com/science/article/pii/S0022202X24001763) | Somatic app | | Generative Haplotype Prediction Outperforms Statistical Methods for Small Variant Detection in NGS Data | -- / [link](https://www.biorxiv.org/content/10.1101/2024.02.27.582327v1) | | | Coexistence of *bla*NDM-5, *bla*CTX-M-15, *bla*OXA-232, *bla*SHV-182 genes in multidrug-resistant *K. pneumoniae* ST437-carrying OmpK36 and OmpK37 porin mutations: First report in Italy | Journal of Global Antimicrobial Resistance / [link](https://www.sciencedirect.com/science/article/pii/S2213716524000420) | v3.9.5 | | Type II Interleukin-4 Receptor Activation in Basal Breast Cancer Cells Promotes Tumor Progression via Metabolic and Epigenetic Modulation | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/25/9/4647) | RNASeq pipeline | | Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc | Genome Biology / [link](https://doi.org/10.1186/s13059-024-03170-5) | v3 | | Characterization and visualization of tandem repeats at genome scale | Nature Biotechnology / [link](https://www.nature.com/articles/s41587-023-02057-3) | | | Multimodal data fusion using sparse canonical correlation analysis and cooperative learning: a COVID-19 cohort study | npj Digital Medicine / [link](https://www.nature.com/articles/s41746-024-01128-2) | COVID Lineage App; BSSH | | Clinical utility of the Oncomine Dx Target Test multi-CDx system and the possibility of utilizing those original sequence data | Cancer Medicine / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/cam4.7077) | v3.8 | | Late-life dietary folate restriction reduces biosynthetic processes without compromising healthspan in mice | -- / [link](https://www.biorxiv.org/content/10.1101/2024.01.12.575290v1) | RNA Seq pipeline | | Clinical Diversity and Outcomes of Progressive Familial Intrahepatic Cholestasis Diagnosed by Whole Genome Sequencing in Pakistani Children | -- / [link](https://www.medrxiv.org/content/10.1101/2024.02.26.24303272v1) | v3.10.4; SV; Indels | | Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review | npj Genomic Medicine / [link](https://www.nature.com/articles/s41525-024-00404-0) | review | | Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer | -- / [link](https://www.biorxiv.org/content/10.1101/2024.05.02.592182v1) | alignment; BSSH | | Replicative senescence and high glucose induce the accrual of self-derived cytosolic nucleic acids in human endothelial cells | Cell Death Discovery / [link](https://www.nature.com/articles/s41420-024-01954-z) | v3.7 | | Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses | BMC Genomics / [link](https://doi.org/10.1186/s12864-024-10080-0) | v3.10 | | Identification of spatially-resolved markers of malignant transformation in Intraductal Papillary Mucinous Neoplasms | Nature Communications / [link](https://www.nature.com/articles/s41467-024-46994-2) | BSSH | | Cell-type-resolved mosaicism reveals clonal dynamics of the human forebrain | Nature / [link](https://www.nature.com/articles/s41586-024-07292-5) | | | Structural rearrangements as a recurrent pathogenic mechanism for SETBP1 haploinsufficiency | Human Genomics / [link](https://doi.org/10.1186/s40246-024-00600-0) | | | Comparative analysis of 136,401 Admixed Americans and 419,228 Europeans reveals ancestry-specific genetic determinants of clonal haematopoiesis | -- / [link](https://www.medrxiv.org/content/10.1101/2024.02.07.24302442v1) | Germline pipeline v3.0.7 | | From GPUs to AI and quantum: three waves of acceleration in bioinformatics | Drug Discovery Today / [link](https://www.sciencedirect.com/science/article/pii/S1359644624001156) | review | | Orthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing | -- / [link](https://www.researchsquare.com/article/rs-3910990/v1) | | | Case report on Reversal of Field Cancerization using Nutraceuticals mapped to the aberrant pathways deciphered via NGS analysis of the neoplastic oral mucosa | Medical Research Archives / [link](https://esmed.org/MRA/mra/article/view/4553) | Somatic pipeline | | Genome-Wide Association Study Reveals a QTL Region for Ashy Stem Blight Resistance in PRA154 Andean Common Bean | Plant Disease / [link](https://apsjournals.apsnet.org/doi/10.1094/PDIS-07-23-1275-RE) | | | Childhood-related neural genotype-phenotype in ATP1A3 mutations: comprehensive analysis | Genes & Genomics / [link](https://link.springer.com/article/10.1007/s13258-023-01481-8) | v3.4.12 | | Molecular Heterogeneity of Osteopetrosis in India: Report of 17 Novel Variants | Indian Journal of Hematology and Blood Transfusion / [link](https://doi.org/10.1007/s12288-023-01732-4) | CNV pipeline | | Whole genome sequencing as a first-tier diagnostic test for infants in neonatal intensive care units: A pilot study in Brazil | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.63544) | | | DNMTs-mediated SOCS3 methylation promotes the occurrence and development of AML | European Journal of Haematology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/ejh.14134) | | | Bi-allelic variants in SNF8 cause a disease spectrum ranging from severe developmental and epileptic encephalopathy to syndromic optic atrophy | The American Journal of Human Genetics / [link](https://linkinghub.elsevier.com/retrieve/pii/S0002929724000375) | | | Targeting prostate tumor low–molecular weight tyrosine phosphatase for oxidation-sensitizing therapy | Science Advances / [link](https://www.science.org/doi/full/10.1126/sciadv.adg7887) | demultiplexing | | HiHo-AID2: boosting homozygous knock-in efficiency enables robust generation of human auxin-inducible degron cells | Genome Biology / [link](https://doi.org/10.1186/s13059-024-03187-w) | v4.2.4 | | Self-reactive B cells traverse a perfect storm of somatic mutagenesis to cause a virus-induced autoimmune disease | -- / [link](https://www.biorxiv.org/content/10.1101/2024.01.07.574561v3) | | | Nasopharyngeal metatranscriptomics reveals host-pathogen signatures of pediatric sinusitis | -- / [link](https://www.medrxiv.org/content/10.1101/2024.03.03.24303663v1) | onboard; demultiplexing | | Multi-Tissue Network Analysis Reveals the Effect of JNK Inhibition on Dietary Sucrose-Induced Metabolic Dysfunction in Rats | -- / [link](https://papers.ssrn.com/abstract=4692602) | BCL convert | | PBK/TOPK mediates Ikaros, Aiolos and CTCF displacement from mitotic chromosomes and alters chromatin accessibility at selected C2H2-zinc finger protein binding sites | -- / [link](https://www.biorxiv.org/content/10.1101/2024.04.23.590758v1) | | | Damaging mutations in LXRα uncouple lipogenesis from hepatotoxicity and implicate hepatic cholesterol sensing in human liver health | -- / [link](https://www.biorxiv.org/content/10.1101/2024.04.28.591512v1) | Germline pipeline v3.7.8 | | 2P-NucTag: on-demand phototagging for molecular analysis of functionally identified cortical neurons | -- / [link](https://www.biorxiv.org/content/10.1101/2024.03.21.586118v1) | De-multiplexing | | Congenital Heart Defects in Patients with Molecularly Confirmed Sotos Syndrome | Diagnostics / [link](https://www.mdpi.com/2075-4418/14/6/594) | BSSH; Germline pipeline | | Single-cell deconvolution reveals high lineage- and location-dependent heterogeneity in mesenchymal multivisceral stage 4 colorectal cancer | The Journal of Clinical Investigation / [link](https://www.jci.org/articles/view/169576) | v3.8.4 | | Proteogenomic analysis reveals adaptive strategies to alleviate the consequences of aneuploidy in cancer | -- / [link](https://www.biorxiv.org/content/10.1101/2024.03.05.583460v1) | | | Targeting circulating labile heme as a defense strategy against malaria | Life Science Alliance / [link](https://www.life-science-alliance.org/content/7/4/e202302276) | | | Engineered interleukin-6-derived cytokines recruit artificial receptor complexes and disclose CNTF signaling via the OSMR | Journal of Biological Chemistry / [link](https://www.jbc.org/article/S0021-9258\(24\)01748-4/abstract) | BCL convert | | A novel T cell-redirecting anti-GPRC5D × CD3 bispecific antibody with potent antitumor activity in multiple myeloma preclinical models | Scientific Reports / [link](https://www.nature.com/articles/s41598-024-55143-0) | alignment | | Protocol for isolating single species of bacteria with swarming ability from human feces | STAR Protocols / [link](https://www.sciencedirect.com/science/article/pii/S2666166724001266) | v3.10.12; onboard | | Mutational rescue of the activity of high-fidelity Cas9 enzymes | Cell Reports Methods / [link](https://www.cell.com/cell-reports-methods/abstract/S2667-2375\(24\)00087-0) | BCL convert | | Clinical application of tumour-in-normal contamination assessment from whole genome sequencing | Nature Communications / [link](https://www.nature.com/articles/s41467-023-44158-2) | alignment; v3.2.22 | | Roles for RERE in lymphatic endothelial cell proliferation and survival, and human cystic lymphatic malformations | -- / [link](https://www.biorxiv.org/content/10.1101/2024.03.24.586490v2) | alignment | | Epigenetic regulation by TET1 in gene-environmental interactions influencing susceptibility to congenital malformations | -- / [link](https://www.biorxiv.org/content/10.1101/2024.02.21.581196v1) | Haplotype variant calling | | Transcriptomic characterization of recombinant Clostridium beijerinckii NCIMB 8052 expressing methylglyoxal synthase and glyoxal reductase from Clostridium pasteurianum ATCC 6013 | -- / [link](https://www.biorxiv.org/content/10.1101/2024.02.27.582317v1) | onboard; v3.10.12 | | Simultaneous blastic plasmacytoid dendritic cell neoplasm and myelofibrosis: A case report | Oncology Letters / [link](https://www.spandidos-publications.com/10.3892/ol.2024.14354) | v3.10.4 | | The usefulness of the genetic panel in the classification and refinement of diagnostic accuracy of Mexican patients with Marfan syndrome and other connective tissue disorders | Biomolecules and Biomedicine / [link](https://www.bjbms.org/ojs/index.php/bjbms/article/view/9578) | | | DMHPpp1r17 neurons regulate aging and lifespan in mice through hypothalamic-adipose inter-tissue communication | Cell Metabolism / [link](https://www.cell.com/cell-metabolism/pdf/S1550-4131\(23\)00462-X.pdf) | DRAGEN server; v3.9.3 | | Hemodynamic and Clinical Profiles of Pulmonary Arterial Hypertension Patients with GDF2 and BMPR2 Variants | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/25/5/2734) | BCL convert | | ATM-deficiency-induced microglial activation promotes neurodegeneration in ataxia-telangiectasia | Cell reports / [link](https://www.cell.com/cell-reports/pdf/S2211-1247\(23\)01634-0.pdf) | DRAGEN-GATK; Germline pipeline | | Pangenome graph construction from genome alignments with Minigraph-Cactus | Nature Biotechnology / [link](https://www.nature.com/articles/s41587-023-01793-w) | | | Nasopharyngeal Bacterial Prevalence and Microbial Diversity at First Treatment for Bovine Respiratory Disease (BRD) and Its Associations with Health and Mortality Outcomes in Feedyard Cattle | Microorganisms / [link](https://www.mdpi.com/2076-2607/12/1/33) | BCL convert | | Assessing Genomic Mutations in SARS-CoV-2: Potential Resistance to Antiviral Drugs in Viral Populations from Untreated COVID-19 Patients | Microorganisms / [link](https://www.mdpi.com/2076-2607/12/1/2) | BSSH; COVID Lineage App v3.5.2 | | Novel Manifestation of Corneal Dystrophy After Keratorefractive Surgery | Cornea / [link](https://journals.lww.com/corneajrnl/abstract/2024/04000/novel_manifestation_of_corneal_dystrophy_after.2.aspx) | | | Deployment of a Vibrio cholerae ordered transposon mutant library in a quorum-competent genetic background | -- / [link](https://www.biorxiv.org/content/10.1101/2023.10.31.564941v2) | v3.10.11; NextSeq2000; DRAGEN onboard | | Cleave and Rescue gamete killers create conditions for gene drive in plants | -- / [link](https://www.biorxiv.org/content/10.1101/2023.10.13.562303v2) | Germline pipeline v3.10.12 | | Agrecanopatías: Reporte de Displasia Espóndiloepifisiaria tipo Kimberley (SEDK) en una familia, producida por variante probablemente patogénica del gen ACAN no descrita previamente | Genetics and Clinical Genomics / [link](https://www.geneticalatam.com/index.php/ggcl/article/view/2338) | CNV caller; Small variant caller | | Detection of Mpox Virus Using a Wastewater Surveillance Approach in Brazil | -- / [link](https://www.preprints.org/manuscript/202405.0571/v1) | BSSH; Microbial Enrichment pipeline | | Metagenomics or Metataxonomics: Best Practice Methods to Uncover the Sinus Microbiome | -- / [link](https://www.researchsquare.com/article/rs-4332600/v1) | BCL convert | | Immunocompetent murine model of Ewing sarcoma reveals role for TGFβ inhibition to enhance immune infiltrates in Ewing tumors during radiation | -- / [link](https://www.biorxiv.org/content/10.1101/2024.05.07.592974v1) | v3.10.12; onboard; demultiplexing | | Toward clinical exomes in diagnostics and management of male infertility | American Journal of Human Genetics / [link](https://doi.org/10.1016/j.ajhg.2024.03.013) | | | CCR2+ monocytes promote white matter injury and cognitive dysfunction after myocardial infarction | Brain, Behavior, and Immunity / [link](https://www.sciencedirect.com/science/article/pii/S088915912400391X) | GeoMx DSP Pipeline | | Combining germline, tissue and liquid biopsy analysis by comprehensive genomic profiling to improve the yield of actionable variants in a real-world cancer cohort | Journal of Translational Medicine / [link](https://doi.org/10.1186/s12967-024-05227-2) | v4; TSO 500 v2.1 | | The Clinical Utility of a Tiered Approach to Pediatric Glioma Molecular Characterization for Resource-Limited Settings | JCO Global Oncology / [link](https://ascopubs.org/doi/10.1200/GO.23.00269) | fusion caller | | A case of T-cell acute lymphoblastic leukemia in retroviral gene therapy for ADA-SCID | Nature Communications / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11061298/) | RNA pipeline | | Mutation analysis of BCR-ABL1 kinase domain in chronic myeloid leukemia patients with tyrosine kinase inhibitors resistance: a Malaysian cohort study | BMC Research Notes / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11031984/) | RNA | | Early-life house dust mite aeroallergen exposure augments cigarette smoke-induced myeloid inflammation and emphysema in mice | Respiratory Research / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11016214/) | BCL convert | | Altered Osteoblast Metabolism with Aging Results in Lipid Accumulation and Oxidative Stress Mediated Bone Loss | Aging and Disease / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10917552/) | RNA pipeline | | The CHK1 inhibitor prexasertib in BRCA wild-type platinum-resistant recurrent high-grade serous ovarian carcinoma: a phase 2 trial | Nature Communications / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10981752/) | v3.9.5 | | SARS-CoV-2 variant with the spike protein mutation F306L in the southern border provinces of Thailand | Scientific Reports / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10987673/) | | | Craniofacial chondrogenesis in organoids from human stem cell-derived neural crest cells | iScience / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11016914/) | onboard | | Protein-truncating variants in BSN are associated with severe adult-onset obesity, type 2 diabetes and fatty liver disease | Nature Genetics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11018524/) | AWS | | De novo variants in the non-coding spliceosomal snRNA gene RNU4-2 are a frequent cause of syndromic neurodevelopmental disorders | medRxiv / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11030480/) | alignment | | Targeting DNMT3A-mediated oxidative phosphorylation to overcome ibrutinib resistance in mantle cell lymphoma | Cell Reports Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11031386/) | v3.10 | | 11p13 microduplication: a differential diagnosis of Silver–Russell syndrome? | Molecular Cytogenetics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10941370/) | v4.0.3 | | Plasma extracellular vesicle microRNAs reflecting the therapeutic effect of the CBP/β-catenin inhibitor PRI-724 in patients with liver cirrhosis | Scientific Reports / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10943077/) | BSSH; RNA pipeline | | Impact of media supplements FGF2, LIF and IGF1 on the genome activity of porcine embryos produced in vitro | Scientific Reports / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10963758/) | | | Immunophenotypic and Gene Expression Analyses of the Inflammatory Microenvironment in High-Grade Oral Epithelial Dysplasia and Oral Lichen Planus | Head and Neck Pathology / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10923754/) | v3.8.4 | | A microfluidic platform integrating functional vascularized organoids-on-chip | Nature Communications / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10873332/) | BSSH; RNA app | | Pangenome graphs improve the analysis of structural variants in rare genetic diseases | Nature Communications / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10803329/) | alignment | | Autoimmune demyelination alters hypothalamic transcriptome and endocrine function | Journal of Neuroinflammation / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10768476/) | v3.8.0 | | Recurrent de novo SPTLC2 variant causes childhood-onset amyotrophic lateral sclerosis (ALS) by excess sphingolipid synthesis | Journal of Neurology, Neurosurgery, and Psychiatry / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10850718/) | v2.03 | | Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023 | Microbiology Spectrum / [link](https://journals.asm.org/doi/10.1128/spectrum.03831-23) | | | Evidence of SARS-CoV-2 Antibody in Mississippi White-Tailed Deer | Vector-Borne and Zoonotic Diseases / [link](https://www.liebertpub.com/doi/abs/10.1089/vbz.2023.0144) | | | Transcriptional features of low-grade neuroepithelial tumors with the BRAF V600E mutation associated with epileptogenicity | Genes to Cells / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/gtc.13096) | | | Integrative multi-region molecular profiling of primary prostate cancer in men with synchronous lymph node metastasis | Nature Communications / [link](https://www.nature.com/articles/s41467-024-48629-y) | DNA pipeline | | The impact of inversions across 33,924 families with rare disease from a national genome sequencing project | The American Journal of Human Genetics / [link](https://www.cell.com/ajhg/abstract/S0002-9297\(24\)00159-9) | v3.8.4 | | Genomic data in the All of Us Research Program | Nature / [link](https://www.nature.com/articles/s41586-023-06957-x) | PopGen | | Challenges in determining the malignant potential of atypical neurofibromas (aNF) using histopathologic features and the potential need for CDKN2A/2B testing: a case report | Journal of Translational Genetics and Genomics / [link](https://www.oaepublish.com/articles/jtgg.2024.02) | | | Diabetes mellitus in Kabuki syndrome 1 on a background of post-transplant diabetes mellitus | Endocrinology, Diabetes & Metabolism Case Reports / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10895327/) | | | Novel variants in *TECRL* leading to catecholaminergic polymorphic ventricular tachycardia | Life Science Alliance / [link](https://www.life-science-alliance.org/lookup/doi/10.26508/lsa.202402572) | | | Type 1 diabetes human enteroid studies reveal major changes in the intestinal epithelial compartment | Scientific Reports / [link](https://www.nature.com/articles/s41598-024-62282-x) | v3.10 | | Limb-girdle muscular dystrophy: A rare clinical case report | Demiroğlu Bilim University Florence Nightingale Journal of Medicine / [link](https://journalmeddbu.com/tur/ozet/323) | v3.6 | | Resolving unsolved whole-genome sequencing data in paediatric neurological disorders: a cohort study | Archives of Disease in Childhood / [link](https://adc.bmj.com/content/early/2024/05/22/archdischild-2024-326985) | v4.0 | | Efficient wastewater sample filtration improves the detection of SARS-CoV-2 variants: An extensive analysis based on sequencing parameters | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0304158) | Metagenomics pipeline | | A Case of Non-Syndromic Congenital Cataracts Caused by a Novel MAF Variant in the C-Terminal DNA-Binding Domain—Case Report and Literature Review | Genes / [link](https://www.mdpi.com/2073-4425/15/6/686) | v3.9 | | Clinician-Driven Reanalysis of Exome Sequencing Data From Patients With Inherited Retinal Diseases | JAMA Network Open / [link](https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2819340) | |
2023 | Title | Publisher / Link | Tags | | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------ | | Reliability of panel-based mutational signatures for immune-checkpoint-inhibition efficacy prediction in non-small cell lung cancer | Lung Cancer / [link](https://linkinghub.elsevier.com/retrieve/pii/S0169500223008243) | DRAGEN server; TSO 500 Analysis software v2.1 | | Viral kinetics of sequential SARS-CoV-2 infections | Nature Communications / [link](https://www.nature.com/articles/s41467-023-41941-z) | BSSH; COVID Lineage App | | Optimization of the Illumina COVIDSeq™ protocol for decentralized, cost-effective genomic surveillance | Practical Laboratory Medicine / [link](https://linkinghub.elsevier.com/retrieve/pii/S2352551723000057) | COVID Lineage App; v3.5.4 | | Mechanism of KMT5B haploinsufficiency in neurodevelopment in humans and mice | Science Advances / [link](https://www.science.org/doi/10.1126/sciadv.ade1463) | v3.6.3 | | De novo MCM6 variants in neurodevelopmental disorders: a recognizable phenotype related to zinc binding residues | Human Genetics / [link](https://link.springer.com/10.1007/s00439-023-02569-7) | | | \[11C]metomidate PET-CT versus adrenal vein sampling for diagnosing surgically curable primary aldosteronism: a prospective, within-patient trial | Nature Medicine / [link](https://www.nature.com/articles/s41591-022-02114-5) | Somatic mode | | Persistent Molecular Disease in Adult Patients With AML Evaluated With Whole-Exome and Targeted Error-Corrected DNA Sequencing | JCO Precision Oncology / [link](https://ascopubs.org/doi/10.1200/PO.22.00559) | v3.9.3 | | Improvement in neoantigen prediction via integration of RNA sequencing data for variant calling | Frontiers in Immunology / [link](https://www.frontiersin.org/articles/10.3389/fimmu.2023.1251603/full) | tumor-normal mode | | Unravelling homologous recombination repair deficiency and therapeutic opportunities in soft tissue and bone sarcoma | EMBO Molecular Medicine / [link](https://www.embopress.org/doi/10.15252/emmm.202216863) | v3.9.5 | | Whole-Genome Sequencing Can Identify Clinically Relevant Variants from a Single Sub-Punch of a Dried Blood Spot Specimen | International Journal of Neonatal Screening / [link](https://www.mdpi.com/2409-515X/9/3/52) | DNA pipeline; v3.9.5 | | PBRM1 mutations might render a subtype of biliary tract cancers sensitive to drugs targeting the DNA damage repair system | npj Precision Oncology / [link](https://www.nature.com/articles/s41698-023-00409-5) | | | Increased clonal hematopoiesis involving DNA damage response genes in patients undergoing lung transplantation | JCI Insight / [link](https://insight.jci.org/articles/view/165609) | | | Molecular and phenotypic characteristics influencing the degree of cytoreduction in high‐grade serous ovarian carcinomas | Cancer Medicine / [link](https://onlinelibrary.wiley.com/doi/10.1002/cam4.6085) | DRAGEN server; v3.8 | | Integrated multi-omics for rapid rare disease diagnosis on a national scale | Nature Medicine / [link](https://www.nature.com/articles/s41591-023-02401-9) | v3.3.7 | | Activation of mitogen-activated protein kinase signaling and development of papillary thyroid carcinoma in thyroid-stimulating hormone receptor D633H knockin mice | European Thyroid Journal / [link](https://etj.bioscientifica.com/view/journals/etj/12/6/ETJ-23-0049.xml) | v3.5.7 | | Androgens show sex-dependent differences in myelination in immune and non-immune murine models of CNS demyelination | Nature Communications / [link](https://www.nature.com/articles/s41467-023-36846-w) | v3.6.3 | | SLC26A1 is a major determinant of sulfate homeostasis in humans | Journal of Clinical Investigation / [link](https://www.jci.org/articles/view/161849) | Germline Pipeline; v3.0.7 | | Disease modeling of ADAMTS9-related nephropathy using kidney organoids reveals its roles in tubular cells and podocytes | Frontiers in Medicine / [link](https://www.frontiersin.org/articles/10.3389/fmed.2023.1089159/full) | Mapping | | Case Report: A new case of YARS1-associated autosomal recessive disorder with compound heterozygous and concurrent 47, XXY | Frontiers in Pediatrics / [link](https://www.frontiersin.org/articles/10.3389/fped.2023.1282253/full) | | | Spike protein mutations and structural insights of pangolin lineage B.1.1.25 with implications for viral pathogenicity and ACE2 binding affinity | Scientific Reports / [link](https://www.nature.com/articles/s41598-023-40005-y) | BSSH; RNA pathogen detection; v3.5.1 | | The genetic determinants of recurrent somatic mutations in 43,693 blood genomes | Science Advances / [link](https://www.science.org/doi/10.1126/sciadv.abm4945) | | | MiR-4521 perturbs FOXM1-mediated DNA damage response in breast cancer | Frontiers in Molecular Biosciences / [link](https://www.frontiersin.org/articles/10.3389/fmolb.2023.1131433/full) | RNA Seq pipeline | | Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer | Nature Communications / [link](https://www.nature.com/articles/s41467-023-40706-y) | COVID Lineage App; v3.5.6 | | The pharmacogenomic landscape of an Indigenous Australian population | Frontiers in Pharmacology / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10241071/) | DRAGEN-GATK; v3.8.4 | | Acquired resistance to a GPRC5D-directed T-cell engager in multiple myeloma is mediated by genetic or epigenetic target inactivation | Nature Cancer / [link](https://www.nature.com/articles/s43018-023-00625-9) | v3.10.8 | | Rapid Whole Genome Sequencing for Diagnosis of Single Locus Genetic Diseases in Critically Ill Children | Clinical Applications of Nucleic Acid Amplification / [link](https://doi.org/10.1007/978-1-0716-2950-5_12) | DRAGEN server; v3.9.3 | | Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy | Microorganisms / [link](https://www.mdpi.com/2076-2607/11/11/2711) | COVID Lineage App; Somatic caller | | Biallellic variants in CACNA1S cause fetal akinesia sequence, progressive hydrops and stillbirth | Prenatal Diagnosis / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/pd.6471) | v3.9.5 | | Characterization of the TRPV6 calcium channel-specific phenotype by RNA-seq in castration-resistant human prostate cancer cells | Frontiers in Genetics / [link](https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1215645/full) | v3.10.4 | | Validation of the BOADICEA model for predicting the likelihood of carrying pathogenic variants in eight breast and ovarian cancer susceptibility genes | Scientific Reports / [link](https://www.nature.com/articles/s41598-023-35755-8) | alignment; Variant calling | | Genomic Tracking of SARS-CoV-2 Variants in Myanmar | Vaccines / [link](https://www.mdpi.com/2076-393X/11/1/6) | COVIDSeq Test pipeline | | Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0288371) | DRAGEN-GATK | | Biallelic variants in TUBGCP6 result in microcephaly and chorioretinopathy 1: Report of four cases and a literature review | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.63203) | CNV | | First sequenced cases of Omicron BA.2 sublineage in Ecuador | Virus Research / [link](https://www.sciencedirect.com/science/article/pii/S0168170223001314) | COVIDSeq Test pipeline; COVID Lineage App; v3.9.3 | | Precision therapy for a medically actionable *ATP1A3* variant from a genomic medicine program in an underserved population | Molecular Genetics & Genomic Medicine / [link](https://onlinelibrary.wiley.com/doi/10.1002/mgg3.2272) | | | Comparative Analysis of Structural Variant Callers on Short-Read Whole-Genome Sequencing Data | Russian Journal of Genetics / [link](https://link.springer.com/10.1134/S102279542306011X) | v3.5.7 | | Identification of allele-specific KIV-2 repeats and impact on Lp (a) measurements for cardiovascular disease risk | bioRxiv / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10168217/) | KIV2 CN caller; LPA caller; v4.2 | | Whole genome sequencing in ROHHAD trios proved inconclusive: what’s beyond? | Frontiers in Genetics / [link](https://www.frontiersin.org/articles/10.3389/fgene.2023.1031074/full) | | | Rapid identification of SARS-CoV-2 variants: Validation of the simplexa SARS-CoV-2 variant direct assay | Journal of Virological Methods / [link](https://www.sciencedirect.com/science/article/pii/S0166093423000848) | COVID Lineage App; v3.5.4 | | Identification of Genetic Risk Factors for Keratinocyte Cancer in Immunosuppressed Solid Organ Transplant Recipients: A Case-Control Study | Cancers / [link](https://www.mdpi.com/2072-6694/15/13/3354) | | | Detection of *ATXN2* Expansions in an Exome Dataset: An Underdiagnosed Cause of Parkinsonism | Movement Disorders Clinical Practice / [link](https://movementdisorders.onlinelibrary.wiley.com/doi/10.1002/mdc3.13699) | ExpansionHunter; v3.9 | | An absolute approach to using whole exome DNA and RNA workflow for cancer biomarker testing | Frontiers in Oncology / [link](https://www.frontiersin.org/articles/10.3389/fonc.2023.1002792/full?trk=public_post_comment-text) | RNA pipeline; Somatic pipeline; v3.6 | | Emergence of SARS-CoV-2 variant of interest B. 1.525 (Eta) in Bangladesh | Biologicals / [link](https://www.sciencedirect.com/science/article/pii/S1045105623000520) | RNA pathogen detection | | Clinical Implementation of MetaFusion for Accurate Cancer-Driving Fusion Detection from RNA Sequencing | The Journal of Molecular Diagnostics / [link](https://www.sciencedirect.com/science/article/pii/S1525157823002118) | BSSH; RNA pipeline; v3.8.4 | | Whole‐exome sequencing analyses in a Saudi Ischemic Stroke Cohort reveal association signals, and shows polygenic risk scores are related to Modified Rankin Scale Risk | Functional & Integrative Genomics / [link](https://link.springer.com/10.1007/s10142-023-01039-7) | Germline Pipeline; Joint genotyping | | NGS implementation for monitoring SARS-CoV-2 variants in Chicagoland: An institutional perspective, successes and challenges | Frontiers in Public Health / [link](https://www.frontiersin.org/articles/10.3389/fpubh.2023.1177695/full) | COVIDSeq Test pipeline; DRAGEN server; NextSeq 550Dx | | Evaluation of Illumina® COVIDSeq™ as a tool for Omicron SARS-CoV-2 characterisation | Journal of Virological Methods / [link](https://www.sciencedirect.com/science/article/pii/S0166093423001520) | BSSH; COVID Lineage App; v3.5.13 | | SARS-CoV-2 variants and mutational patterns: relationship with risk of ventilator-associated pneumonia in critically ill COVID-19 patients in the era of dexamethasone | Scientific Reports / [link](https://www.nature.com/articles/s41598-023-33639-5) | COVIDSeq Test pipeline; DRAGEN server | | Genomic Surveillance of SARS-CoV-2 Sequence Variants at Universities in Southwest Idaho | COVID / [link](https://www.mdpi.com/2673-8112/4/1/3) | BSSH; COVID Lineage App; v3.5.12 | | Midline brain hamartomatous lesions in fibrodysplasia ossificans progressiva with *ACVR1* mutations | Neuropathology / [link](https://onlinelibrary.wiley.com/doi/10.1111/neup.12892) | | | Biphenotypic Immunohistochemical Features and NTRK1 Amplification in Intermediate Cell Carcinoma of the Liver | International Journal of Surgical Pathology / [link](http://journals.sagepub.com/doi/10.1177/10668969221142043) | | | Comparative analysis of tumor content estimation methods based on simu-lated tumor samples identified their impact on somatic variant detection in cancer whole genome sequencing | Biomedical Research / [link](https://www.jstage.jst.go.jp/article/biomedres/44/4/44_161/_article/-char/ja/) | | | Novel association of Dandy–Walker malformation with *CAPN15* variants expands the phenotype of oculogastrointestinal neurodevelopmental syndrome | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/10.1002/ajmg.a.63363) | | | Nicotine, THC, and Dolutegravir Modulate E-Cigarette-Induced Changes in Addiction-and Inflammation-Associated Genes in Rat Brains and Astrocytes | Brain Sciences / [link](https://www.mdpi.com/2076-3425/13/11/1556) | | | epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data | GigaScience / [link](https://doi.org/10.1093/gigascience/giad087) | v3.9.5; Methylation pipeline | | Clinical Validation of Tagmentation-Based Genome Sequencing for Germline Disorders | The Journal of Molecular Diagnostics / [link](https://www.sciencedirect.com/science/article/pii/S1525157823000776) | SV caller; v3.8.4 | | Low-pass whole-genome and targeted sequencing of cell-free DNA from cerebrospinal fluid in pediatric patients with central nervous system tumors | Neuro-Oncology Advances / [link](https://academic.oup.com/noa/article-abstract/5/1/vdad077/7209725) | tumor-only liquid-biopsy variant calling pipeline; v3.5.7 | | The incorporation of next-generation sequencing into pediatric care | Pediatrics & Neonatology / [link](https://www.sciencedirect.com/science/article/pii/S1875957222002480) | | | The clinical characteristics of pediatric patients infected by SARS-CoV-2 Omicron variant and whole viral genome sequencing analysis | Plos one / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0282389) | COVID Lineage | | Scalable, high quality, whole genome sequencing from archived, newborn, dried blood spots | NPJ Genomic Medicine / [link](https://www.nature.com/articles/s41525-023-00349-w) | | | Effects of protein-coding variants on blood metabolite measurements and clinical biomarkers in the UK Biobank | The American Journal of Human Genetics / [link](https://www.cell.com/ajhg/pdf/S0002-9297\(23\)00046-0.pdf) | Germline Pipeline v3.0.7 | | Monogenic diabetes clinic (MDC): 3-year experience | Acta Diabetologica / [link](https://doi.org/10.1007/s00592-022-01972-2) | BSSH; Germline Enrichment app | | Identification of *RP1* as the genetic cause of retinitis pigmentosa in a multi-generational pedigree using Extremely Low-Coverage Whole Genome Sequencing (XLC-WGS) | Gene / [link](https://www.sciencedirect.com/science/article/pii/S0378111922007764) | | | Evaluation of Breast Implant–Associated Anaplastic Large Cell Lymphoma With Whole Exome and Genome Sequencing | Aesthetic Surgery Journal / [link](https://doi.org/10.1093/asj/sjac282) | v3.8 | | The Genomic landscape of short tandem repeats across multiple ancestries | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0279430) | | | Flavored E-cigarette product aerosols induce transformation of human bronchial epithelial cells | Lung Cancer / [link](https://www.sciencedirect.com/science/article/pii/S0169500223001034) | RNA pipeline; Differential Expression App | | Design and implementation of a hybrid cloud system for large-scale human genomic research | Human Genome Variation / [link](https://www.nature.com/articles/s41439-023-00231-2) | | | Association between hepatic angiosarcoma and end-stage renal disease: nationwide population-based evidence and enriched mutational signature of aristolochic acid exposure | The Journal of Pathology / [link](https://pathsocjournals.onlinelibrary.wiley.com/doi/10.1002/path.6072) | | | Rapid Whole Genome Sequencing Diagnoses and Guides Treatment in Critically Ill Children in Belgium in Less than 40 Hours | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/24/4/4003) | BSSH | | Fibroblast-expressed LRRC15 is a receptor for SARS-CoV-2 spike and controls antiviral and antifibrotic transcriptional programs | PLOS Biology / [link](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001967) | Differential Expression | | Combined low-pass whole genome and targeted sequencing in liquid biopsies for pediatric solid tumors | npj Precision Oncology / [link](https://www.nature.com/articles/s41698-023-00357-0) | alignment; v3.7.3 | | Integrated genetic profiling of archival pediatric high-grade glial tumors and reassessment with 2021 WHO classification of paediatric CNS tumours | Cancer Genetics / [link](https://www.sciencedirect.com/science/article/pii/S221077622300008X) | | | Somatic small-variant calling methods in Illumina DRAGEN™ Secondary Analysis | -- / [link](https://www.biorxiv.org/content/10.1101/2023.03.23.534011v2) | | | Somatic mutation detection workflow validity distinctly influences clinical decision | -- / [link](https://www.biorxiv.org/content/10.1101/2023.10.26.562640v1) | | | Genomic perspectives of SARS CoV-2 in liver disease patients with its clinical correlation: A single centre retrospective study | -- / [link](https://www.biorxiv.org/content/10.1101/2023.02.26.530067v1) | COVID Lineage App | | An accessible patient-derived xenograft model of low-risk myelodysplastic syndromes | Haematologica / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10772503/) | Enrichment pipeline v4.0.3 | | Genetic Profiling of African American Patients With Prostatic Adenocarcinoma Metastatic to the Lymph Nodes: A Pilot Study | Archives of Pathology & Laboratory Medicine / [link](https://doi.org/10.5858/arpa.2022-0274-OA) | BCL convert | | Experimental Evaluation of the Possibility to Detect Cross-Contaminated DNA Samples Based on Genetic Data | Russian Journal of Genetics / [link](https://doi.org/10.1134/S1022795423060066) | alignment | | Identification of copy number variants with genome sequencing: Clinical experiences from the NYCKidSeq program | Clinical Genetics / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/cge.14365) | | | RNA Sequencing Reveals Novel Oncogenic Fusions and Depicts Detailed Fusion Transcripts of *FN1-FGFR1* in Phosphaturic Mesenchymal Tumors | Modern Pathology / [link](https://www.sciencedirect.com/science/article/pii/S0893395223001710) | BSSH; RNA pipeline v3.3.7 | | Fast and reliable detection of repeat expansions in spinocerebellar ataxia using exomes | Journal of Medical Genetics / [link](https://jmg.bmj.com/content/60/7/717) | | | KMT2A-rearranged sarcoma with unusual fusion gene CBX6::KMT2A::PYGO1 | Virchows Archiv / [link](https://doi.org/10.1007/s00428-023-03639-x) | fusion analysis; RNA app v3.10.4 | | An SPG7 mutation as a novel cause of monogenic progressive muscular atrophy | Neurological Sciences / [link](https://doi.org/10.1007/s10072-023-06867-w) | Variant annotation | | A short-term three dimensional culture-based drug sensitivity test is feasible for malignant bone tumors | Human Cell / [link](https://doi.org/10.1007/s13577-023-00982-8) | BSSH; RNA pipeline | | Variants in CLDN5 cause a syndrome characterized by seizures, microcephaly and brain calcifications | Brain / [link](https://doi.org/10.1093/brain/awac461) | | | Transcriptomic Profiling of Placental Cells in Preeclampsia as an Effective Tool for Personalized Medicine | Russian Journal of Genetics / [link](https://doi.org/10.1134/S102279542312013X) | | | SARS-CoV-2 Sequencing for Variant Surveillance | Clinical Applications of Nucleic Acid Amplification / [link](https://doi.org/10.1007/978-1-0716-2950-5_16) | COVID Lineage App; procedure | | Recurrent FOXP4 nonsense variant in two unrelated patients: Association with neurodevelopmental disease and congenital diaphragmatic hernia | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.63006) | | | Hydrolysis of pea protein differentially modulates its effect on iron bioaccessibility, sulfur availability, composition and activity of gut microbial communities in vitro | Food & Function / [link](https://pubs.rsc.org/en/content/articlelanding/2023/fo/d3fo00504f) | | | SNV/indel hypermutator phenotype in biallelic RAD51C variant: Fanconi anemia | Human Genetics / [link](https://link.springer.com/article/10.1007/s00439-023-02550-4) | v3.4.15 | | Hyperinsulinemia acts via acinar insulin receptors to initiate pancreatic cancer by increasing digestive enzyme production and inflammation | Cell Metabolism / [link](https://www.cell.com/cell-metabolism/abstract/S1550-4131\(23\)00372-8) | alignment; BCL convert; BSSH; RNA app | | Respective roles of Pik3ca mutations and cyproterone acetate impregnation in mouse meningioma tumorigenesis | Cancer Gene Therapy / [link](https://www.nature.com/articles/s41417-023-00621-2) | | | An autosomal-dominant childhood-onset disorder associated with pathogenic variants in VCP | American Journal of Human Genetics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10645565/) | alignment; Germline pipeline v3.2.8 | | Identification of human exTreg cells as CD16+CD56+ cytotoxic CD4+ T cells | Nature Immunology / [link](https://www.nature.com/articles/s41590-023-01589-9) | FASTQ toolkit; read trimming | | Generation of quality-controlled SARS-CoV-2 variant stocks | Nature Protocols / [link](https://www.nature.com/articles/s41596-023-00897-6) | BSSH; COVID Lineage App v3.5.11 | | KDM2B-Rearranged Soft Tissue Sarcomas Expand the Concept of BCOR-Associated Sarcoma | Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc / [link](https://doi.org/10.1016/j.modpat.2023.100317) | RNA app; RNA fusion; RNA-Seq Alignment app | | Overexpression of FRA1 (FOSL1) Leads to Global Transcriptional Perturbations, Reduced Cellular Adhesion and Altered Cell Cycle Progression | Cells / [link](https://www.mdpi.com/2073-4409/12/19/2344) | Differential Expression; RNA | | Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations | Cancer Research Communications / [link](https://doi.org/10.1158/2767-9764.CRC-22-0364) | CNV pipeline; HRD caller; v3.9 | | Induction of macrophages matriptase and activation of macrophage stimulating protein 1 in sickle cell anemia - related chronic kidney disease | Physiology / [link](https://journals.physiology.org/doi/abs/10.1152/physiol.2023.38.S1.5734971) | Differential Expression v3.6.3 | | Accurate tumor purity determination is critical for the analysis of homologous recombination deficiency (HRD) | Translational Oncology / [link](https://www.sciencedirect.com/science/article/pii/S193652332300092X) | DRAGEN server; v3.8; somatic tumor-normal workflow; Germline only workflow | | Low microsatellite instability: A distinct instability type in gastric cancer? | Journal of Cancer Research and Clinical Oncology / [link](https://doi.org/10.1007/s00432-023-05430-6) | Somatic mode | | Effects of S-Adenosylhomocysteine Hydrolase Downregulation on Wnt Signaling Pathway in SW480 Cells | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/24/22/16102) | BSSH; RNA Pipeline v3.9.5; Differential Expression App | | Rapid Genome Sequencing Diagnosis in Pediatric Patients with Liver Dysfunction | The Journal of Pediatrics / [link](https://www.sciencedirect.com/science/article/pii/S0022347623003827) | | | Dominant negative variants in IKZF2 cause ICHAD syndrome, a new disorder characterised by immunodysregulation, craniofacial anomalies, hearing impairment, athelia and developmental delay | Journal of Medical Genetics / [link](https://jmg.bmj.com/content/60/11/1092) | | | Chronic stress targets mitochondrial respiratory efficiency in the skeletal muscle of C57BL/6 mice | Cellular and Molecular Life Sciences / [link](https://doi.org/10.1007/s00018-023-04761-4) | v3.9.5; Reference builder v3.10.4; Illumina cloud; Methylation pipeline v3.9.5 | | Replicative Study in Performance-Related Genes of Brazilian Elite Soccer Players Highlights Genetic Differences from African Ancestry and Similarities between Professional and U20 Youth Athletes | Genes / [link](https://www.mdpi.com/2073-4425/14/7/1446) | Germline app | | Whole genome sequencing of CCR5 CRISPR-Cas9-edited Mauritian cynomolgus macaque blastomeres reveals large-scale deletions and off-target edits | Frontiers in Genome Editing / [link](https://www.frontiersin.org/articles/10.3389/fgeed.2022.1031275) | v3.7 | | Genetic testing and family screening in idiopathic pediatric cardiomyopathy: a prospective observational study from a tertiary care center in North India | Egyptian Journal of Medical Human Genetics / [link](https://doi.org/10.1186/s43042-023-00414-0) | haplotype caller | | Distinct Molecular Profiles and Drug Vulnerabilities in Pancreatic Metastases of Renal Cell Carcinoma | -- / [link](https://www.researchsquare.com/article/rs-3375800/v1) | v3.9 | | SARS-CoV-2 Next Generation Sequencing (NGS) data from clinical isolates from the East Texas Region of the United States | Data in Brief / [link](https://www.sciencedirect.com/science/article/pii/S2352340923004304) | | | A Panel-Agnostic Strategy ‘HiPPo’ Improves Diagnostic Efficiency in the UK Genomic Medicine Service | Healthcare / [link](https://www.mdpi.com/2227-9032/11/24/3179) | alignment; CNV caller; small variant caller; v3.2.22; Variant calling | | Trio-based GWAS identifies novel associations and subtype-specific risk factors for cleft palate | Human Genetics and Genomics Advances / [link](https://www.cell.com/hgg-advances/pdf/S2666-2477\(23\)00066-0.pdf) | BSSH; Germline | | Clinical phenotypes and outcomes associated with SARS-CoV-2 Omicron variants BA.2, BA.5 and BQ.1.1 in critically ill patients with COVID-19: a prospective, multicenter cohort study | Intensive Care Medicine Experimental / [link](https://doi.org/10.1186/s40635-023-00536-0) | COVIDSeq Test pipeline; DRAGEN server | | Genetic mapping and prediction for novel lesion mimic in maize demonstrates quantitative effects from genetic background, environment and epistasis | Theoretical and Applied Genetics / [link](https://doi.org/10.1007/s00122-023-04394-y) | Germline small variant caller | | Enhanced production of eicosanoids in plasma and activation of DNA damage pathways in PBMCs are correlated with the severity of ancestral COVID-19 infection | -- / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10516085/) | BSSH; Differential Expression App; RNA Seq app | | Effect of an obesogenic high-fat and high-sucrose diet on hepatic gene expression signatures in male Collaborative Cross mice | American Journal of Physiology-Gastrointestinal and Liver Physiology / [link](https://journals.physiology.org/doi/full/10.1152/ajpgi.00225.2022) | RNA pipeline; Differential expression pipeline | | Dissemination of the Omicron Variant and Its Sub-Lineages among Residents and Travelers in Its First Year of Emergence in Venezuela | Viruses / [link](https://www.mdpi.com/1999-4915/15/7/1460) | | | Population genetic testing and SERPINA1 sequencing identifies unidentified alpha-1 antitrypsin deficiency alleles and gene-environment interaction with hepatitis C infection | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0286469) | BSSH; Germline small variant caller | | Whole-genome sequencing of half-a-million UK Biobank participants | -- / [link](https://www.medrxiv.org/content/10.1101/2023.12.06.23299426v1) | | | In Silico Analysis and In-depth Assessment of a Female Patient with a Missense Mutation in the F12 Gene Associated with Hereditary Angioedema Symptoms: A Case Study | -- / [link](https://www.researchsquare.com/article/rs-3382724/v1) | | | \[Clinical practice of whole-genome sequencing in the rapid diagnosis of critically ill neonates] | Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics / [link](https://europepmc.org/articles/PMC9979393) | | | Investigation of SNP markers for the melatonin production trait in the Hu sheep with bulked segregant analysis | BMC Genomics / [link](https://doi.org/10.1186/s12864-023-09494-z) | Genome pipeline | | HostSeq: a Canadian whole genome sequencing and clinical data resource | BMC Genomic Data / [link](https://doi.org/10.1186/s12863-023-01128-3) | | | Combining cell-free RNA with cell-free DNA in liquid biopsy for hematologic and solid tumors | Heliyon / [link](https://www.cell.com/heliyon/pdf/S2405-8440\(23\)03468-0.pdf) | BSSH; RNA Seq pipeline; v3.8 | | Genomic integration and expression of Felis catus papillomavirus type 2 oncogenes in feline Merkel cell carcinoma | Veterinary Pathology / [link](https://doi.org/10.1177/03009858221139197) | | | Genome-wide analysis for the melatonin trait associated genes and SNPs in dairy goat (Capra hircus) as the molecular breeding markers | Frontiers in Genetics / [link](https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1118367/full) | Genome pipeline | | Activation of thousands of genes in the lungs and kidneys by sepsis is countered by the selective nuclear blockade | Frontiers in Immunology / [link](https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1221102/full) | RNA pipeline v3.3.7; Differential Expression analysis | | Understanding the Impact of Population and Cancer Type on Tumor Mutation Burden Scores: A Comprehensive Whole-Exome Study in Cancer Patients From India | JCO Global Oncology / [link](https://ascopubs.org/doi/full/10.1200/GO.23.00047) | Somatic pipeline; v3.6 | | Limitations in next-generation sequencing-based genotyping of breast cancer polygenic risk score loci | -- / [link](https://www.medrxiv.org/content/10.1101/2023.12.15.23298835v1) | | | STIM1 signals through NFAT1 independently of Orai1 and SOCE to regulate breast cancer cell migration | Cell Calcium / [link](https://www.sciencedirect.com/science/article/pii/S014341602300091X) | Differential Expression; BSSH; RNA-Seq | | Analysis of a hit-and-run tumor model by HPV in oropharyngeal cancers | Journal of Medical Virology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.28260) | v3.9.3; Somatic small variant calling | | Wastewater Genomic Surveillance Captures Early Detection of Omicron in Utah | Microbiology Spectrum / [link](https://journals.asm.org/doi/full/10.1128/spectrum.00391-23) | COVIDSeq Test pipeline | | Evaluation of an automated genome interpretation model for rare disease routinely used in a clinical genetic laboratory | Genetics in Medicine / [link](https://www.sciencedirect.com/science/article/pii/S1098360023008432) | v3.1.5 | | Rare variant associations with plasma protein levels in the UK Biobank | Nature / [link](https://www.nature.com/articles/s41586-023-06547-x) | UK Biobank | | Whole genome and RNA sequencing analyses for 254 Taiwanese hepatocellular carcinomas | Biomarker Research / [link](https://doi.org/10.1186/s40364-023-00492-7) | | | Newborn screening for X-linked adrenoleukodystrophy in Italy: Diagnostic algorithm and disease monitoring | Frontiers in Neurology / [link](https://www.frontiersin.org/journals/neurology/articles/10.3389/fneur.2022.1072256/full) | v3.0 | | Homozygous CDH2 variant may be associated with hypopituitarism without neurological disorders | Endocrine Connections / [link](https://ec.bioscientifica.com/view/journals/ec/12/8/EC-22-0473.xml) | CNV pipeline | | Reinfection rate and disease severity of the BA.5 Omicron SARS-CoV-2 lineage compared to previously circulating variants of concern in the Canary Islands (Spain) | Emerging Microbes & Infections / [link](https://doi.org/10.1080/22221751.2023.2202281) | v1.3 | | Cellular myofibromas with *SRF* fusions: clinicopathological and molecular study of 3 cases of a rare entity and a potential mimic of sarcoma | Human Pathology / [link](https://www.sciencedirect.com/science/article/pii/S0046817723001235) | RNA pipeline; BSSH | | Rapid Whole-Genomic Sequencing and a Targeted Neonatal Gene Panel in Infants With a Suspected Genetic Disorder | JAMA / [link](https://doi.org/10.1001/jama.2023.9350) | v3.7 | | Applications of artificial intelligence in clinical laboratory genomics | American Journal of Medical Genetics Part C: Seminars in Medical Genetics / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.c.32057) | review | | Intermediate repeat expansions of *TBP* and *STUB1*: Genetic modifier or pure digenic inheritance in spinocerebellar ataxias? | Genetics in Medicine / [link](https://www.sciencedirect.com/science/article/pii/S1098360022009959) | Variant calling; alignment | | Genomic surveillance identifies SARS-CoV-2 transmission patterns in local university populations, Wisconsin, USA, 2020–2022 | Microbial Genomics / [link](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000970) | COVID Lineage Pipeline | | SCN1A Gene Mutations in Indian Children With Epilepsy: Single Center Experience | Indian Pediatrics / [link](https://doi.org/10.1007/s13312-023-2964-4) | | | Immune evasion and membrane fusion of SARS-CoV-2 XBB subvariants EG.5.1 and XBB.2.3 | Emerging Microbes & Infections / [link](https://doi.org/10.1080/22221751.2023.2270069) | COVID Lineage | | Genomic analysis identifies risk factors in restless legs syndrome | -- / [link](https://www.medrxiv.org/content/10.1101/2023.12.19.23300211v1) | v3.4.12 | | Capicua (CIC) mutations in gliomas in association with MAPK activation for exposing a potential therapeutic target | Medical Oncology / [link](https://doi.org/10.1007/s12032-023-02071-0) | BCL convert | | Clinical characteristics and outcomes of laboratory-confirmed SARS-CoV-2 cases infected with omicron subvariants and the XBB recombinant variant | Cureus / [link](https://www.cureus.com/articles/138573-clinical-characteristics-and-outcomes-of-laboratory-confirmed-sars-cov-2-cases-infected-with-omicron-subvariants-and-the-xbb-recombinant-variant.pdf) | alignment; COVID Lineage App | | Comprehensive prenatal diagnostics: Exome versus genome sequencing | Prenatal Diagnosis / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/pd.6402) | | | Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia | Leukemia / [link](https://www.nature.com/articles/s41375-022-01806-8) | | | Report of two cases of Schaaf‐Yang syndrome: Same genotype and different phenotype | Clinical Case Reports / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10387585/) | SNV | | Dysfunctional mitophagy associated mutation in THP-1 cells | Atherosclerosis / [link](https://www.atherosclerosis-journal.com/article/S0021-9150\(23\)04291-0/fulltext) | | | Balanced Translocation Disrupting *JAG1* Identified by Optical Genomic Mapping in Suspected Alagille Syndrome | Human Mutation / [link](https://www.hindawi.com/journals/humu/2023/5396281/) | v3.2.8 | | Disentangling archaic introgression and genomic signatures of selection at human immunity genes | Infection, Genetics and Evolution / [link](https://www.sciencedirect.com/science/article/pii/S1567134823001260) | v3.6.4 | | Intracranial mesenchymal tumor with (novel) COX14::PTEN rearrangement | Acta Neuropathologica Communications / [link](https://doi.org/10.1186/s40478-023-01596-9) | v3.7.5; RNA | | Impaired neutralizing antibody efficacy of tixagevimab-cilgavimab 150+150 mg as pre-exposure prophylaxis against Omicron BA.5. A real-world experience in booster vaccinated immunocompromised patients | Journal of Clinical Virology / [link](https://www.sciencedirect.com/science/article/pii/S138665322300207X) | COVID Lineage v3.5.13 | | Direct Saliva Analysis by MALDI Mass Spectrometry: A Workflow Suitable for Future Clinical Applications | The Journal of Liquid Biopsy / [link](https://www.journalofliquidbiopsy.com/article/S2950-1954\(23\)00055-3/fulltext) | | | Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs | Journal of Computational Biology / [link](https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0186) | v3.10.4 | | Associations of MYPN, TTN, SCN5A, MYO6 and ELN Mutations With Arrhythmias and Subsequent Sudden Cardiac Death: A Case Report of an Ecuadorian Individual | Cardiology Research / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10627373/) | Enrichment pipeline v3.9.5 | | Detection of an *MN1::ETV6* Gene Fusion in a Case of Acute Myeloid Leukemia with Erythroid Differentiation: A Case Report and Review of the Literature | Case Reports in Hematology / [link](https://www.hindawi.com/journals/crihem/2023/9771388/) | Somatic pipeline v3.8.4 | | Metastatic insulinoma: exploration from clinicopathological signatures and genetic characteristics | Frontiers in Oncology / [link](https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2023.1109330/full) | | | Preliminary analysis of oral and gut microbiome of an elderly patient with late-diagnosed phenylketonuria | Annals of Agricultural and Environmental Medicine / [link](http://agro.icm.edu.pl/agro/element/bwmeta1.element.agro-e59fc564-20e1-478e-a8f5-5309b3b718cb) | | | Expanding individualized therapeutic options via genoproteomics | Cancer Letters / [link](https://www.sciencedirect.com/science/article/pii/S0304383523000745) | | | Hypolipidemic treatment increases lipoprotein(a) levels in patients with mixed hyperlipidemia | Atherosclerosis / [link](https://www.atherosclerosis-journal.com/article/S0021-9150\(23\)04293-4/fulltext) | | | An overview of SARS-CoV-2 variants circulating in the 2020–2022 period in Lombardy | Diagnostic Microbiology and Infectious Disease / [link](https://www.sciencedirect.com/science/article/pii/S0732889323001797) | COVID Lineage App | | Insights into the Rare cis-AB Blood Group: In Silico Genotyping and Analysis in the Indian Subcontinent | -- / [link](https://osf.io/f4xr7) | v3.4 | | Novel STAT3 variant causing infantile-onset autoimmune disease | Frontiers in Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10666157/) | BSSH; Germline pipeline | | Adipose tissue insulin resistance exacerbates liver inflammation and fibrosis in a diet-induced NASH model | Hepatology Communications / [link](https://journals.lww.com/hepcomm/fulltext/2023/06010/Adipose_tissue_insulin_resistance_exacerbates.20.aspx) | v3.6.3 | | Immune dysregulation, polyendocrinopathy and enteropathy, X-linked (IPEX) syndrome due to a mutation in FOXP3, modified by a pathogenic variant in SON (SON DNA-binding protein) | Journal of Applied Genetics / [link](https://doi.org/10.1007/s13353-022-00728-6) | Variant calling; alignment | | Personalized neoantigen-based T cell therapy triggers cytotoxic lymphocytes expressing polyclonal TCR against metastatic ovarian cancer | Biomedicine & Pharmacotherapy / [link](https://www.sciencedirect.com/science/article/pii/S0753332223017262) | | | High mortality and morbidity among vaccinated residents infected with the SARS-CoV-2 Omicron variant during an outbreak in a nursing home in Kyoto City, Japan | American Journal of Infection Control / [link](https://www.sciencedirect.com/science/article/pii/S0196655322006757) | COVID Lineage App | | Myosin Mutations and Sudden Sensorineural Hearing Loss: Results of Whole Exome Sequencing | Otology & Neurotology / [link](https://journals.lww.com/otology-neurotology/abstract/2023/01000/myosin_mutations_and_sudden_sensorineural_hearing.5.aspx) | | | Genomic alterations in chronic myeloid leukaemia patients who failed second generation tyrosine kinase inhibitor | Pathology / [link](https://www.pathologyjournal.rcpa.edu.au/article/S0031-3025\(22\)00648-1/fulltext) | | | Exome-First Strategy in Adult Patients With CKD: A Cohort Study | Kidney International Reports / [link](https://www.sciencedirect.com/science/article/pii/S2468024922019027) | BCL convert | | Genomic Surveillance Reveals the Rapid Expansion of the XBB Lineage among Circulating SARS-CoV-2 Omicron Lineages in Southeastern Wisconsin, USA | Viruses / [link](https://www.mdpi.com/1999-4915/15/9/1940) | COVID Lineage | | Development of a somatic variant registry in a National Cancer Center: towards Molecular Real World Data preparedness | Journal of Biomedical Informatics / [link](https://www.sciencedirect.com/science/article/pii/S1532046423001156) | | | The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub | Viruses / [link](https://www.mdpi.com/1999-4915/15/4/888) | | | Success and Pitfalls of Genetic Testing in Undiagnosed Diseases: Whole Exome Sequencing and Beyond | Genes / [link](https://www.mdpi.com/2073-4425/14/6/1241) | | | FUS-ERG induces late-onset azacitidine resistance in acute myeloid leukaemia cells | Scientific Reports / [link](https://www.nature.com/articles/s41598-023-41230-1) | v3.9.5 | | Novel compound heterozygous variants (c.971delA/c.542C > T) in SLC1A4 causes spastic tetraplegia, thin corpus callosum, and progressive microcephaly: a case report and mutational analysis | Frontiers in Pediatrics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10369183/) | | | Genetic insights into childhood-onset schizophrenia: The yield of clinical exome sequencing | Schizophrenia Research / [link](https://www.sciencedirect.com/science/article/pii/S0920996422004807) | v2.5.1 | | Short-term Weight Trajectory of Severely Obese Individuals With and Without Pathogenic Satiety-Regulation Melanocortin 3/4 Receptor (MC3/4R) Mutations From a Multi-ethnic Asian Large Bariatric Surgery Program | Journal of Investigative Medicine High Impact Case Reports / [link](https://doi.org/10.1177/23247096231168108) | DNA amplicon app | | Clinical and molecular features of four Brazilian families with multiple endocrine neoplasia type 1 | Frontiers in Endocrinology / [link](https://www.frontiersin.org/journals/endocrinology/articles/10.3389/fendo.2023.1117873/full) | Germline pipeline v3.5.7 | | A concurrent dual analysis of genomic data augments diagnoses: Experiences of 2 clinical sites in the Undiagnosed Diseases Network | Genetics in Medicine / [link](https://www.sciencedirect.com/science/article/pii/S1098360022010589) | CNV pipeline | | Concurrent predictors of an immune responsive tumor microenvironment within tumor mutational burden-high breast cancer | Frontiers in Oncology / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10457522/) | | | Genetic heterogeneity and enrichment of variants in DNA-repair genes in ameloblastoma | Journal of Oral Pathology & Medicine / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/jop.13410) | v3.2.8; alignment | | Functional and Molecular Heterogeneity in Glioma Stem Cells Derived from Multiregional Sampling | Cancers / [link](https://www.mdpi.com/2072-6694/15/24/5826) | | | Complex Microphthalmia due to a Homozygous Novel Variant in SIX Homeobox 6 Gene | Delhi Journal of Ophthalmology / [link](https://journals.lww.com/djo/fulltext/2023/33010/Complex_Microphthalmia_due_to_a_Homozygous_Novel.10.aspx?context=LatestArticles) | Variant calling | | Extracellular matrix remodelling and stiffening contributes to tumorigenesis of salivary carcinoma ex pleomorphic adenoma——A study based on patient-derived organoids | Cell & Bioscience / [link](https://doi.org/10.1186/s13578-023-01071-x) | | | Kohlschutter-Tonz syndrome (amelo-cerebro-hypohidrotic syndrome) in an Indian family with a novel ROGD1 mutation | Clinical Dysmorphology / [link](https://journals.lww.com/clindysmorphol/citation/2023/10000/kohlschutter_tonz_syndrome.5.aspx) | | | GAMT Deficiency Among Pediatric Population: Clinical and Molecular Characteristics and Management | Child Neurology Open / [link](https://doi.org/10.1177/2329048X231215630) | v3.4.12 | | Loss of Nudt15 thiopurine detoxification increases direct DNA damage in hematopoietic stem cells | Scientific Reports / [link](https://www.nature.com/articles/s41598-023-38952-7) | v3.7.5 | | SLC25A48 is a human mitochondrial choline transporter | -- / [link](https://www.medrxiv.org/content/10.1101/2023.12.04.23299390v1) | Germline pipeline | | Fetal de novo heterozygous variant in the isocitrate dehydrogenase 1 gene associated with growth restriction, skeletal, cerebral and vascular anomalies | Prenatal Diagnosis / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/pd.6433) | | | Diagnosis of Kidney Diseases of Unknown Etiology Through Biopsy-Genetic Analysis | Kidney International Reports / [link](https://www.sciencedirect.com/science/article/pii/S2468024923013815) | BCL convert | | Pompe disease ascertained through The Lantern Project, 2018–2021: Next-generation sequencing and enzymatic testing to overcome obstacles to diagnosis | Molecular Genetics and Metabolism / [link](https://www.sciencedirect.com/science/article/pii/S1096719223001956) | v3.4.12 | | Comprehensive Analysis and Drug Modulation of Human Endogenous Retrovirus in Hepatocellular Carcinomas | Cancers / [link](https://www.mdpi.com/2072-6694/15/14/3664) | | | Impact of High-to-Moderate Penetrance Genes on Genetic Testing: Looking over Breast Cancer | Genes / [link](https://www.mdpi.com/2073-4425/14/8/1530) | Enrichment software v4.0.3 | | Factor XIII Deficiency in Three Iraqi patients with a Variations in Gene F13A1 Detected by Next Generation Sequencing | Migration Letters / [link](https://migrationletters.com/index.php/ml/article/view/5204) | Germline pipeline | | Circulating Variants of SARS-CoV-2 Among Macedonian COVID - 19 Patients in the First Year of Pandemic | PRILOZI / [link](https://www.sciendo.com/article/10.2478/prilozi-2023-0018) | BSSH; RNA pathogen detection app v3.5.15 | | A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India | Journal of Infection and Public Health / [link](https://www.sciencedirect.com/science/article/pii/S1876034123002113) | alignment; BSSH | | 3′ UTR Deletion of FBXO28 in a Patient with Brain Abnormalities and Developmental Delay | Genes / [link](https://www.mdpi.com/2073-4425/14/9/1687) | Variant calling; v3.8.4 | | DNA Methylation Near CPT1A and Changes in Triglyceride-rich Lipoproteins in Response to Weight-loss Diet Interventions | The Journal of Clinical Endocrinology & Metabolism / [link](https://doi.org/10.1210/clinem/dgad086) | | | Differential outcomes and immune checkpoint inhibitor response among endometrial cancer patients with *MLH1* hypermethylation versus *MLH1* “Lynch-like” mismatch repair gene mutation | Gynecologic Oncology / [link](https://www.sciencedirect.com/science/article/pii/S0090825823014579) | BCL convert | | Dynamics of disease characteristics and viral RNA decay in patients with asymptomatic and mild infections during the Omicron wave in Shanghai, China: A retrospective cohort study | International Journal of Infectious Diseases / [link](https://www.sciencedirect.com/science/article/pii/S120197122300067X) | | | Biallelic truncating variants in children with titinopathy represent a recognizable condition with distinctive muscular and cardiac characteristics: a report on five patients | Frontiers in Cardiovascular Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10415037/) | alignment; BSSH; Enrichment app | | Duplication at 19q13.32q13.33 Segregating with Neuropsychiatric Phenotype in a Three-Generation Family: Towards the Definition of a Critical Region | Genes / [link](https://www.mdpi.com/2073-4425/14/12/2157) | Germline Pipeline | | A transgenerational mutational signature from ionizing radiation exposure | -- / [link](https://www.medrxiv.org/content/10.1101/2023.11.20.23298689v1) | Variant calling | | RNA analysis of intronic variants in the LAMA2 gene detected by whole genome sequencing confirms a rare dual diagnosis of incontinentia pigmenti with limb-girdle muscular dystrophy | Clinical Case Reports / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ccr3.7165) | v2.0.3 | | Discrepancies in tumor mutation burden reporting from sequential endobronchial ultrasound transbronchial needle aspiration samples within single lymph node stations - brief report | Frontiers in Oncology / [link](https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2023.1259882/full) | v2.1 | | A New Case of Autosomal-Dominant POLR3B-Related Disorder: Widening Genotypic and Phenotypic Spectrum | Brain Sciences / [link](https://www.mdpi.com/2076-3425/13/11/1567) | BSSH; Enrichment app | | Limitations of gene editing assessments in human preimplantation embryos | Nature Communications / [link](https://www.nature.com/articles/s41467-023-36820-6) | Germline pipeline; Joint genotyping pipeline | | Three cases of colon cancer in four generations of the Saudi family, caused by endogamous germline mutations | Cellular and Molecular Biology / [link](http://www.cellmolbiol.org/index.php/CMB/article/view/4890) | | | A novel de novo pathogenic variant in TBL1XR1 as a new proposed cause of Pierpont syndrome | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.63162) | | | Technical feasibility of newborn screening for spinal muscular atrophy by next-generation DNA sequencing | Frontiers in Genetics / [link](https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1095600/full) | BCL convert | | Clinical Performance of BD Veritor™ Assay Across SARS-CoV-2 Variants | -- / [link](https://www.medrxiv.org/content/10.1101/2023.04.11.23288130v1) | COVID Lineage App v3.5.9 | | Genomic Characterization of Rare Primary Cardiac Sarcoma Entities | Diagnostics / [link](https://www.mdpi.com/2075-4418/13/2/214) | RNA app | | Deep Intronic LINE-1 Insertions in NF1: Expanding the Spectrum of Neurofibromatosis Type 1-Associated Rearrangements | Biomolecules / [link](https://www.mdpi.com/2218-273X/13/5/725) | | | Genomic Signatures of Positive Selection in Human Populations of the OXT, OXTR, AVP, AVPR1A and AVR1B Gene Variants Related to the Regulation of Psychoemotional Response | Genes / [link](https://www.mdpi.com/2073-4425/14/11/2053) | alignment | | The current benefit of genome sequencing compared to exome sequencing in patients with developmental or epileptic encephalopathies | Molecular Genetics & Genomic Medicine / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/mgg3.2148) | | | Comprehensive genomic profiling of penile squamous cell carcinoma and the impact of human papillomavirus status on immune-checkpoint inhibitor-related biomarkers | Cancer / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/cncr.34982) | | | Chromosomal instability and a deregulated cell cycle are intrinsic features of high-risk gastrointestinal stromal tumours with a metastatic potential | Molecular Oncology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/1878-0261.13514) | Germline pipeline v3.9 | | Mouse and human studies support *DSTYK* loss of function as a low-penetrance and variable expressivity risk factor for congenital urinary tract anomalies | Genetics in Medicine / [link](https://www.sciencedirect.com/science/article/pii/S1098360023009991) | v3 | | Genomic Strategies in Mitochondrial Diagnostics | Mitochondrial DNA: Methods and Protocols / [link](https://doi.org/10.1007/978-1-0716-2922-2_27) | protocol | | EndoC-βH5 cells are storable and ready-to-use human pancreatic beta cells with physiological insulin secretion | Molecular Metabolism / [link](https://www.sciencedirect.com/science/article/pii/S2212877823001060) | v3.8.4 | | HER2+ endometrioid endometrial cancer possesses distinct molecular and immunologic features associated with a more active immune microenvironment and worse prognosis | Gynecologic Oncology / [link](https://www.sciencedirect.com/science/article/pii/S0090825823001415) | BCL convert | | Breaking Barriers to Rapid Whole Genome Sequencing in Pediatrics: Michigan’s Project Baby Deer | Children / [link](https://www.mdpi.com/2227-9067/10/1/106) | CNV | | The Effect of Long-Term Inorganic Iodine on Intrathyroidal Iodothyronine Content and Gene Expression in Mice with Graves' Hyperthyroidism | Thyroid® / [link](https://www.liebertpub.com/doi/full/10.1089/thy.2022.0496) | v3.6.3 | | Mucopolysaccharidosis Type I Presenting with Persistent Neonatal Respiratory Distress: A Case Report | Diseases / [link](https://www.mdpi.com/2079-9721/11/2/67) | v3.4.12 | | Anti-inflammatory effects of cold atmospheric plasma irradiation on the THP-1 human acute monocytic leukemia cell line | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0292267) | v3.6.3 | | Genetic Sequencing of Breakthrough Severe Acute Respiratory Syndrome Coronavirus 2 Infections in Fully Vaccinated Healthcare Workers | Infectious Diseases in Clinical Practice / [link](https://journals.lww.com/infectdis/fulltext/2023/01000/genetic_sequencing_of_breakthrough_severe_acute.23.aspx) | BSSH | | DNA methylation signature in NSD2 loss-of-function variants appeared similar to that in Wolf-Hirschhorn syndrome | -- / [link](https://www.biorxiv.org/content/10.1101/2023.01.06.522834v1) | | | Combined sequence and copy number analysis improves diagnosis of limb girdle and other myopathies | Annals of Clinical and Translational Neurology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/acn3.51896) | v3.4.12 | | Presence of known feline ALMS1 and MYBPC3 variants in a diverse cohort of cats with hypertrophic cardiomyopathy in Japan | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0283433) | v3.6 | | Plant GARDEN: a portal website for cross-searching between different types of genomic and genetic resources in a wide variety of plant species | BMC Plant Biology / [link](https://doi.org/10.1186/s12870-023-04392-8) | | | Whole Exome Sequence Analysis for Inborn Errors of IL-12/IFN-*γ* Axis in Patient with Recurrent Typhoid Fever | BioMed Research International / [link](https://www.hindawi.com/journals/bmri/2023/1761283/) | Genome pipeline | | Long-Term Culturing of FreeStyle 293-F Cells Affects Immunoglobulin G Glycome Composition | Biomolecules / [link](https://www.mdpi.com/2218-273X/13/8/1245) | Differential Expression tool | | Commercially available SARS-CoV-2 RT-qPCR diagnostic tests need obligatory internal validation | Scientific Reports / [link](https://www.nature.com/articles/s41598-023-34220-w) | COVID Lineage Pipeline | | Expanding the spectrum of neonatal-onset AIFM1-associated disorders | Annals of Clinical and Translational Neurology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/acn3.51876) | | | Genomic and Transcriptomic Landscape of RET Wild-Type Medullary Thyroid Cancer and Potential Use of Mitogen-Activated Protein Kinase-Targeted Therapy | Journal of the American College of Surgeons / [link](https://journals.lww.com/journalacs/abstract/9900/genomic_and_transcriptomic_landscape_of_ret.967.aspx) | | | Diagnostic Utility of Exome Sequencing Among Israeli Children With Kidney Failure | Kidney International Reports / [link](https://www.sciencedirect.com/science/article/pii/S2468024923013980) | CNV | | In-Depth Comparison of Genetic Variants Demonstrates a Close Relationship Between Invasive and Intraductal Components of Prostate Cancer | Modern Pathology / [link](https://www.sciencedirect.com/science/article/pii/S0893395223000352) | | | Mutation in Chek2 triggers von Hippel-Lindau hemangioblastoma growth | Acta Neurochirurgica / [link](https://doi.org/10.1007/s00701-023-05825-x) | v3.6.3 | | Genomic analysis of a Palestinian family with inherited cancer syndrome: a next-generation sequencing study | Frontiers in Genetics / [link](https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2023.1230241/full) | | | Non-invasive harvesting of conjunctival cells for whole transcriptome sequencing | Experimental Eye Research / [link](https://www.sciencedirect.com/science/article/pii/S0014483523002348) | BCL convert | | RNA Sequencing in Hypoxia-Adapted T98G Glioblastoma Cells Provides Supportive Evidence for IRE1 as a Potential Therapeutic Target | Genes / [link](https://www.mdpi.com/2073-4425/14/4/841) | v3.3.7 | | Systematic lung ultrasound in Omicron-type vs. wild-type COVID-19 | European Heart Journal - Cardiovascular Imaging / [link](https://doi.org/10.1093/ehjci/jeac212) | | | Influence of scat ageing on the gut microbiome: how old is too old? | BMC Genomics / [link](https://doi.org/10.1186/s12864-023-09520-0) | BCL convert | | Genome characterization, phylogenomic assessment and spatio-temporal dynamics study of highly mutated BA variants from India | Indian Journal of Medical Microbiology / [link](https://www.sciencedirect.com/science/article/pii/S0255085722002328) | BSSH; COVID Lineage | | Interplay between Nrf2 and αB-crystallin in the lens and heart of zebrafish under proteostatic stress | Frontiers in Molecular Biosciences / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10422029/) | Differential Expression; RNA Seq pipeline | | Genomic surveillance reveals circulation of multiple variants and lineages of SARS-CoV-2 during COVID-19 pandemic in Indian city of Bengaluru | -- / [link](https://www.biorxiv.org/content/10.1101/2023.03.14.532352v1) | COVID Lineage App | | The Expanding Phenotype of ZTTK Syndrome Due to the Heterozygous Variant of SON Gene Focusing on Liver Involvement: Patient Report and Literature Review | Genes / [link](https://www.mdpi.com/2073-4425/14/3/739) | Germline Enrichment app | | Whole exome data prioritization unveils the hidden weight of Mendelian causes of male infertility. A report from the first Italian cohort | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0288336) | Germline pipeline | | Mutational Analysis of Circulating Omicron SARS-CoV-2 Lineages in the Al-Baha Region of Saudi Arabia | Journal of Multidisciplinary Healthcare / [link](https://www.tandfonline.com/doi/full/10.2147/JMDH.S419859) | | | The Suitability of RNA from Positive SARS-CoV-2 Rapid Antigen Tests for Whole Virus Genome Sequencing and Variant Identification to Maintain Genomic Surveillance | Diagnostics / [link](https://www.mdpi.com/2075-4418/13/24/3618) | BSSH; COVID Lineage | | High incidence of occult familial SDHD cases amongst Czech patients with head and neck paragangliomas | Frontiers in Endocrinology / [link](https://www.frontiersin.org/journals/endocrinology/articles/10.3389/fendo.2023.1278175/full) | | | The emergence of Omicron VOC and its rapid spread and persistence in the Western Amazon | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0285742) | BSSH; COVID Lineage | | Polygenic Risk of Epilepsy and Post-Stroke Epilepsy | -- / [link](https://www.medrxiv.org/content/10.1101/2023.09.18.23295739v1) | v3.4.12 | | Pharmacogenetics of tuberculosis treatment toxicity and effectiveness in a large Brazilian cohort | -- / [link](https://www.medrxiv.org/content/10.1101/2023.08.30.23294860v1) | BSSH; Joint genotyping pipeline; Germline app | | Productive infection of primary human hepatocytes with SARS-CoV-2 induces antiviral and proinflammatory responses | Gut / [link](https://gut.bmj.com/content/early/2023/12/12/gutjnl-2023-330961) | | | Genomic variants exclusively identified in children with birth defects and concurrent malignant tumors predispose to cancer development | Molecular Cancer / [link](https://doi.org/10.1186/s12943-023-01828-5) | | | Timeline of SARS-CoV-2 Transmission in Sabah, Malaysia: Tracking the Molecular Evolution | Pathogens / [link](https://www.mdpi.com/2076-0817/12/8/1047) | | | Neutropenia associated with delay to processing FBC samples | Pathology / [link](https://www.pathologyjournal.rcpa.edu.au/article/S0031-3025\(22\)00646-8/fulltext) | | | Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial | -- / [link](https://www.researchsquare.com/article/rs-3723914/v1) | | | Blood transcriptome responses in patients correlate with severity of COVID-19 disease | Frontiers in Immunology / [link](https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2022.1043219/full) | BCL convert | | Precision Medicine in a Community Cancer Center: Pan-Cancer DNA/RNA Sequencing of Tumors Reveals Clinically Relevant Gene Fusions | Biologics / [link](https://www.mdpi.com/2673-8449/3/3/11) | demultiplexing | | High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol | Genes / [link](https://www.mdpi.com/2073-4425/14/3/681) | BCL convert | | Investigation of SARS-CoV-2 Transmission in The Tabernacle Choir at Temple Square in the Context of Prevention Protocols, Utah, September–November 2021 | Public Health Reports® / [link](https://doi.org/10.1177/00333549231152198) | | | The Influenza B Virus Victoria and Yamagata Lineages Display Distinct Cell Tropism and Infection-Induced Host Gene Expression in Human Nasal Epithelial Cell Cultures | Viruses / [link](https://www.mdpi.com/1999-4915/15/9/1956) | RNA pathogen detection pipeline | | Fecal microbiota transplanted from old mice promotes more colonic inflammation, proliferation, and tumor formation in azoxymethane-treated A/J mice than microbiota originating from young mice | Gut Microbes / [link](https://doi.org/10.1080/19490976.2023.2288187) | DRAGEN server; BCL convert | | The clinical utility of rapid exome sequencing in a consanguineous population | Genome Medicine / [link](https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-023-01192-5) | DRAGEN server v3 | | Etiology of acute febrile illness in the peruvian amazon as determined by modular formatted quantitative PCR: a protocol for RIVERA, a health facility-based case-control study | BMC Public Health / [link](https://doi.org/10.1186/s12889-023-15619-6) | COVID Lineage App v3.5.7 | | Use of Optical Genome Mapping to Detect Structural Variants in Neuroblastoma | Cancers / [link](https://www.mdpi.com/2072-6694/15/21/5233) | alignment | | Inhibition of oxidative stress-induced epithelial-mesenchymal transition in retinal pigment epithelial cells of age-related macular degeneration model by suppressing ERK activation | Journal of Advanced Research / [link](https://www.sciencedirect.com/science/article/pii/S2090123223001674) | mRNA quantification pipeline | | Prenatal diagnosis of lanosterol synthase deficiency: Fetal ultrasound findings as a window on family genetics | European Journal of Medical Genetics / [link](https://www.sciencedirect.com/science/article/pii/S1769721223001313) | SNV; CNV | | Amp(1q) and tetraploidy are commonly acquired chromosomal abnormalities in relapsed multiple myeloma | European Journal of Haematology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/ejh.13905) | BSSH; Somatic app v3.8.4; tumor-only mode | | Functional Epicardial Conduction Disturbances Due to a SCN5A Variant Associated With Brugada Syndrome | JACC: Clinical Electrophysiology / [link](https://www.jacc.org/doi/full/10.1016/j.jacep.2023.03.009) | | | CoVEx: SARS-CoV-2 Mutation Explorer for genomic surveillance | Infection, Genetics and Evolution / [link](https://www.sciencedirect.com/science/article/pii/S1567134823001193) | COVID Lineage App v3.5.13 | | Quantification of the escape from X chromosome inactivation with the million cell-scale human single-cell omics datasets reveals heterogeneity of escape across cell types and tissues | -- / [link](https://www.biorxiv.org/content/10.1101/2023.10.14.561800v1) | v3.8.4; Single cell RNA pipeline | | Identifying Genomic Signatures of Positive Selection to Predict Protective Genomic Loci in the Cohort of Lithuanian Clean-Up Workers of the Chornobyl Nuclear Disaster | Current Issues in Molecular Biology / [link](https://www.mdpi.com/1467-3045/45/4/195) | v3.6.4 | | Comparative Genomic Analysis of Pancreatic Acinar Cell Carcinoma (PACC) and Pancreatic Ductal Adenocarcinoma (PDAC) Unveils New Actionable Genomic Aberrations in PACC | Clinical Cancer Research / [link](https://doi.org/10.1158/1078-0432.CCR-22-3724) | | | Prevalence of familial BRCA1/2 mutation in four cancer types in the United Arab Emirates and of Arab Nationals | -- / [link](https://www.researchsquare.com/article/rs-3705910/v1) | BSSH; Enrichment app | | Strong protective effect of the APOL1 p.N264K variant against G2-associated focal segmental glomerulosclerosis and kidney disease | Nature Communications / [link](https://www.nature.com/articles/s41467-023-43020-9) | | | Improving the response to oxaliplatin by targeting chemotherapy-induced CLDN1 in resistant metastatic colorectal cancer cells | Cell & Bioscience / [link](https://doi.org/10.1186/s13578-023-01015-5) | v3.8.4 | | Epidermal differentiation complex genetic variation in atopic dermatitis and peanut allergy | Journal of Allergy and Clinical Immunology / [link](https://www.sciencedirect.com/science/article/pii/S0091674922015664) | Germline small variant caller | | An aptamer-mediated base editing platform for simultaneous knock-in and multiple gene knockout for allogeneic CAR-T cells generation | -- / [link](https://www.biorxiv.org/content/10.1101/2023.06.20.545315v1) | SV caller v3.8.4; RNA pipeline v3.7.5 | | Danon Disease: Entire LAMP2 Gene Deletion with Unusual Clinical Presentation—Case Report and Review of the Literature | Genes / [link](https://www.mdpi.com/2073-4425/14/8/1539) | v3.6 | | Genomic and Epidemiologic Surveillance of SARS-CoV-2 in the Pandemic Period: Sequencing Network of the Lazio Region, Italy | Viruses / [link](https://www.mdpi.com/1999-4915/15/11/2192) | BSSH | | PTPA variants and impaired PP2A activity in early-onset parkinsonism with intellectual disability | Brain / [link](https://doi.org/10.1093/brain/awac326) | | | Sensitive Detection of Cell-Free Tumour DNA Using Optimised Targeted Sequencing Can Predict Prognosis in Gastro-Oesophageal Cancer | Cancers / [link](https://www.mdpi.com/2072-6694/15/4/1160) | BCL convert | | Biallelic loss of function variants in WBP4, encoding a spliceosome protein, result in a variable neurodevelopmental delay syndrome | -- / [link](https://www.medrxiv.org/content/10.1101/2023.06.19.23291425v1) | Variant calling; alignment; SNV; CNV; SV | | Ependymoma-like tumor with mesenchymal differentiation (ELTMD) with ZFTA:NCOA1 fusion: A diagnostic challenge | Neuropathology: Official Journal of the Japanese Society of Neuropathology / [link](https://onlinelibrary.wiley.com/doi/10.1111/neup.12952) | BSSH; RNA pipeline | | The Cold-Adapted, Temperature-Sensitive SARS-CoV-2 Strain TS11 Is Attenuated in Syrian Hamsters and a Candidate Attenuated Vaccine | Viruses / [link](https://www.mdpi.com/1999-4915/15/1/95) | | | Emergence and Persistent Dominance of Omicron BA.2.3.7 Variant in Community Outbreaks in Taiwan | -- / [link](https://www.medrxiv.org/content/10.1101/2022.09.27.22280238v2) | BSSH; COVID Lineage App v3.5.9 | | Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern | Viruses / [link](https://www.mdpi.com/1999-4915/15/1/108) | COVIDSeq Test RUO v1.3.0 | | Analytical performance of the rapid qualitative antigen kit for the detection of SARS-CoV-2 during widespread circulation of the Omicron variant | Journal of Infection and Chemotherapy / [link](https://www.sciencedirect.com/science/article/pii/S1341321X22003130) | COVIDSeq Test pipeline | | Cognitive impairment in long-living adults: a genome-wide association study, polygenic risk score model and molecular modeling of the APOE protein | Frontiers in Aging Neuroscience / [link](https://www.frontiersin.org/articles/10.3389/fnagi.2023.1273825) | alignment | | Developmental and epileptic encephalopathy in a young Italian woman with a *de novo* missense variant in the *CLCN4* gene: A case report | Brain and Development / [link](https://www.sciencedirect.com/science/article/pii/S0387760423000888) | BSSH; Germline Enrichment app | | Exome-based genome-wide screening of rare variants associated with the risk of polycystic ovary syndrome | Reproductive Medicine and Biology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/rmb2.12504) | v3.9.5 | | Prevalence of SARS-CoV-2 Variants and Disease Outcome of COVID-19 Patients in the Amazonas Region of Peru | The American Journal of Tropical Medicine and Hygiene / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10484257/) | | | Genomic epidemiology of SARS-CoV-2 in large university hospital cohort: the UnCoVER-Brazil project | Epidemiology & Infection / [link](https://www.cambridge.org/core/journals/epidemiology-and-infection/article/genomic-epidemiology-of-sarscov2-in-large-university-hospital-cohort-the-uncoverbrazil-project/3602091448619664DE0849FB98A2ED60) | BSSH; COVID Lineage | | SARS-CoV-2: Air pollution highly correlated to the increase in mortality. The case of Guadalajara, Jalisco, México | Infectious Disease Modelling / [link](https://www.sciencedirect.com/science/article/pii/S2468042723000295) | | | Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022 | mSphere / [link](https://journals.asm.org/doi/full/10.1128/msphere.00232-23) | COVID Lineage | | Genomic Landscape Comparison of Cardiac versus Extra-Cardiac Angiosarcomas | Biomedicines / [link](https://www.mdpi.com/2227-9059/11/12/3290) | RNA app | | Spinal cord extracts of amyotrophic lateral sclerosis spread TDP-43 pathology in cerebral organoids | PLOS Genetics / [link](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010606) | v3.8 | | GWAS reveals genetic basis of a predisposition to severe COVID-19 through in silico modeling of the FYCO1 protein | Frontiers in Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10399629/) | alignment | | Data Analysis Pipeline for Detection and Quantification of Pseudouridine (ψ) in RNA by HydraPsiSeq | Computational Epigenomics and Epitranscriptomics / [link](https://doi.org/10.1007/978-1-0716-2962-8_14) | BCL convert | | Cardiomyocyte-Targeting Peptide to Deliver Amiodarone | Pharmaceutics / [link](https://www.mdpi.com/1999-4923/15/8/2107) | v3.8.4; BCL convert | | Muscle spasms as presenting feature of Nivelon-Nivelon-Mabile syndrome | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.63000) | | | NOTCH1 Gene as a Novel Cause of Thoracic Aortic Aneurysm in Patients with Tricuspid Aortic Valve: Two Cases Reported | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/24/10/8644) | v4.0.3 | | Whole Sequencing and Detailed Analysis of SARS-CoV-2 Genomes in Southeast Spain: Identification of Recurrent Mutations in the 20E (EU1) Variant with Some Clinical Implications | Diseases / [link](https://www.mdpi.com/2079-9721/11/2/54) | COVID Lineage App | | Genome-wide association study of the age of onset of type 1 diabetes reveals HTATIP2 as a novel T cell regulator | Frontiers in Immunology / [link](https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2023.1101488/full) | DRAGEN server | | The Impact of Phase-Specific Macrophage Depletion on Intestinal Anastomotic Healing | Cells / [link](https://www.mdpi.com/2073-4409/12/7/1039) | demultiplexing | | Rapid genome diagnosis of alveolar capillary dysplasia leading to treatment in a child with respiratory and cardiac failure | Molecular Case Studies / [link](http://molecularcasestudies.cshlp.org/content/9/4/a006292) | | | Role of Royal Jelly Treated Adipose-Derived Stem Cell-Extracellular Vesicles on Fibroblast Proliferation, Migration, and Collagen Production | Dermatologic Therapy / [link](https://www.hindawi.com/journals/dth/2023/7950026/) | v3.6.3; Differential Expression | | Clinical predominance of whole-exome sequencing to evaluate microsatellite instability status | Cancer Science / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/cas.15813) | v3.8 | | In-depth genetic characterization of the SARS-CoV-2 pandemic in a two-year frame in North Macedonia using second and third generation sequencing technologies | Frontiers in Virology / [link](https://www.frontiersin.org/articles/10.3389/fviro.2022.1064882) | v3.5.13 | | Koala Genome Survey: An Open Data Resource to Improve Conservation Planning | Genes / [link](https://www.mdpi.com/2073-4425/14/3/546) | v3.8.4; alignment; Koala reference genome | | Biallelic NEXN variants and fetal onset dilated cardiomyopathy: two independent case reports and revision of literature. | -- / [link](https://www.researchsquare.com/article/rs-3230381/v1) | BSSH; Enrichment app | | NGS method for parallel processing of high quality, damaged or fragmented input material using target enrichment | -- / [link](https://www.biorxiv.org/content/10.1101/2023.01.15.524106v1) | BCL convert | | Detection of mosaic variants using genome sequencing in a large pediatric cohort | American Journal of Medical Genetics. Part A / [link](https://onlinelibrary.wiley.com/doi/10.1002/ajmg.a.63062) | | | Systematic identification of disease-causing promoter and untranslated region variants in 8,040 undiagnosed individuals with rare disease | -- / [link](https://www.medrxiv.org/content/10.1101/2023.09.12.23295416v1) | | | Enhanced microglial dynamics and paucity of tau seeding in the amyloid plaque microenvironment contributes to cognitive resilience in Alzheimer’s disease | -- / [link](https://www.biorxiv.org/content/10.1101/2023.07.27.550884v1) | DRAGEN server v4 | | Immuno-oncologic profiling of pediatric CNS tumors reveals major clinical significance of the tumor immune microenvironment | -- / [link](https://www.researchsquare.com/article/rs-2655807/v1) | BSSH | | SARS-CoV-2 variants-associated outbreaks of COVID-19 in a tertiary institution, North-Central Nigeria: Implications for epidemic control | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0280756) | | | Phase I Study and Cell-Free DNA Analysis of T-DM1 and Metronomic Temozolomide for Secondary Prevention of HER2-Positive Breast Cancer Brain Metastases | Clinical Cancer Research / [link](https://doi.org/10.1158/1078-0432.CCR-22-0855) | v4.0.3; tumor-only | | Short-read aligner performance in germline variant identification | Bioinformatics / [link](https://doi.org/10.1093/bioinformatics/btad480) | Germline | | Reclassification of the Etiology of Infant Mortality With Whole-Genome Sequencing | JAMA Network Open / [link](https://doi.org/10.1001/jamanetworkopen.2022.54069) | | | The Impact of Muscarinic Antagonism on Psychosis-Relevant Behaviors and Striatal \[11C] Raclopride Binding in Tau Mouse Models of Alzheimer’s Disease | Biomedicines / [link](https://www.mdpi.com/2227-9059/11/8/2091) | v3.9.0 | | Assessment of Apolipoprotein(a) Isoform Size Using Phenotypic and Genotypic Methods | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/24/18/13886) | KIV2 CN caller | | A systematic review of the barcoding strategy that contributes to COVID-19 diagnostics at a population level | Frontiers in Molecular Biosciences / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10366608/) | COVIDSeq Test pipeline; review | | A Genome-Wide Association Study of Nigerien and Senegalese Sorghum Germplasm of Exserohilum turcicum, the Causal Agent of Leaf Blight | Plants / [link](https://www.mdpi.com/2223-7747/12/23/4010) | DRAGEN-GATK | | Severe NAD(P)HX Dehydratase (NAXD) Neurometabolic Syndrome May Present in Adulthood after Mild Head Trauma | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/24/4/3582) | | | Germline- and Somatic-Inactivating FLCN Variants in Parathyroid Cancer and Atypical Parathyroid Tumors | The Journal of Clinical Endocrinology & Metabolism / [link](https://doi.org/10.1210/clinem/dgad136) | | | FLAIRR-Seq: A Method for Single-Molecule Resolution of Near Full-Length Antibody H Chain Repertoires | The Journal of Immunology / [link](https://doi.org/10.4049/jimmunol.2200825) | | | Elucidating the Proximal Tubule HNF4A Gene Regulatory Network in Human Kidney Organoids | Journal of the American Society of Nephrology / [link](https://journals.lww.com/jasn/abstract/2023/10000/elucidating_the_proximal_tubule_hnf4a_gene.10.aspx) | | | Advanced Age in Humans and Mouse Models of Glioblastoma Show Decreased Survival from Extratumoral Influence | Clinical Cancer Research / [link](https://doi.org/10.1158/1078-0432.CCR-23-0834) | BCL convert | | mRNA vaccine quality analysis using RNA sequencing | Nature Communications / [link](https://www.nature.com/articles/s41467-023-41354-y) | BCL convert | | Determining the impact of vaccination on SARS-CoV-2 RT-PCR cycle threshold values and infectious viral titres | Access Microbiology / [link](https://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000597.v3) | BSSH; COVID Lineage App v3.5.2 | | Polygenic risk alters the penetrance of monogenic kidney disease | Nature Communications / [link](https://www.nature.com/articles/s41467-023-43878-9) | v3.4.12 | | Heterogeneity in the half-life of factor VIII concentrate in patients with hemophilia A is due to variability in the clearance of endogenous von Willebrand factor | Journal of Thrombosis and Haemostasis / [link](https://www.sciencedirect.com/science/article/pii/S1538783623000417) | Germline pipeline; v3.7 | | A pilot study of lymphodepletion intensity for peripheral blood mononuclear cell-derived neoantigen-specific CD8 + T cell therapy in patients with advanced solid tumors | Nature Communications / [link](https://www.nature.com/articles/s41467-023-39225-7) | alignment | | Evaluation of low-cost SARS-CoV-2 RNA purification methods for viral quantification by RT-qPCR and next-generation sequencing analysis: Implications for wider wastewater-based epidemiology adoption | Heliyon / [link](https://www.sciencedirect.com/science/article/pii/S2405844023033376) | COVID Lineage App v3.5.9 | | Integrated Multi-omics Analysis of Early Lung Adenocarcinoma Links Tumor Biological Features with Predicted Indolence or Aggressiveness | Cancer Research Communications / [link](https://doi.org/10.1158/2767-9764.CRC-22-0373) | Enrichment pipeline v3.7.5 | | A Breast Cancer Polygenic Risk Score Is Feasible for Risk Stratification in the Norwegian Population | Cancers / [link](https://www.mdpi.com/2072-6694/15/16/4124) | DRAGEN-GATK | | A “Two-in-One Hit” Model of Shortcut Carcinogenesis in MLH1 Lynch Syndrome Carriers | Gastroenterology / [link](https://www.gastrojournal.org/article/S0016-5085\(23\)00261-5/fulltext) | DRAGEN server; somatic tumor-normal workflow; germline-only workflow | | Coupling of metabolomics and exome sequencing reveals graded effects of rare damaging heterozygous variants on gene function and resulting traits and diseases | -- / [link](https://www.medrxiv.org/content/10.1101/2023.10.17.23297094v1) | Germline pipeline v3.0.7 | | 2019–2020 H1N1 clade A5a.1 viruses have better in vitro fitness compared with the co-circulating A5a.2 clade | Scientific Reports / [link](https://www.nature.com/articles/s41598-023-37122-z) | RNA pathogen detection | | The reference genome of the paradise fish (Macropodus opercularis) | -- / [link](https://www.biorxiv.org/content/10.1101/2023.08.10.552018v1) | | | SARS-CoV-2 viral variants can rapidly be identified for clinical decision making and population surveillance using a high-throughput digital droplet PCR assay | Scientific Reports / [link](https://www.nature.com/articles/s41598-023-34188-7) | | | Interplay of gene expression and regulators under salinity stress in gill of Labeo rohita | BMC Genomics / [link](https://doi.org/10.1186/s12864-023-09426-x) | BCL convert | | PAK1 c.1409 T > a (p. Leu470Gln) de novo variant affects the protein kinase domain, leading to epilepsy, macrocephaly, spastic quadriplegia, and hydrocephalus: Case report and review of the literature | American Journal of Medical Genetics. Part A / [link](https://onlinelibrary.wiley.com/doi/10.1002/ajmg.a.63177) | | | Phase II trial of CDK4/6 inhibitor palbociclib in advanced sarcoma based on mRNA expression of CDK4/CDKN2A | Signal Transduction and Targeted Therapy / [link](https://www.nature.com/articles/s41392-023-01661-8) | Variant calling | | Deep genomic characterization highlights complexities and prognostic markers of pediatric acute myeloid leukemia | Communications Biology / [link](https://www.nature.com/articles/s42003-023-04732-2) | Somatic pipeline; RNA pipeline | | Pathway and Network Analyses Identify Growth Factor Signaling and MMP9 as Potential Mediators of Mitochondrial Dysfunction in Severe COVID-19 | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/24/3/2524) | BCL convert | | Human Induced Pluripotent Stem Cell based Hepatic-Modeling of Lipid metabolism associated TM6SF2 E167K variant | -- / [link](https://www.biorxiv.org/content/10.1101/2023.12.18.572248v1) | RNA; v3.10.12 | | De novo TRPM3 missense variant associated with neurodevelopmental delay and manifestations of cerebral palsy | Molecular Case Studies / [link](http://molecularcasestudies.cshlp.org/content/9/4/a006293) | Germline pipeline v3.9.5 | | A Novel RUNX1 Genetic Variant Identified in a Young Male with Severe Osteoporosis | JBMR Plus / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/jbm4.10791) | Variant calling; alignment; Enrichment pipeline | | Placental Infection Associated with SARS-CoV-2 Wildtype Variant and Variants of Concern | Viruses / [link](https://www.mdpi.com/1999-4915/15/9/1918) | COVID Lineage App | | Genetic landscape of homologous recombination repair genes in early-onset/familial prostate cancer patients | Genes, Chromosomes and Cancer / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/gcc.23190) | | | Next-Generation sequencing transforming clinical practice and precision medicine | Clinica Chimica Acta / [link](https://www.sciencedirect.com/science/article/pii/S0009898123003704) | review | | At-Risk Genomic Findings for Pediatric-Onset Disorders From Genome Sequencing vs Medically Actionable Gene Panel in Proactive Screening of Newborns and Children | JAMA Network Open / [link](https://doi.org/10.1001/jamanetworkopen.2023.26445) | | | Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort | Nature Communications / [link](https://www.nature.com/articles/s41467-023-38782-1) | alignment | | Congenital heart defects in CTNNB1 syndrome: Raising clinical awareness | Clinical Genetics / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/cge.14404) | Germline pipeline | | Multi-omic profiling reveals discrepant immunogenic properties and a unique tumor microenvironment among melanoma brain metastases | npj Precision Oncology / [link](https://www.nature.com/articles/s41698-023-00471-z) | | | The importance of genome sequencing: unraveling SSBP1 variant missed by exome sequencing | Ophthalmic Genetics / [link](https://doi.org/10.1080/13816810.2022.2109685) | | | Skim resequencing finely maps the downy mildew resistance loci RPF2 and RPF3 in spinach cultivars whale and Lazio | Horticulture Research / [link](https://doi.org/10.1093/hr/uhad076) | v3.8.4 | | Modelling population genetic screening in rare neurodegenerative diseases | -- / [link](https://www.medrxiv.org/content/10.1101/2023.07.03.23292187v1) | | | A confinable female-lethal population suppression system in the malaria vector, Anopheles gambiae | Science Advances / [link](https://www.science.org/doi/full/10.1126/sciadv.ade8903) | v3.8.4; BCL convert | | Characterization of an *in vitro* steatosis model simulating activated *de novo* lipogenesis in MAFLD patients | iScience / [link](https://www.sciencedirect.com/science/article/pii/S2589004223018047) | v3.9.5; BCL convert | | Semaphorin 4B is an ADAM17-cleaved adipokine that inhibits adipocyte differentiation and thermogenesis | Molecular Metabolism / [link](https://www.sciencedirect.com/science/article/pii/S2212877823000650) | | | Secondary findings in a large Pakistani cohort tested with whole genome sequencing | Life Science Alliance / [link](https://www.life-science-alliance.org/content/6/3/e202201673) | v3.10.4 | | The molecular epidemiology of SARS-CoV-2 in the Pityusic Islands shows multiple introductions and fast replacements of variants in a touristic worldwide hot spot | Scientific Reports / [link](https://www.nature.com/articles/s41598-023-44668-5) | | | The Quebec Dental Anomalies Registry: Identifying genes for rare disorders | PNAS Nexus / [link](https://doi.org/10.1093/pnasnexus/pgad196) | Enrichment pipeline v3.9.5 | | Codon affinity in mitochondrial DNA shapes evolutionary and somatic fitness | -- / [link](https://www.biorxiv.org/content/10.1101/2023.04.23.537997v1) | alignment; small variant caller; Germline pipeline v3.7.8 | | The T Cell Receptor β Chain Repertoire of Tumor Infiltrating Lymphocytes Improves Neoantigen Prediction and Prioritization | -- / [link](https://www.biorxiv.org/content/10.1101/2023.11.16.567478v1) | | | Identification of 13 Novel Loci in a Genome-Wide Association Study on Taiwanese with Hepatocellular Carcinoma | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/24/22/16417) | RNA; v3.7 | | Streptococcus mutans inhibits the growth of Enterococcus via the non-ribosomal cyclic peptide mutanobactin | -- / [link](https://www.biorxiv.org/content/10.1101/2023.09.12.557362v1) | v3.10.12 | | Efficient sex separation by exploiting differential alternative splicing of a dominant marker in Aedes aegypti | PLOS Genetics / [link](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011065) | v3.8.4; BCL convert | | Targeting Sex Determination to Suppress Mosquito Populations | eLife / [link](https://elifesciences.org/reviewed-preprints/90199) | v3.8.4 | | Genetic architecture of telomere length in 462,675 UK Biobank whole-genome sequences | -- / [link](https://www.medrxiv.org/content/10.1101/2023.09.18.23295715v2) | Germline pipeline | | Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression | Proceedings of the National Academy of Sciences / [link](https://www.pnas.org/doi/full/10.1073/pnas.2306494120) | | | Sex and molecular differences in cardiovascular parameters at peak influenza disease in mice | Physiological Genomics / [link](https://journals.physiology.org/doi/full/10.1152/physiolgenomics.00146.2022) | RNA app; BSSH; Differential Expression App | | First-in-human prospective trial of sonobiopsy in high-grade glioma patients using neuronavigation-guided focused ultrasound | npj Precision Oncology / [link](https://www.nature.com/articles/s41698-023-00448-y) | DRAGEN server; v3.9.3 | | Next-Generation Sequencing Technology: Current Trends and Advancements | Biology / [link](https://www.mdpi.com/2079-7737/12/7/997) | review | | Pharmacological inhibition of TBK1/IKKε blunts immunopathology in a murine model of SARS-CoV-2 infection | Nature Communications / [link](https://www.nature.com/articles/s41467-023-41381-9) | BCL convert | | *IRF7* and *UNC93B1* variants in an infant with recurrent herpes simplex virus infection | The Journal of Clinical Investigation / [link](https://www.jci.org/articles/view/154016) | v3.6.3 | | Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants | Communications Biology / [link](https://www.nature.com/articles/s42003-023-04782-6) | COVID Lineage | | Syngap1 Disruption Induced by Recombination between Inverted loxP Sites Is Associated with Hippocampal Interneuron Dysfunction | eNeuro / [link](https://www.eneuro.org/content/10/5/ENEURO.0475-22.2023) | | | ApoE isoform– and microbiota-dependent progression of neurodegeneration in a mouse model of tauopathy | Science / [link](https://www.science.org/doi/full/10.1126/science.add1236) | abstract; DRAGEN server; remove; v3.9.3 | | Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation | Nature Communications / [link](https://www.nature.com/articles/s41467-023-37843-9) | Germline pipeline v3.9.3 | | A novel, RAS-independent role for NF1 in microtubular dynamics and damage repair dictates sensitivity to T-DM1 in HER2-positive breast cancer | -- / [link](https://www.biorxiv.org/content/10.1101/2023.12.06.569572v1) | v4.0; Variant calling | | Functional assessment of homozygous ALDH18A1 variants reveals alterations in amino acid and antioxidant metabolism | Human Molecular Genetics / [link](https://doi.org/10.1093/hmg/ddac226) | | | Cytokimera GIL-11 rescued IL-6R deficient mice from partial hepatectomy-induced death by signaling via non-natural gp130:LIFR:IL-11R complexes | Communications Biology / [link](https://www.nature.com/articles/s42003-023-04768-4) | BCL convert | | Deep amplicon sequencing reveals extensive allelic diversity in the *erg11*/*CYP51* promoter and allows multi-population DMI fungicide resistance monitoring in the canola pathogen *Leptosphaeria maculans* | Fungal Genetics and Biology / [link](https://www.sciencedirect.com/science/article/pii/S1087184523000452) | BCL convert | | 25-hydroxycholesterol mediates brain cytokine production and neutrophil infiltration in a mouse model of lipopolysaccharide-induced neuroinflammation | -- / [link](https://www.biorxiv.org/content/10.1101/2023.10.09.561598v1) | DRAGEN server; alignment; v3.9.3; RNA quantification | | Non-invasive mapping of systemic neutrophil dynamics upon cardiovascular injury | Nature Cardiovascular Research / [link](https://www.nature.com/articles/s44161-022-00210-w) | BCL convert | | Advanced cell-based products generated via automated and manual manufacturing platforms under the quality by design principle: Are they equivalent or different? | Heliyon / [link](https://www.sciencedirect.com/science/article/pii/S2405844023031535) | Variant calling; DRAGEN-GATK | | The miR-221/222 cluster regulates hematopoietic stem cell quiescence and multipotency by suppressing both Fos/AP-1/IEG pathway activation and stress-like differentiation to granulocytes | PLOS Biology / [link](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002015) | | | Genotypic and phenotypic homogeneity of vaginal and rectal yeast isolates from recurrent vulvovaginal candidiasis | -- / [link](https://www.biorxiv.org/content/10.1101/2023.07.19.549743v1) | | | Tirap controls Mycobacterium tuberculosis phagosomal acidification | PLOS Pathogens / [link](https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1011192) | v3.8.4 | | The Landscape of Clinical Whole Genome Sequencing and the Emergence of Rapid Genetic Diagnosis in Critical Care | Advances in Molecular Pathology / [link](https://www.advancesinmolecularpathology.com/article/S2589-4080\(23\)00021-2/fulltext) | review | | Advances in the discovery and analyses of human tandem repeats | Emerging topics in life sciences / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10806765/) | review | | iPSC–derived retinal pigmented epithelial cells from patients with macular telangiectasia show decreased mitochondrial function | The Journal of Clinical Investigation / [link](https://www.jci.org/articles/view/163771) | alignment; v2.5.1 | | Selective adaptation of SARS-CoV-2 Omicron under booster vaccine pressure: a multicentre observational study | eBioMedicine / [link](https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964\(23\)00409-7/fulltext) | | | Functional analysis of recurrent CDC20 promoter variants in human melanoma | Communications Biology / [link](https://www.nature.com/articles/s42003-023-05526-2) | DRAGEN server; v3.9.3 | | Insight into spatial intratumoral genomic evolution in glioblastoma | -- / [link](https://www.biorxiv.org/content/10.1101/2023.09.11.557112v1) | alignment | | A thin-film optogenetic visual prosthesis | -- / [link](https://www.biorxiv.org/content/10.1101/2023.01.31.526482v2) | BCL convert | | Histone H3 E50K mutation confers oncogenic activity and supports an EMT phenotype | -- / [link](https://www.biorxiv.org/content/10.1101/2023.10.11.561775v1) | | | Real-Time Analysis of SARS-CoV-2-Induced Cytolysis Reveals Distinct Variant-Specific Replication Profiles | Viruses / [link](https://www.mdpi.com/1999-4915/15/9/1937) | | | Investigation into the genetics of fetal congenital lymphatic anomalies | Prenatal Diagnosis / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/pd.6345) | alignment | | APC-Related Phenotypes and Intellectual Disability in 5q Interstitial Deletions: A New Case and Review of the Literature | Genes / [link](https://www.mdpi.com/2073-4425/14/7/1505) | | | A survey of CIN measures across mechanistic models | -- / [link](https://www.biorxiv.org/content/10.1101/2023.06.15.544840v1) | alignment | | NLRP3 inflammasome activation and symptom burden in *KRAS*-mutated CMML patients is reverted by IL-1 blocking therapy | Cell Reports Medicine / [link](https://www.sciencedirect.com/science/article/pii/S2666379123005463) | BSSH; Germline; Somatic | | The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization | Medizinische Genetik / [link](https://www.degruyter.com/document/doi/10.1515/medgen-2023-2065/html) | | | Whole-Exome Sequencing and cfDNA Analysis Uncover Genetic Determinants of Melanoma Therapy Response in a Real-World Setting | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/24/5/4302) | Germline pipeline; Somatic pipeline | | Luminal-Type Invasive Carcinoma in Association With Microglandular Adenosis/Atypical Microglandular Adenosis: A Case Report and Molecular Comparison | Cureus / [link](https://www.cureus.com/articles/148184-luminal-type-invasive-carcinoma-in-association-with-microglandular-adenosisatypical-microglandular-adenosis-a-case-report-and-molecular-comparison#!/) | Somatic small variant caller; tumor-normal mode | | From amaurotic idiocy to biochemically defined lipid storage diseases: the first identification of GM1-Gangliosidosis | Free Neuropathology / [link](https://doi.org/10.17879/freeneuropathology-2023-4845) | | | The Bioinformatics Application in Detecting Germline and Somatic Variants towards Breast Cancer using Next Generation Sequencing | Journal of Applied Science, Engineering, Technology, and Education / [link](https://jpabdimas.idjournal.eu/index.php/asci/article/view/1608) | | | Generation of anti-GD2 CAR macrophages from human pluripotent stem cells for cancer immunotherapies | Stem Cell Reports / [link](https://doi.org/10.1016/j.stemcr.2022.12.012) | | | A genetic mosaic mouse model illuminates the pre-malignant progression of basal-like breast cancer | Disease Models & Mechanisms / [link](https://journals.biologists.com/dmm/article/16/11/dmm050219/334680/A-genetic-mosaic-mouse-model-illuminates-the-pre) | CNV; Somatic mode; Somatic mutation | | Accurate long-read sequencing identified GBA1 as major risk factor in the Luxembourgish Parkinson’s study | npj Parkinson's Disease / [link](https://www.nature.com/articles/s41531-023-00595-w) | DNA pipeline; GBA caller; v4 | | Prenatal BRCA1 epimutations contribute significantly to triple-negative breast cancer development | Genome Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10698991/) | v3.6.3 | | vcfdist: accurately benchmarking phased small variant calls in human genomes | Nature Communications / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10710436/) | | | Performance analysis of conventional and AI-based variant callers using short and long reads | BMC Bioinformatics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10720095/) | DRAGEN-GATK | | Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases | Genome Research / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10760520/) | DRAGMAP | | Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases | Scientific Data / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10662356/) | | | Talniflumate abrogates mucin immune suppressive barrier improving efficacy of gemcitabine and nab-paclitaxel treatment in pancreatic cancer | Journal of Translational Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10668479/) | BSSH; Nanostring GeoMx Digital Spatial Profiling | | Multimodal Biomedical Data Fusion Using Sparse Canonical Correlation Analysis and Cooperative Learning: A Cohort Study on COVID-19 | Research Square / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10690316/) | COVID Lineage App | | Identification of IncA Plasmid, Harboring blaVIM-1 Gene, in S. enterica Goldcoast ST358 and C. freundii ST62 Isolated in a Hospitalized Patient | Antibiotics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10741216/) | | | Rare variant analyses validate known ALS genes in a multi-ethnic population and identifies ANTXR2 as a candidate in PLS | medRxiv / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10593055/) | alignment | | Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1 | -- / [link](https://www.biorxiv.org/content/10.1101/2023.11.08.566246v1) | BCL convert | | Fibrolamellar hepatocellular carcinoma: a case report and gene analysis | Surgical Case Reports / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10511385/) | RNA pipeline v3.5.7 | | Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets | Nature Communications / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10533562/) | v3.1 | | Combined Presence in Heterozygosis of Two Variant Usher Syndrome Genes in Two Siblings Affected by Isolated Profound Age-Related Hearing Loss | Biomedicines / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10604119/) | v4.2 | | PALB2 Variants Extend the Mutational Profile of Hungarian Patients with Breast and Ovarian Cancer | Cancers / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10487218/) | Enrichment pipeline | | Integrative miRNA-mRNA network analysis to identify crucial pathways of salinity adaptation in brain transcriptome of Labeo rohita | Frontiers in Genetics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10500595/) | BCL convert | | Health Assessments of Koalas after Wildfire: A Temporal Comparison of Rehabilitated and Non-Rescued Resident Individuals | Animals : an Open Access Journal from MDPI / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10525633/) | Germline; Joint genotyping | | The choroidal nervous system: a link between mineralocorticoid receptor and pachychoroid | Acta Neuropathologica / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10564818/) | v3.8.4 | | LINE-1 regulates cortical development by acting as long non-coding RNAs | Nature Communications / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10435495/) | Germline pipeline v3 | | Long-term follow-up in a pediatric patient with Ligneous Conjunctivitis due to PLG gene mutation in topical plasminogen treatment after successful use of ocular prosthesis for aesthetic rehabilitation: a case report | Italian Journal of Pediatrics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10463973/) | Germline pipeline | | Challenging interpretation of germline TP53 variants based on the experience of a national comprehensive cancer centre | Scientific Reports / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10471726/) | BSSH; Germline pipeline | | Antigen concentration, viral load, and test performance for SARS-CoV-2 in multiple specimen types | PLOS ONE / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10355390/) | BSSH; COVID Lineage App | | Tumor biology and immune infiltration define primary liver cancer subsets linked to overall survival after immunotherapy | Cell Reports Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10313915/) | tumor-only mode | | Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas | Nature Communications / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10089528/) | BSSH | | Genome-wide expression analysis reveals different heat shock responses in indigenous (Bos indicus) and crossbred (Bos indicus X Bos taurus) cattle | Genes and Environment / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10152620/) | RNA | | A draft human pangenome reference | Nature / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10172123/) | | | Resilience to autosomal dominant Alzheimer’s disease in a Reelin-COLBOS heterozygous man | Nature Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10202812/) | | | Neutrophil extracellular traps formed during chemotherapy confer treatment resistance via TGFβ activation | Cancer cell / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10228050/) | onboard | | The role of genetic testing in the diagnostic workflow of pediatric patients with kidney diseases: the experience of a single institution | Human Genomics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9926680/) | Enrichment | | Comparison of the mutation patterns between tumor tissue and cell-free DNA in stage IV gastric cancer | Aging (Albany NY) / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9970310/) | Somatic mutation pipeline | | Cardiologic Manifestations in Omicron‐Type Versus Wild‐Type COVID‐19: A Systematic Echocardiographic Study | Journal of the American Heart Association: Cardiovascular and Cerebrovascular Disease / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9973649/) | COVIDSeq | | From gene to dose: Long-read sequencing and \*-allele tools to refine phenotype predictions of CYP2C19 | Frontiers in Pharmacology / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10014917/) | | | Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021 | Frontiers in Public Health / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10018007/) | | | SEQUIN is an R/Shiny framework for rapid and reproducible analysis of RNA-seq data | Cell Reports Methods / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10088091/) | | | Genetic Variants Associated with Bronchial Asthma Specific to the Population of the Russian Federation | Acta Naturae / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10154776/) | | | Long-term risk associated with clonal hematopoiesis in patients with severe aortic valve stenosis undergoing TAVR | Clinical Research in Cardiology / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10160205/) | Enrichment app | | Navigating bottlenecks and trade-offs in genomic data analysis | Nature reviews. Genetics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10204111/) | review | | Classification and genetics of pediatric B-other acute lymphoblastic leukemia by targeted RNA sequencing | Blood Advances / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10320209/) | RNA pipeline | | A hyper-quiescent chromatin state formed during aging is reversed by regeneration | -- / [link](https://www.biorxiv.org/content/10.1101/2023.02.14.528512v1) | | | A pathological autopsy of a case dying from omicron variant of COVID-19 | Open Journal of Clinical & Medical Case Reports / [link](https://jclinmedcasereports.com/articles/OJCMCR-2030.pdf) | BaseSpace Sequence Hub; BSSH; RNA pathogen detection | | Validating Clinical Exome Sequencing (CES) Test for Copy Number Variation (CNV) Analysis in Patients with Autism Spectrum Disorder | American Journal of Medical and Clinical Sciences / [link](https://www.ajrms.com/articles/Validating%20Clinical%20Exome%20Sequencing%20%20CES%20%20Test%20for%20Copy%20Number%20Variation%20%20CNV%20%20Analysis%20in%20Patients%20with%20Autism%20Spectrum%20Disorder) | Enrichment CNV calling | | The Hong Kong genome project: building genome sequencing capacity and capability for advancing genomic science in Hong Kong | Journal of Translational Genetics and Genomics / [link](https://www.oaepublish.com/articles/jtgg.2023.22) | v4.1.5 | | An Integrated Pipeline for Trio‐Rapid Genome Sequencing in Critically Ill Infants | Current Protocols / [link](https://currentprotocols.onlinelibrary.wiley.com/doi/10.1002/cpz1.706) | | | Comparative molecular profiling of pancreatic ductal adenocarcinoma of the head versus body/tail reveals differences in the tumor immune microenvironment (TIME) | -- / [link](https://www.researchsquare.com/article/rs-3317962/v1) | | | Genetic landscape of homologous recombination repair genes in early-onset/familial prostate cancer patients | -- / [link](https://www.researchsquare.com/article/rs-2403119/v1) | |
2022 | Title | Publisher / Link | Tags | | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------- | | Analysis of the Plastid Genome Sequence During Maize Seedling Development | Frontiers in Genetics / [link](https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.870115/full) | v3.8 | | An Upgrade on the Surveillance System of SARS-CoV-2: Deployment of New Methods for Genetic Inspection | International Journal of Molecular Sciences / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8950365/) | COVID Lineage App v3.5.3 | | Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function | Human Mutation / [link](https://onlinelibrary.wiley.com/doi/10.1002/humu.24435) | Variant calling | | Precocious puberty in a case of Simpson–Golabi–Behmel syndrome with a de novo 240-kb deletion including GPC3 | Human Genome Variation / [link](https://www.nature.com/articles/s41439-022-00196-8) | v3.5 | | A patient with compound heterozygosity of *SMPD4* : Another example of utility of exome‐based copy number analysis in autosomal recessive disorders | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/10.1002/ajmg.a.62535) | | | Diagnosis of SLC25A46-related pontocerebellar hypoplasia in two siblings with fulminant neonatal course: role of postmortem CT and whole genomic analysis: a case report | BMC Neurology / [link](https://bmcneurol.biomedcentral.com/articles/10.1186/s12883-021-02540-x) | v3.5 | | Whole‐exome sequencing of a Saudi epilepsy cohort reveals association signals in known and potentially novel loci | Human Genomics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9764464/) | | | Acute stress induces severe neural inflammation and overactivation of glucocorticoid signaling in interleukin-18-deficient mice | Translational Psychiatry / [link](https://www.nature.com/articles/s41398-022-02175-7) | alignment | | Rapid Displacement of SARS-CoV-2 Variants within Japan Correlates with Cycle Threshold Values on Routine RT-PCR Testing | Archives of Clinical and Biomedical Research / [link](http://www.fotunejournals.com/rapid-displacement-of-sarscov2-variants-within-japan-correlates-with-cycle-threshold-values-on-routine-rtpcr-testing.html) | | | Whole-genome sequencing as an investigational device for return of hereditary disease risk and pharmacogenomic results as part of the All of Us Research Program | Genome Medicine / [link](https://doi.org/10.1186/s13073-022-01031-z) | | | Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift | Genes / [link](https://www.mdpi.com/2073-4425/13/4/569) | | | Genome Analysis in Sick Neonates and Infants: High-yield Phenotypes and Contribution of Small Copy Number Variations | The Journal of Pediatrics / [link](https://www.sciencedirect.com/science/article/pii/S0022347622000646) | v3.4 | | Differentially methylated CpGs in response to growth hormone administration in children with idiopathic short stature | Clinical Epigenetics / [link](https://doi.org/10.1186/s13148-022-01281-z) | | | Concurrent inhibition of CDK2 adds to the anti-tumour activity of CDK4/6 inhibition in GIST | British Journal of Cancer / [link](https://www.nature.com/articles/s41416-022-01990-5) | | | Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample | Genome Biology / [link](https://doi.org/10.1186/s13059-021-02592-9) | DRAGEN comparison to other technologies | | Cutting-Edge AI Technologies Meet Precision Medicine to Improve Cancer Care | Biomolecules / [link](https://www.mdpi.com/2218-273X/12/8/1133) | review | | A Splice Variant of the MYH7 Gene Is Causative in a Family with Isolated Left Ventricular Noncompaction Cardiomyopathy | Genes / [link](https://www.mdpi.com/2073-4425/13/10/1750) | SNP calling | | Whole-genome sequencing reveals host factors underlying critical COVID-19 | Nature / [link](https://www.nature.com/articles/s41586-022-04576-6) | | | Lymphocytes Utilize Somatic Mutations, Epigenetic Silencing, and the Proteasome to Escape Truncated WASP Expression | Journal of Clinical Immunology / [link](https://doi.org/10.1007/s10875-022-01224-6) | | | Rapid genome sequencing for pediatrics | Human Mutation / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.24466) | | | Somatic copy number alteration and fragmentation analysis in circulating tumor DNA for cancer screening and treatment monitoring in colorectal cancer patients | Journal of Hematology & Oncology / [link](https://doi.org/10.1186/s13045-022-01342-z) | | | Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program | BMC Infectious Diseases / [link](https://doi.org/10.1186/s12879-022-07374-7) | | | 28MO Real-world whole sequencing data of ovarian cancer patients | Annals of Oncology / [link](https://www.sciencedirect.com/science/article/pii/S0923753422007311) | HRD | | Cardiovascular Involvement in Pediatric FLNC Variants: A Case Series of Fourteen Patients | Journal of Cardiovascular Development and Disease / [link](https://www.mdpi.com/2308-3425/9/10/332) | BSSH; Enrichment app | | Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment | Scientific Reports / [link](https://www.nature.com/articles/s41598-022-26181-3) | comparison of DRAGEN with other technologies; v3.8.4 | | Molecular Epidemiological Investigations of Localized SARS-CoV-2 Outbreaks-Utility of Public Algorithms | Epidemiologia / [link](https://www.mdpi.com/2673-3986/3/3/31) | | | High-level gonosomal mosaicism for a pathogenic non-coding CNV deletion of the lung-specific FOXF1 enhancer in an unaffected mother of an infant with ACDMPV | Molecular Genetics & Genomic Medicine / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/mgg3.2062) | | | Whole genome sequencing identifies candidate genes for familial essential tremor and reveals biological pathways implicated in essential tremor aetiology | eBioMedicine / [link](https://www.sciencedirect.com/science/article/pii/S2352396422004728) | DNA pipeline; SV caller | | The Brazilian Rare Genomes Project: Validation of Whole Genome Sequencing for Rare Diseases Diagnosis | Frontiers in Molecular Biosciences / [link](https://www.frontiersin.org/articles/10.3389/fmolb.2022.821582) | | | Genetic Dissection of TLR9 Reveals Complex Regulatory and Cryptic Pro-inflammatory Roles in Murine Lupus | Nature immunology / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9561083/) | BCL convert | | Whole-genome sequencing analysis of clozapine-induced myocarditis | The Pharmacogenomics Journal / [link](https://www.nature.com/articles/s41397-022-00271-x) | haplotype caller | | Evaluation of an optimized protocol and Illumina ARTIC V4 primer pool for sequencing of SARS-CoV-2 using COVIDSeq™ and DRAGEN™ COVID Lineage App workflow | -- / [link](https://www.biorxiv.org/content/10.1101/2022.01.07.475443v1) | COVID Lineage App; BSSH | | Molecular Profiling of Liquid Biopsies for Precision Oncology | Advances in Experimental Medicine and Biology / [link](https://link.springer.com/chapter/10.1007/978-3-030-91836-1_13) | review | | Frequent HLA-DR loss on hematopoietic stem progenitor cells in patients with cyclosporine-dependent aplastic anemia carrying HLA-DR15 | Leukemia / [link](https://www.nature.com/articles/s41375-022-01549-6) | | | Congenital heart defects in molecularly confirmed KBG syndrome patients | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.62632) | | | Low rate of RNAemia in blood donations collected during the first wave of COVID-19 in France | Transfusion / [link](https://onlinelibrary.wiley.com/doi/10.1111/trf.16812) | | | Genomic characterization of the dominating Beta, V2 variant carrying vaccinated (Oxford−AstraZeneca) and nonvaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole-genome approach | Journal of Medical Virology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.27537) | | | RNA-seq Fusion Detection in Clinical Oncology | Computational Methods for Precision Oncology / [link](https://doi.org/10.1007/978-3-030-91836-1_9) | review | | Identification of a QTL region for ashy stem blight resistance using genome-wide association and linage analysis in common bean recombinant inbred lines derived from BAT 477 and NY6020-4 | Frontiers in Plant Science / [link](https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1019263/full) | v3.8.4 | | PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions | Cell Genomics / [link](https://www.sciencedirect.com/science/article/pii/S2666979X22000581) | PrecisionFDA | | Characteristics of Amelanotic Acantholytic-Like Melanoma Resembling Squamous Cell Carcinoma | Journal of cutaneous pathology / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9473664/) | v3.8 | | Novel mutation of *IFT140* in an infant with Mainzer-Saldino syndrome presenting with retinal dystrophy | Molecular Genetics and Metabolism Reports / [link](https://www.sciencedirect.com/science/article/pii/S2214426922000970) | | | MixviR: an R Package for Exploring Variation Associated with Genomic Sequence Data from Environmental SARS-CoV-2 and Other Mixed Microbial Samples | Applied and Environmental Microbiology / [link](https://journals.asm.org/doi/full/10.1128/aem.00874-22) | BSSH; COVID Lineage App v3.5.10 | | A complete pedigree-based graph workflow for rare candidate variant analysis | Genome Research / [link](https://genome.cshlp.org/content/32/5/893) | v3.7.5 | | Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking | Computational and Structural Biotechnology Journal / [link](https://www.sciencedirect.com/science/article/pii/S2001037022001891) | COVID Lineage App; RNA pathogen detection app; COVIDSeq Test RUO | | Early Emergence and Dispersal of Delta SARS-CoV-2 Lineage AY.99.2 in Brazil | Frontiers in Medicine / [link](https://www.frontiersin.org/articles/10.3389/fmed.2022.930380) | COVID Lineage App; BSSH | | Genome sequencing as a first-line diagnostic test for hospitalized infants | Genetics in Medicine / [link](https://www.sciencedirect.com/science/article/pii/S1098360021054009) | | | SARS-CoV-2 BA.1 and BA.2 coinfection detected by genomic surveillance in Brazil, January 2022 | Archives of Virology / [link](https://doi.org/10.1007/s00705-022-05532-5) | | | Whole-exome sequencing of BRCA-negative breast cancer patients and case–control analyses identify variants associated with breast cancer susceptibility | Human Genomics / [link](https://doi.org/10.1186/s40246-022-00435-7) | BSSH; v3.5.7 | | Evaluating use of changing technologies for rapid next-generation sequencing in pediatrics | Pediatric Research / [link](https://www.nature.com/articles/s41390-022-01965-5) | CNV | | Chronic Myeloid Leukemia Failed Second Generation Tyrosine Kinase Inhibitor Patients' Molecular Interrogation Using Next Generation Sequencing | Blood / [link](https://ashpublications.org/blood/article/140/Supplement%201/11544/492595) | alignment; Variant calling | | SARS-CoV-2 Omicron Variant Wave in India: Advent, Phylogeny and Evolution | -- / [link](https://www.biorxiv.org/content/10.1101/2022.05.14.491911v1) | | | Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity | Human Genetics / [link](https://doi.org/10.1007/s00439-021-02397-7) | v3.5.7; v3.6.3 | | Successful Laparoscopic Oviductal Artificial Insemination in the Endangered Tsushima Leopard Cat (Prionailurus bengalensis euptilurus) | Animals / [link](https://www.mdpi.com/2076-2615/12/6/777) | | | *CYP2C8, CYP2C9,* and *CYP2C19* Characterization Using Next-Generation Sequencing and Haplotype Analysis | The Journal of Molecular Diagnostics / [link](https://www.sciencedirect.com/science/article/pii/S1525157822000198) | v3.4.12; v2.0.4 | | miR-671-5p Inhibition by MSI1 Promotes Glioblastoma Tumorigenesis via Radioresistance, Tumor Motility and Cancer Stem-like Cell Properties | Biomedicines / [link](https://www.mdpi.com/2227-9059/10/1/21) | RNA pipeline; miRNA expression | | Fetal pharmacogenomics: A promising addition to complex neonatal care | Molecular Genetics and Metabolism / [link](https://www.sciencedirect.com/science/article/pii/S1096719222003894) | v3.4.12; PGx star alleles | | Return of non-ACMG recommended incidental genetic findings to pediatric patients: considerations and opportunities from experiences in genomic sequencing | Genome Medicine / [link](https://doi.org/10.1186/s13073-022-01139-2) | | | Bioinformatic Challenges Detecting Genetic Variation in Precision Medicine Programs | Frontiers in Medicine / [link](https://www.frontiersin.org/articles/10.3389/fmed.2022.806696) | review | | CRAM compression: practical across-technologies considerations for large-scale sequencing projects | -- / [link](https://www.biorxiv.org/content/10.1101/2022.12.21.521516v1) | DRAGEN server; v3.9 | | Age Estimate of GJB2-p.(Arg143Trp) Founder Variant in Hearing Impairment in Ghana, Suggests Multiple Independent Origins across Populations | Biology / [link](https://www.mdpi.com/2079-7737/11/3/476) | alignment; Germline pipeline v3.2.8 | | Clonal Myeloid Heterogeneity in Older Autopsy Patients Determined By Multiple Bone Marrow Site Sequencing | Blood / [link](https://ashpublications.org/blood/article/140/Supplement%201/2874/488671) | | | ISGylation is increased in the peripheral blood mononuclear cells derived from symptomatic COVID-19 patients | Experimental Biology and Medicine / [link](https://doi.org/10.1177/15353702221075606) | COVIDSeq Test pipeline; COVID Lineage App; BSSH | | Clinical Validation of Genome Reference Consortium Human Build 38 in a Laboratory Utilizing Next-Generation Sequencing Technologies | Clinical Chemistry / [link](https://doi.org/10.1093/clinchem/hvac113) | v3.9.3; v3.3.7 | | A novel frameshift homozygous mutation in FAT1 gene causes ptosis, nephropathy, and syndactyly in an Emirati family: case report and literature review | Journal of Biochemical and Clinical Genetics / [link](https://jbcgenetics.com/fulltext/183-1645370249.pdf) | SV caller | | Secure secondary utilization system of genomic data using quantum secure cloud | Scientific Reports / [link](https://www.nature.com/articles/s41598-022-22804-x) | | | Genotyping of Circulating Free DNA Enables Monitoring of Tumor Dynamics in Synovial Sarcomas | Cancers / [link](https://www.mdpi.com/2072-6694/14/9/2078) | Somatic pipeline; Enrichment pipeline; BSSH | | LINE-1 insertion in the RP1 gene in a family with retinitis pigmentosa | Acta Ophthalmologica / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1755-3768.2022.0582) | | | Evaluating the analytical validity of mutation calling pipeline for tumor whole exome sequencing | -- / [link](https://www.biorxiv.org/content/10.1101/2022.11.17.516840v1) | DRAGEN comparison to other technologies | | HiCUP-Plus: a fast open-source pipeline for accurately processing large scale Hi-C sequence data | -- / [link](https://www.biorxiv.org/content/10.1101/2022.05.18.492393v1) | | | Performance of a high-throughput, automated enzyme immunoassay for the detection of SARS-CoV-2 antigen, including in viral “variants of concern”: Implications for clinical use | Journal of Clinical Virology / [link](https://www.sciencedirect.com/science/article/pii/S1386653221003152) | | | Assessing the risk stratification of breast cancer polygenic risk scores in two Brazilian samples | -- / [link](https://www.medrxiv.org/content/10.1101/2022.09.09.22279721v1) | DRAGEN-GATK; DNA pipeline; v3.6.4 | | Germline Variants Associated with Nasopharyngeal Carcinoma Predisposition Identified through Whole-Exome Sequencing | Cancers / [link](https://www.mdpi.com/2072-6694/14/15/3680) | v3.8.4 | | 1029 genomes of self-declared healthy individuals from India reveal prevalent and clinically relevant cardiac ion channelopathy variants | Human Genomics / [link](https://doi.org/10.1186/s40246-022-00402-2) | Variant calling; v3.4 | | Canine Oncopanel: A capture-based, NGS platform for evaluating the mutational landscape and detecting putative driver mutations in canine cancers | Veterinary and Comparative Oncology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/vco.12746) | | | Forensic Application of Snp-Targeted Next-Generation Sequencing on Korean Kinship Analysis | -- / [link](https://papers.ssrn.com/abstract=4279141) | BSSH; Germline pipeline | | Somatic and Germline Variant Calling from Next-Generation Sequencing Data | Computational Methods for Precision Oncology / [link](https://doi.org/10.1007/978-3-030-91836-1_3) | | | Chronic reduction of store operated Ca2+ entry is viable therapeutically but is associated with cardiovascular complications | The Journal of Physiology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1113/JP283811) | Differential expression pipeline v3.6.3; RNA pipeline v3.6.3 | | SARS-CoV-2 infection in free-ranging white-tailed deer | Nature / [link](https://www.nature.com/articles/s41586-021-04353-x) | | | SARS-CoV-2 Genomic Characteristics and Clinical Impact of SARS-CoV-2 Viral Diversity in Critically Ill COVID-19 Patients: A Prospective Multicenter Cohort Study | Viruses / [link](https://www.mdpi.com/1999-4915/14/7/1529) | | | A Study Protocol for Validation and Implementation of Whole-Genome and -Transcriptome Sequencing as a Comprehensive Precision Diagnostic Test in Acute Leukemias | Frontiers in Medicine / [link](https://www.frontiersin.org/articles/10.3389/fmed.2022.842507) | protocol | | Refining the Camelus dromedarius Myostatin Gene Polymorphism through Worldwide Whole-Genome Sequencing | Animals / [link](https://www.mdpi.com/2076-2615/12/16/2068) | BSSH; Germline app | | Case report: EWSR1-TFCP2 in an adolescent represents an extremely rare and aggressive form of intraosseous spindle cell rhabdomyosarcomas | Molecular Case Studies / [link](http://molecularcasestudies.cshlp.org/content/8/5/a006209) | RNA pipeline v3.6.3 | | Assessing reproducibility of inherited variants detected with short-read whole genome sequencing | Genome Biology / [link](https://doi.org/10.1186/s13059-021-02569-8) | BSSH; Germline pipeline v3.2.8 | | A monoallelic variant in EYA1 is associated with Branchio-Otic syndrome in a Malian family | Molecular Genetics & Genomic Medicine / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/mgg3.1995) | alignment; v3.4.12; Germline Pipeline v3.2.8 | | Glioblastoma CD105+ cells define a SOX2− cancer stem cell-like subpopulation in the pre-invasive niche | Acta Neuropathologica Communications / [link](https://doi.org/10.1186/s40478-022-01422-8) | | | Inhibition of the Phosphatidylinositol-3 Kinase Pathway Using Bimiralisib in Loss-of-Function NOTCH1-Mutant Head and Neck Cancer | The Oncologist / [link](https://doi.org/10.1093/oncolo/oyac185) | v3 | | Whole-genome Sequencing of SARS-CoV-2: Using Phylogeny and Structural Modeling to Contextualize Local Viral Evolution | Military Medicine / [link](https://doi.org/10.1093/milmed/usab031) | | | A guide for the diagnosis of rare and undiagnosed disease: beyond the exome | Genome Medicine / [link](https://doi.org/10.1186/s13073-022-01026-w) | review | | CD19 expression is maintained in DLBCL patients after treatment with tafasitamab plus lenalidomide in the L-MIND study | Leukemia & Lymphoma / [link](https://doi.org/10.1080/10428194.2021.1986219) | v3.4 | | A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability | Genes / [link](https://www.mdpi.com/2073-4425/13/7/1270) | BSSH; Germline pipeline v3.7.5 | | Sequencing SARS-CoV-2 from antigen tests | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0263794) | | | Emergence and spreading of the largest SARS-CoV-2 deletion in the Delta AY.20 lineage from Uruguay | Gene Reports / [link](https://www.sciencedirect.com/science/article/pii/S2452014422002114) | BSSH | | Genomic and epidemiologic surveillance of SARS-CoV-2 in Southern Brazil and identification of a new Omicron-L452R sublineage | Virus Research / [link](https://www.sciencedirect.com/science/article/pii/S0168170222002350) | BSSH | | Similarity Index–Probabilistic Confidence Estimation of SARS-CoV-2 Strain Relatedness in Localized Outbreaks | Epidemiologia / [link](https://www.mdpi.com/2673-3986/3/2/19) | COVID Lineage | | Clinical phenotypes and outcomes associated with SARS-CoV-2 variant Omicron in critically ill French patients with COVID-19 | Nature Communications / [link](https://www.nature.com/articles/s41467-022-33801-z) | COVIDSeq Test pipeline; DRAGEN server | | The spike gene target failure (SGTF) genomic signature is highly accurate for the identification of Alpha and Omicron SARS-CoV-2 variants | Scientific Reports / [link](https://www.nature.com/articles/s41598-022-21564-y) | COVID Lineage App | | Evaluation of EPISEQ SARS-CoV-2 and a Fully Integrated Application to Identify SARS-CoV-2 Variants from Several Next-Generation Sequencing Approaches | Viruses / [link](https://www.mdpi.com/1999-4915/14/8/1674) | COVID Lineage App | | Xanthogranulomatous epithelial tumors and keratin-positive giant cell-rich soft tissue tumors: two aspects of a single entity with frequent *HMGA2-NCOR2* fusions | Modern Pathology / [link](https://www.sciencedirect.com/science/article/pii/S0893395222002320) | BSSH; RNA app; v3.8.4 | | Association of Clonal Hematopoiesis of Indeterminate Potential with Worse Kidney Function and Anemia in Two Cohorts of Patients with Advanced Chronic Kidney Disease | Journal of the American Society of Nephrology / [link](https://journals.lww.com/jasn/fulltext/2022/05000/association_of_clonal_hematopoiesis_of.13.aspx) | Somatic mode; v3.8; tumor-only mode | | Treatment with metformin glycinate reduces SARS-CoV-2 viral load: An *in vitro* model and randomized, double-blind, Phase IIb clinical trial | Biomedicine & Pharmacotherapy / [link](https://www.sciencedirect.com/science/article/pii/S0753332222006126) | | | Biological proof of a hit-and-run tumour formation in oropharyngeal cancers | -- / [link](https://www.researchsquare.com/article/rs-1991904/v1) | v3.9.3 | | Blood DNA methylation at TXNIP and glycemic changes in response to weight-loss diet interventions: the POUNDS Lost Trial | International journal of obesity (2005) / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9156542/) | v3.6 | | Rapid syndromic testing for respiratory viral infections in children attending the emergency department during COVID-19 pandemic in Lille, France, 2021–2022 | Journal of Clinical Virology / [link](https://www.sciencedirect.com/science/article/pii/S1386653222001548) | COVIDSeq Test pipeline | | Immediate reinfection with Omicron variant after clearance of a previous SARS-CoV-2 infection | Journal of Infection and Public Health / [link](https://www.sciencedirect.com/science/article/pii/S1876034122001903) | | | Next 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| Science Advances / [link](https://www.science.org/doi/full/10.1126/sciadv.abl9051) | Methylation pipeline | | Transmissibility of SARS-CoV-2 B.1.1.214 and Alpha Variants during 4 COVID-19 Waves, Kyoto, Japan, January 2020–June 2021 | Emerging Infectious Diseases / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9328921/) | | | Monitoring the SARS-CoV-2 pandemic: screening algorithm with single nucleotide polymorphism detection for the rapid identification of established and emerging variants | Clinical Microbiology and Infection / [link](https://www.sciencedirect.com/science/article/pii/S1198743X21004973) | COVIDSeq Test pipeline | | An exceptional biallelic N-terminal frame shift mutation in *ZMPSTE24* leads to non-lethal progeria due to possible utilization of a downstream alternative start codon | Gene / [link](https://www.sciencedirect.com/science/article/pii/S0378111922004012) | BSSH; Germline pipeline v3.2.8 | | HLA-B\*07:02 and HLA-C\*07:02 are associated with trimethoprim-sulfamethoxazole respiratory failure | The pharmacogenomics journal / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9125581/) | v3.3.7 | | Curated variation benchmarks for challenging medically relevant autosomal genes | Nature Biotechnology / [link](https://www.nature.com/articles/s41587-021-01158-1) | v3.6.3 | | Virological and Serological Characterisation of SARS-CoV-2 Infections Diagnosed After mRNA BNT162b2 Vaccination Between December 2020 and March 2021 | Frontiers in Medicine / [link](https://www.frontiersin.org/articles/10.3389/fmed.2021.815870) | RNA pathogen detection | | TRAPPC9-CDG: A novel congenital disorder of glycosylation with dysmorphic features and intellectual disability | Genetics in Medicine / [link](https://www.sciencedirect.com/science/article/pii/S109836002105471X) | v3.8.4 | | Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City | Viruses / [link](https://www.mdpi.com/1999-4915/14/3/545) | | | COVID-19 & differential effects in twins: Insights from Placenta Pathology | Placenta / [link](https://www.sciencedirect.com/science/article/pii/S0143400422002569) | BSSH; COVID Lineage Pipeline | | Recurrent switch 2 domain RAC2 mutations in intravascular large B-cell lymphoma | Blood Advances / [link](https://ashpublications.org/bloodadvances/article/6/23/6051/484639/Recurrent-switch-2-domain-RAC2-mutations-in) | v3.8 | | Simultaneous production of cellobiose and xylobiose from alkali-treated bagasse using cellulase secreted by Fe-ion-irradiated *Trichoderma reesei* mutant | Journal of Bioscience and Bioengineering / [link](https://www.sciencedirect.com/science/article/pii/S1389172322002559) | v3.6.3 | | Whole exome sequencing reveals potentially pathogenic variants in a small subset of premenopausal women with idiopathic osteoporosis | Bone / [link](https://www.sciencedirect.com/science/article/pii/S8756328221004191) | alignment | | Immunoinformatics approach to epitope-based vaccine design against the SARS-CoV-2 in Bangladeshi patients | Journal of Genetic Engineering and Biotechnology / [link](https://doi.org/10.1186/s43141-022-00410-8) | RNA pathogen detection; BSSH; v3.5.14 | | Breakthrough Covid‐19 infections in vaccinated recipients of allogeneic stem cell transplantation | EJHaem / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9349499/) | COVIDSeq Test pipeline; DRAGEN server | | Benefits of tailored disease management in improving tremor, white matter hyperintensities, and liver enzymes in a child with heterozygous X-linked ornithine transcarbamylase deficiency | Molecular Genetics and Metabolism Reports / [link](https://www.sciencedirect.com/science/article/pii/S2214426922000519) | Variant calling; alignment | | ALS2-related disorders in Spanish children: a severely affected case of infantile ascending spastic paraplegia due to homozygous R704X mutation | Neurological Sciences / [link](https://doi.org/10.1007/s10072-022-05884-5) | CNV caller | | Clinical and Molecular Spectrum of Sporadic Vascular Malformations: A Single-Center Study | Biomedicines / [link](https://www.mdpi.com/2227-9059/10/6/1460) | mosaicism; Somatic pipeline v3.6.3 | | Human genetics uncovers MAP3K15 as an obesity-independent therapeutic target for diabetes | Science Advances / [link](https://www.science.org/doi/full/10.1126/sciadv.add5430) | Germline pipeline v3.0.7 | | Mutations in SCNM1 cause orofaciodigital syndrome due to minor intron splicing defects affecting primary cilia | American Journal of Human Genetics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9606384/) | Variant calling; v3.6.3 | | Molecular characterization of ESR1 variants in breast cancer | Breast Cancer Research and Treatment / [link](https://doi.org/10.1007/s10549-022-06740-y) | demultiplexing | | Familial exudative vitreoretinopathy in a 4 generations family of South-East Asian Descendent with FZD4 mutation (c.1501\_1502del) | International Journal of Retina and Vitreous / [link](https://doi.org/10.1186/s40942-022-00384-2) | v2.03 | | Antibody titers and neutralizing activity in cases of COVID-19 after a single dose of vaccination | Journal of Infection and Chemotherapy / [link](https://www.sciencedirect.com/science/article/pii/S1341321X22002525) | COVID Lineage App v3.5.9 | | Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2 | eBioMedicine / [link](https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964\(22\)00118-9/fulltext) | COVIDSeq Test pipeline; DRAGEN server | | Understanding the mechanism of the SARS CoV-2 coinfection with other respiratory viruses | -- / [link](https://www.biorxiv.org/content/10.1101/2022.12.15.520197v1) | Pathogen detection app | | Genetic impact of non-consanguineous marriages in Saudi Arabia | -- / [link](https://www.researchsquare.com/article/rs-1876191/v1) | v3.7 | | Identification of risk variants related to malignant tumors in children with birth defects by whole genome sequencing | Biomarker Research / [link](https://doi.org/10.1186/s40364-022-00431-y) | | | Genome Sequences of 408 SARS-CoV-2 Strains Obtained from Nasopharyngeal Swabs in La Araucanía Region, Southern Chile | Microbiology Resource Announcements / [link](https://journals.asm.org/doi/full/10.1128/mra.00121-22) | COVID Lineage App; BSSH | | Multi-Design Differential Expression Profiling of COVID-19 Lung Autopsy Specimens Reveals Significantly Deregulated Inflammatory Pathways and SFTPC Impaired Transcription | Cells / [link](https://www.mdpi.com/2073-4409/11/6/1011) | COVID Lineage Pipeline v3.5.0 | | Genomic surveillance of SARS-CoV-2 in the state of Delaware reveals tremendous genomic diversity | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0262573) | RNA pathogen detection pipeline v3.5.15 | | Description of a One-Year Succession of Variants of Interest and Concern of SARS-CoV-2 in Venezuela | Viruses / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9317613/) | | | Benchmarking challenging small variants with linked and long reads | Cell Genomics / [link](https://doi.org/10.1016/j.xgen.2022.100128) | v3.2; v3.3.7 | | A novel autosomal dominant GREB1L variant associated with non-syndromic hearing impairment in Ghana | BMC Medical Genomics / [link](https://doi.org/10.1186/s12920-022-01391-w) | alignment; Germline pipeline v3.4.12 | | Genetic Appraisal of Hereditary Muscle Disorders In A Cohort From Mumbai, India | Journal of Neuromuscular Diseases / [link](https://content.iospress.com/articles/journal-of-neuromuscular-diseases/jnd220801) | | | Genetics of Pediatric Epilepsy: Next-Generation Sequencing in Clinical Practice | Genes / [link](https://www.mdpi.com/2073-4425/13/8/1466) | | | Gene-SCOUT: identifying genes with similar continuous trait fingerprints from phenome-wide association analyses | Nucleic Acids Research / [link](https://doi.org/10.1093/nar/gkac274) | Germline pipeline v3.0.7 | | A year living with SARS-CoV-2: an epidemiological overview of viral lineage circulation by whole-genome sequencing in Barcelona city (Catalonia, Spain) | Emerging Microbes & Infections / [link](https://doi.org/10.1080/22221751.2021.2011617) | BSSH; COVID Lineage App v3.5.2 | | Probable Aerosol Transmission of SARS-CoV-2 through Floors and Walls of Quarantine Hotel, Taiwan, 2021 | Emerging Infectious Diseases / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9707602/) | | | Genome Sequencing of Omicron Variants of SARS-CoV-2 Circulating in Bangladesh during the Third Wave of the COVID-19 Pandemic | Microbiology Resource Announcements / [link](https://journals.asm.org/doi/full/10.1128/mra.00381-22) | BSSH; COVID Lineage App v3.5.8 | | Clustering of Genetic Anomalies of Cilia Outer Dynein Arm and Central Apparatus in Patients with Transposition of the Great Arteries | Genes / [link](https://www.mdpi.com/2073-4425/13/9/1662) | Germline pipeline v3.2.8 | | Intragenic inversions in NF1 gene as pathogenic mechanism in neurofibromatosis type 1 | European Journal of Human Genetics / [link](https://www.nature.com/articles/s41431-022-01153-3) | | | Gene fusions and oncogenic mutations in MLH1 deficient and BRAFV600E wild-type colorectal cancers | Virchows Archiv / [link](https://doi.org/10.1007/s00428-022-03302-x) | v3.8.4 | | Syndromic Microphthalmia 9: Role of rapid genome sequencing and novel mutations in *STRA6* gene | Progress in Pediatric Cardiology / [link](https://www.sciencedirect.com/science/article/pii/S1058981321001223) | | | Syrian hamsters as a model of lung injury with SARS-CoV-2 infection: Pathologic, physiologic, and detailed molecular profiling | Translational Research / [link](https://www.sciencedirect.com/science/article/pii/S1931524421002632) | | | Whole exome sequencing reveals novel risk genes of pituitary neuroendocrine tumors | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0265306) | Somatic pipeline | | SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic | Viruses / [link](https://www.mdpi.com/1999-4915/14/9/1878) | | | Congenital idiopathic megaesophagus in the German shepherd dog is a sex-differentiated trait and is associated with an intronic variable number tandem repeat in Melanin-Concentrating Hormone Receptor 2 | PLOS Genetics / [link](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010044) | | | Whole Exome Sequencing of Patients With Heritable and Idiopathic Pulmonary Arterial Hypertension in Central Taiwan | Frontiers in Cardiovascular Medicine / [link](https://www.frontiersin.org/articles/10.3389/fcvm.2022.911649) | | | Case report: Genomic screening for inherited cardiac conditions in Ecuadorian mestizo relatives: Improving familial diagnose | Frontiers in Cardiovascular Medicine / [link](https://www.frontiersin.org/articles/10.3389/fcvm.2022.1037370) | Enrichment pipeline v3.9.5 | | UMOD Mutations in Chronic Kidney Disease in Taiwan | Biomedicines / [link](https://www.mdpi.com/2227-9059/10/9/2265) | Variant calling | | Identification of genomic signatures and multiple lineage markers from the second and third wave samples of COVID-19 in Western Rajasthan, India | -- / [link](https://www.biorxiv.org/content/10.1101/2022.12.10.518819v1) | COVID Lineage App | | SARS-CoV-2 RT-PCR to Screen for B.1.617.2 (Delta) Variant of Concern | Diagnostics / [link](https://www.mdpi.com/2075-4418/12/9/2056) | | | Pathogenic Variants in ZSWIM7 Cause Primary Ovarian Insufficiency | The Journal of Clinical Endocrinology & Metabolism / [link](https://doi.org/10.1210/clinem/dgac090) | v3.8.4 | | GATA2 Deficiency in Adult Life Is Characterized by Phenotypic Diversity and Delayed Diagnosis | Frontiers in Immunology / [link](https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2022.886117/full) | v3.8 | | A patient with mosaic USP9X gene variant | European Journal of Medical Genetics / [link](https://www.sciencedirect.com/science/article/pii/S1769721222002191) | BSSH; Enrichment app; Variant annotation; Variant calling | | Local genomic sequencing enhances COVID-19 surveillance in the Northern Territory of Australia | Pathology / [link](https://www.pathologyjournal.rcpa.edu.au/article/S0031-3025\(22\)00156-8/fulltext) | BSSH; COVID Lineage Pipeline | | Genome Sequencing in the Parkinson Disease Clinic | Neurology Genetics / [link](https://www.neurology.org/doi/full/10.1212/NXG.0000000000200002) | | | Rapid genome sequencing identifies novel variants in complement factor I | Molecular Case Studies / [link](http://molecularcasestudies.cshlp.org/content/8/7/a006239) | SNV | | Increased prevalence of clonal hematopoiesis of indeterminate potential in hospitalized patients with COVID-19 | Frontiers in Immunology / [link](https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2022.968778/full) | Enrichment app | | A Multi-Disciplinary Team Approach to Genomic Testing for Drug-Resistant Epilepsy Patients—The GENIE Study | Journal of Clinical Medicine / [link](https://www.mdpi.com/2077-0383/11/14/4238) | Germline Pipeline v3.2.8 | | The Contribution of Deleterious Rare Alleles in ENPP1 and Osteomalacia Causative Genes to Atypical Femoral Fracture | The Journal of Clinical Endocrinology & Metabolism / [link](https://doi.org/10.1210/clinem/dgac022) | v3.6.3 | | Clinical and Infection Prevention Applications of Severe Acute Respiratory Syndrome Coronavirus 2 Genotyping: an Infectious Diseases Society of America/American Society for Microbiology Consensus Review Document | Journal of Clinical Microbiology / [link](https://journals.asm.org/doi/full/10.1128/jcm.01659-21) | | | Characteristics of 24 SARS-CoV-2-Sequenced Reinfection Cases in a Tertiary Hospital in Spain | Frontiers in Microbiology / [link](https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.876409/full) | COVID Lineage App | | Blockade of the protease ADAM17 ameliorates experimental pancreatitis | Proceedings of the National Academy of Sciences / [link](https://www.pnas.org/doi/abs/10.1073/pnas.2213744119) | BCL convert | | Transcriptional Profiling of Malignant Melanoma Reveals Novel and Potentially Targetable Gene Fusions | Cancers / [link](https://www.mdpi.com/2072-6694/14/6/1505) | | | Systematic sequencing of imported cases leads to detection of SARS-CoV-2 B.1.1.529 (Omicron) variant in central Viet Nam | Western Pacific Surveillance and Response / [link](https://ojs.wpro.who.int/ojs/index.php/wpsar/article/view/977) | | | Identical IFT140 Variants Cause Variable Skeletal Ciliopathy Phenotypes—Challenges for the Accurate Diagnosis | Frontiers in Genetics / [link](https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.931822/full) | v3.7.5; RNA pipeline; BSSH | | Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage | Global Health, Epidemiology and Genomics / [link](https://www.cambridge.org/core/journals/global-health-epidemiology-and-genomics/article/confirming-multiplex-rtqpcr-use-in-covid19-with-nextgeneration-sequencing-strategies-for-epidemiological-advantage/9D5CD091C7DB82D1F6777B29D9607F1E) | COVID Lineage App; BSSH | | Genomic study of nonsyndromic hearing loss in unaffected individuals: Frequency of pathogenic and likely pathogenic variants in a Brazilian cohort of 2,097 genomes | Frontiers in Genetics / [link](https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.921324/full) | Germline pipeline v3.6.3 | | Rapid Weight Loss and Severe Failure to Thrive Mimicking Lipodystrophy Syndrome in a 1-Year-Old Taiwanese Girl with Costello Syndrome | Children / [link](https://www.mdpi.com/2227-9067/9/6/905) | BSSH; Enrichment | | Establishment of Novel Neuroendocrine Carcinoma Patient-Derived Xenograft Models for Receptor Peptide-Targeted Therapy | Cancers / [link](https://www.mdpi.com/2072-6694/14/8/1910) | | | A Polymorphism Cluster at the 2q12 locus May Predict Response to Piromelatine in Patients with Mild Alzheimer’s Disease | The Journal of Prevention of Alzheimer's Disease / [link](https://doi.org/10.14283/jpad.2021.61) | SNP calling | | Genetic analysis for type 1 diabetes genes in juvenile dermatomyositis unveils genetic disease overlap | Rheumatology / [link](https://doi.org/10.1093/rheumatology/keac100) | v3.3.7 | | Muscle Biopsy: A Requirement for Precision Medicine in Adult-Onset Myopathy | Journal of Clinical Medicine / [link](https://www.mdpi.com/2077-0383/11/6/1580) | v3.7.5 | | Whole mitochondrial genome sequencing of Malaysian patients with cardiomyopathy | PeerJ / [link](https://peerj.com/articles/13265) | | | Comparison of different sequencing techniques for identification of SARS-CoV-2 variants of concern with multiplex real-time PCR | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0265220) | Somatic pipeline; BSSH | | Phylogenetic and amino acid signature analysis of the SARS-CoV-2s lineages circulating in Tunisia | Infection, Genetics and Evolution / [link](https://www.sciencedirect.com/science/article/pii/S1567134822000971) | RNA pathogen detection pipeline | | A patient with Beta-Propeller Protein-Associated Neurodegeneration: a new missense mutation of the gene | Journal of Epileptology / [link](https://sciendo.com/article/10.2478/joepi-2022-0001) | alignment; Variant calling | | TBX3 and EFNA4 Variant in a Family with Ulnar-Mammary Syndrome and Sagittal Craniosynostosis | Genes / [link](https://www.mdpi.com/2073-4425/13/9/1649) | Germline; v3.9 | | Characterization of RNF43 frameshift mutations that drive Wnt ligand- and R-spondin-dependent colon cancer | The Journal of Pathology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/path.5868) | | | The study of cancer cell in stromal environment through induced pluripotent stem cell–derived mesenchymal stem cells | Journal of the Chinese Medical Association / [link](https://journals.lww.com/jcma/fulltext/2022/08000/The_study_of_cancer_cell_in_stromal_environment.4.aspx) | | | Convergence between germline and somatic mutations in pancreatic neuroendocrine tumors | European Journal of Endocrinology / [link](https://doi.org/10.1530/EJE-21-0893) | | | A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases | American Journal of Human Genetics / [link](https://doi.org/10.1016/j.ajhg.2022.08.003) | AWS; ICA; v3.8; v3.9 | | Precocious Puberty in a Boy With Bilateral Leydig Cell Tumors due to a Somatic Gain-of-Function LHCGR Variant | Journal of the Endocrine Society / [link](https://doi.org/10.1210/jendso/bvac127) | Germline pipeline v3.4.5 | | Genetic Characterization in High-Risk Individuals from a Low-Resource City of Peru | Cancers / [link](https://www.mdpi.com/2072-6694/14/22/5603) | v3.6.3 | | Dominant-negative signal transducer and activator of transcription (STAT)3 variants in adult patients: A single center experience | Frontiers in Immunology / [link](https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2022.1044933/full) | v3.9 | | The Identification of Novel CYP2D6 Variants in US Hmong: Results From Genome Sequencing and Clinical Genotyping | Frontiers in Pharmacology / [link](https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2022.867331/full) | v2.5.3 | | Somatic mosaicism reveals clonal distributions of neocortical development | Nature / [link](https://www.nature.com/articles/s41586-022-04602-7) | | | A Randomized Controlled Trial of Combined Ivermectin and Zinc Sulfate versus Combined Hydroxychloroquine, Darunavir/Ritonavir, and Zinc Sulfate among Adult Patients with Asymptomatic or Mild Coronavirus-19 Infection | Journal of Global Infectious Diseases / [link](https://journals.lww.com/jgid/fulltext/2022/14020/a_randomized_controlled_trial_of_combined.6.aspx) | Variant calling; BSSH; COVID Lineage App v3.5.3 | | Performance of 22 Rapid Lateral Flow Tests for SARS-CoV-2 Antigen Detection and Influence of “Variants of Concern”: Implications for Clinical Use | Microbiology Spectrum / [link](https://journals.asm.org/doi/full/10.1128/spectrum.01157-22) | | | Human Papillomavirus Integration Strictly Correlates with Global Genome Instability in Head and Neck Cancer | Molecular Cancer Research / [link](https://doi.org/10.1158/1541-7786.MCR-21-0831) | Somatic mutation | | A de novo ACTB gene pathogenic variant in identical twins with phenotypic variation for hydrops and jejunal atresia | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.62631) | | | Bi-allelic PAGR1 variants are associated with microcephaly and a severe neurodevelopmental disorder: Genetic evidence from two families | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.62513) | | | Phylodynamic analysis of SARS-CoV-2 spread in Rio de Janeiro, Brazil, highlights how metropolitan areas act as dispersal hubs for new variants | Microbial Genomics / [link](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000859) | COVID Lineage Pipeline | | Downregulation of METTL6 mitigates cell progression, migration, invasion and adhesion in hepatocellular carcinoma by inhibiting cell adhesion molecules | International Journal of Oncology / [link](https://www.spandidos-publications.com/10.3892/ijo.2021.5294) | v3.6.3 | | Successful use of casirivimab/imdevimab anti-spike monoclonal antibodies to enhance neutralizing antibodies in a woman on anti-CD20 treatment with refractory COVID-19 | Journal of Infection and Chemotherapy / [link](https://www.sciencedirect.com/science/article/pii/S1341321X22000769) | | | From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures | Computational and Structural Biotechnology Journal / [link](https://www.sciencedirect.com/science/article/pii/S2001037022003531) | review | | SARS-CoV-2 Variants Identification: Overview of Molecular Existing Methods | Pathogens / [link](https://www.mdpi.com/2076-0817/11/9/1058) | review | | Case Report: Bi-allelic missense variant in the desmocollin 3 gene causes hypotrichosis and recurrent skin vesicles | Frontiers in Genetics / [link](https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.994509/full) | BSSH; SV caller | | *Capsicum* hypocotyls mycobiome diversity is unaffected by *Phytophthora capsici* inoculation | Physiological and Molecular Plant Pathology / [link](https://www.sciencedirect.com/science/article/pii/S0885576522000169) | BSSH | | Longitudinal Characterization of a Neutralizing and Total Antibody Response in Patients with Severe COVID-19 and Fatal Outcomes | Vaccines / [link](https://www.mdpi.com/2076-393X/10/12/2063) | COVIDSeq Test pipeline; BSSH | | SARS-CoV-2 Omicron Variant in Croatia—Rapid Detection of the First Case and Cross-Border Spread | Pathogens / [link](https://www.mdpi.com/2076-0817/11/5/511) | | | Whole genome sequencing identifies rare genetic variants in familial pancreatic cancer patients | Annals of Human Genetics / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/ahg.12464) | v3.7 | | Chagas Disease Megaesophagus Patients Carrying Variant MRPS18B P260A Display Nitro-Oxidative Stress and Mitochondrial Dysfunction in Response to IFN-γ Stimulus | Biomedicines / [link](https://www.mdpi.com/2227-9059/10/9/2215) | alignment | | GATA1 controls numbers of hematopoietic progenitors and their response to autoimmune neuroinflammation | Blood Advances / [link](https://doi.org/10.1182/bloodadvances.2022008234) | Genome pipeline | | Validation of reduced S-gene target performance and failure for rapid surveillance of SARS-CoV-2 variants | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0275150) | COVID Lineage App | | Surveillance genome sequencing reveals multiple SARS-CoV-2 variants circulating in central Texas, USA, with a predominance of delta variant and review of vaccine breakthrough cases | Journal of Medical Virology / [link](https://onlinelibrary.wiley.com/doi/10.1002/jmv.27373) | | | Validation of the RT-LAMP assay in a large cohort of nasopharyngeal swab samples shows that it is a useful screening method for detecting SARS-CoV-2 and its VOC variants | -- / [link](https://www.medrxiv.org/content/10.1101/2022.02.15.22270954v1) | v3.3.4 | | Preliminary Experience of Liquid Biopsy in Lung Cancer Compared to Conventional Assessment: Light and Shadows | Journal of Personalized Medicine / [link](https://www.mdpi.com/2075-4426/12/11/1896) | DRAGEN server; TSO app | | Artificial-Intelligence-Assisted Discovery of Genetic Factors for Precision Medicine of Antiplatelet Therapy in Diabetic Peripheral Artery Disease | Biomedicines / [link](https://www.mdpi.com/2227-9059/10/1/116) | v3.6.3; Germline pipeline | | STRipy: A graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data | Human Mutation / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.24382) | ExpansionHunter | | Simple Saliva Sample Collection for the Detection of SARS-CoV-2 Variants Compared With Nasopharyngeal Swab Sample | Archives of Pathology & Laboratory Medicine / [link](https://doi.org/10.5858/arpa.2022-0298-SA) | | | Genetic Subtyping and Phenotypic Characterization of the Immune Microenvironment and MYC/BCL2 Double Expression Reveal Heterogeneity in Diffuse Large B-cell Lymphoma | Clinical Cancer Research / [link](https://doi.org/10.1158/1078-0432.CCR-21-2949) | Somatic pipeline; tumor-only | | Low-frequency variants in mildly symptomatic vaccine breakthrough infections presents a doubled-edged sword | Journal of Medical Virology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.27726) | | | SARS-CoV-2 Lineage P.4 Detection in Southeast Brazil: A Retrospective Genomic and Clinical Overview | COVID / [link](https://www.mdpi.com/2673-8112/2/12/127) | | | The SARS-CoV-2 Delta (B.1.617.2) variant with spike N501Y mutation in the shadow of Omicron emergence | Heliyon / [link](https://www.sciencedirect.com/science/article/pii/S240584402203938X) | COVID Lineage Pipeline | | Seminal Microbiota of Idiopathic Infertile Patients and Its Relationship With Sperm DNA Integrity | Frontiers in Cell and Developmental Biology / [link](https://www.frontiersin.org/articles/10.3389/fcell.2022.937157) | v3.5; BSSH; Metagenomics pipeline | | Novel De Novo Heterozygous Variants in the SON Gene Causing ZTTK Syndrome: A Case Report of Two Patients and Review of Neurological Findings | Child Neurology Open / [link](https://doi.org/10.1177/2329048X221119658) | alignment | | A thermostable Cas12b from Brevibacillus leverages one-pot discrimination of SARS-CoV-2 variants of concern | eBioMedicine / [link](https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964\(22\)00110-4/fulltext) | | | Sclerostin ablation prevents aortic valve stenosis in mice | American Journal of Physiology-Heart and Circulatory Physiology / [link](https://journals.physiology.org/doi/full/10.1152/ajpheart.00355.2022) | | | Pharmaceutical Potential of Casein-Derived Tripeptide Met-Lys-Pro: Improvement in Cognitive Impairments and Suppression of Inflammation in APP/PS1 Mice | Journal of Alzheimer's Disease / [link](https://content.iospress.com/articles/journal-of-alzheimers-disease/jad220192) | v3.7.5 | | The variant catalogue pipeline: A workflow to generate a background variant library from Whole Genome Sequences | -- / [link](https://www.biorxiv.org/content/10.1101/2022.10.03.508010v2) | | | Inhibition of KRAS, MEK and PI3K Demonstrate Synergistic Anti-Tumor Effects in Pancreatic Ductal Adenocarcinoma Cell Lines | Cancers / [link](https://www.mdpi.com/2072-6694/14/18/4467) | BCL convert; onboard | | Efficacy of the adjuvanted subunit protein COVID-19 vaccine, SCB-2019: a phase 2 and 3 multicentre, double-blind, randomised, placebo-controlled trial | The Lancet / [link](https://www.thelancet.com/journals/lancet/article/PIIS0140-6736\(22\)00055-1/fulltext) | COVIDSeq Test pipeline | | Sudden child death with acute encephalitis due to human herpesvirus 7: A case report and review of the literature | Forensic Science International: Reports / [link](https://www.sciencedirect.com/science/article/pii/S2665910721000803) | | | SARS-CoV-2 and post-donation information: a one-year experience of the French haemovigilance network | Blood Transfusion = Trasfusione Del Sangue / [link](https://www.bloodtransfusion.it/bt/article/view/247) | | | Disruption of the HIF-1 pathway in individuals with Ollier disease and Maffucci syndrome | PLOS Genetics / [link](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010504) | Variant calling; alignment | | Cancer-driving mutations are enriched in genic regions intolerant to germline variation | Science Advances / [link](https://www.science.org/doi/full/10.1126/sciadv.abo6371) | | | Effectiveness and protection duration of Covid-19 vaccines and previous infection against any SARS-CoV-2 infection in young adults | Nature Communications / [link](https://www.nature.com/articles/s41467-022-31469-z) | COVID Lineage App | | miR-200c-3p, miR-222-5p, and miR-512-3p Constitute a Biomarker Signature of Sorafenib Effectiveness in Advanced Hepatocellular Carcinoma | Cells / [link](https://www.mdpi.com/2073-4409/11/17/2673) | BCL convert | | Genomic Snapshot of SARS-CoV-2 in Migrants Entering Through Mediterranean Sea Routes | Frontiers in Public Health / [link](https://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2022.846115/full) | COVID Lineage App | | A Complex Genomic Rearrangement Resulting in Loss of Function of SCN1A and SCN2A in a Patient with Severe Developmental and Epileptic Encephalopathy | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/23/21/12900) | TruSight Software Suite | | A Mesenchymal Tumor Cell State Confers Increased Dependency on the BCL-XL Antiapoptotic Protein in Kidney Cancer | Clinical Cancer Research / [link](https://doi.org/10.1158/1078-0432.CCR-22-0669) | BCL convert | | Technical Performance of a 430-Gene Preventative Genomics Assay to Identify Multiple Variant Types Associated with Adult-Onset Monogenic Conditions, Susceptibility Loci, and Pharmacogenetic Insights | Journal of Personalized Medicine / [link](https://www.mdpi.com/2075-4426/12/5/667) | | | Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern | Viruses / [link](https://www.mdpi.com/1999-4915/14/9/1865) | DNA pipeline | | Modeling colorectal cancer: A bio-resource of 50 patient-derived organoid lines | Journal of Gastroenterology and Hepatology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/jgh.15818) | alignment; v2.4.5 | | HLA-associated outcomes in peanut oral immunotherapy trials identify mechanistic and clinical determinants of therapeutic success | Frontiers in Immunology / [link](https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2022.941839/full) | Germline small variant caller | | Cost Efficacy of Rapid Whole Genome Sequencing in the Pediatric Intensive Care Unit | Frontiers in Pediatrics / [link](https://www.frontiersin.org/articles/10.3389/fped.2021.809536) | Variant calling; alignment | | RNA sequence analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic patients with COVID-19 | International Journal of Infectious Diseases / [link](https://www.sciencedirect.com/science/article/pii/S120197122200368X) | | | Targeting MLL Methyltransferases Enhances the Antitumor Effects of PI3K Inhibition in Hormone Receptor–positive Breast Cancer | Cancer Research Communications / [link](https://doi.org/10.1158/2767-9764.CRC-22-0158) | | | Distinct diagnostic trajectories in NBAS-associated acute liver failure highlights the need for timely functional studies | JIMD Reports / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/jmd2.12280) | alignment | | Temporal dynamics of SARS-CoV-2 genome and detection of variants of concern in wastewater influent from two metropolitan areas in Arkansas | Science of The Total Environment / [link](https://www.sciencedirect.com/science/article/pii/S0048969722046447) | BSSH; COVID Lineage App | | Analytical Performances of the COVISTIXTM Antigen Rapid Test for SARS-CoV-2 Detection in an Unselected Population (All-Comers) | Pathogens / [link](https://www.mdpi.com/2076-0817/11/6/628) | COVID Lineage App v3.3.4 | | Candidate Modifier Genes for the Penetrance of Leber’s Hereditary Optic Neuropathy | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/23/19/11891) | v3.7.5 | | Stratum Corneum Ceramide Profiles Provide Reliable Indicators of Remission and Potential Flares in Atopic Dermatitis | Journal of Investigative Dermatology / [link](https://www.sciencedirect.com/science/article/pii/S0022202X22016645) | | | Endocannabinoid dysfunction in neurological disease: neuro-ocular DAGLA-related syndrome | Brain / [link](https://doi.org/10.1093/brain/awac223) | v3.8 | | SWAN pathway-network identification of common aneuploidy-based oncogenic drivers | Nucleic Acids Research / [link](https://doi.org/10.1093/nar/gkac200) | | | From Alpha to Delta—Genetic Epidemiology of SARS-CoV-2 (hCoV-19) in Southern Poland | Pathogens / [link](https://www.mdpi.com/2076-0817/11/7/780) | COVID Lineage App; BSSH; RNA pathogen detection app | | Clinical, genetic, and epidemiological survey of Polish children and adolescents with severe obesity: A study protocol of the Polish–German study project on severe early-onset obesity | Frontiers in Endocrinology / [link](https://www.frontiersin.org/journals/endocrinology/articles/10.3389/fendo.2022.972174/full) | Enrichment pipeline | | Adaptive immune responses in vaccinated patients with symptomatic SARS-CoV-2 Alpha infection | JCI Insight / [link](https://insight.jci.org/articles/view/155944) | BSSH; Pathogen detection app | | Dispatches from Biotech beginning BeginNGS: Rapid newborn genome sequencing to end the diagnostic and therapeutic odyssey | American Journal of Medical Genetics Part C: Seminars in Medical Genetics / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.c.32005) | v3.10; ICA | | Topical therapy for regression and melanoma prevention of congenital giant nevi | Cell / [link](https://doi.org/10.1016/j.cell.2022.04.025) | | | The Protective Effect of Edaravone on TDP-43 Plus Oxidative Stress-Induced Neurotoxicity in Neuronal Cells: Analysis of Its Neuroprotective Mechanisms Using RNA Sequencing | Pharmaceuticals / [link](https://www.mdpi.com/1424-8247/15/7/842) | v3.6.3 | | \[Rapidly progressive Alport syndrome in a young woman: case report] | Giornale Italiano Di Nefrologia: Organo Ufficiale Della Societa Italiana Di Nefrologia / [link](https://pubmed.ncbi.nlm.nih.gov/35191625/) | | | Sequential Appearance and Isolation of a SARS-CoV-2 Recombinant between Two Major SARS-CoV-2 Variants in a Chronically Infected Immunocompromised Patient | Viruses / [link](https://doi.org/10.3390/v14061266) | | | Pharmacogenomic study of heart failure and candesartan response from the CHARM programme | ESC Heart Failure / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ehf2.14026) | AWS; Germline pipeline | | LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays | Briefings in Bioinformatics / [link](https://doi.org/10.1093/bib/bbac252) | Variant calling | | A systems biology approach identifies candidate drugs to reduce mortality in severely ill patients with COVID-19 | Science Advances / [link](https://www.science.org/doi/full/10.1126/sciadv.abm2510) | alignment; Epigenome pipeline v3.4.5 | | Balanced chromosomal rearrangements offer insights into coding and noncoding genomic features associated with developmental disorders | -- / [link](https://www.medrxiv.org/content/10.1101/2022.02.15.22270795v1) | | | Ethylmalonic encephalopathy masquerading as meningococcemia | Cold Spring Harbor Molecular Case Studies / [link](https://molecularcasestudies.cshlp.org/content/8/2/a006193) | | | Individualized Mini-Panel Sequencing of ctDNA Allows Tumor Monitoring in Complex Karyotype Sarcomas | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/23/18/10215) | Enrichment pipeline; BSSH | | Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil | Microbiology Spectrum / [link](https://journals.asm.org/doi/full/10.1128/spectrum.02366-21) | BSSH; COVID Lineage | | Changes in the transcriptome and long non-coding RNAs but not the methylome occur in human cells exposed to Borrelia burgdorferi | -- / [link](https://www.biorxiv.org/content/10.1101/2022.07.11.499513v1) | Methylation pipeline; BSSH | | Identifying SARS-CoV-2 Variants of Concern through Saliva-Based RT-qPCR by Targeting Recurrent Mutation Sites | Microbiology Spectrum / [link](https://journals.asm.org/doi/full/10.1128/spectrum.00797-22) | v3.5.3 | | Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota | Communications Biology / [link](https://www.nature.com/articles/s42003-022-03347-3) | COVID Lineage App; BSSH | | Massively parallel identification of functionally consequential noncoding genetic variants in undiagnosed rare disease patients | Scientific Reports / [link](https://www.nature.com/articles/s41598-022-11589-8) | v3.6.3 | | Severe acute respiratory syndrome coronavirus 2 spike ARTIC amplicon 76 dropout in relation to primers, viral load, and variants | Journal of The Arab Society for Medical Research / [link](https://journals.lww.com/asmr/fulltext/2022/17020/severe_acute_respiratory_syndrome_coronavirus_2.10.aspx) | | | Tracing the trajectories of SARS-CoV-2 variants of concern between December 2020 and September 2021 in the Canary Islands (Spain) | Frontiers in Cellular and Infection Microbiology / [link](https://www.frontiersin.org/articles/10.3389/fcimb.2022.919346) | | | PathoLive—Real-Time Pathogen Identification from Metagenomic Illumina Datasets | Life / [link](https://www.mdpi.com/2075-1729/12/9/1345) | | | Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/23/2/986) | | | Characterization of the First SARS-CoV-2 Isolates from Aotearoa New Zealand as Part of a Rapid Response to the COVID-19 Pandemic | Viruses / [link](https://www.mdpi.com/1999-4915/14/2/366) | Variant calling | | Resistome and Virulome of Multi-Drug Resistant E. coli ST131 Isolated from Residents of Long-Term Care Facilities in the Northern Italian Region | Diagnostics / [link](https://www.mdpi.com/2075-4418/12/1/213) | | | Aberrant expression of agouti signaling protein (ASIP) as a cause of monogenic severe childhood obesity | Nature Metabolism / [link](https://www.nature.com/articles/s42255-022-00703-9) | v3.7.5 | | Whole-Genome Sequencing of ST2 A. baumannii Causing Bloodstream Infections in COVID-19 Patients | Antibiotics / [link](https://www.mdpi.com/2079-6382/11/7/955) | | | Rare and common variants in ROM1 and PRPH2 genes trans-modify Stargardt/ABCA4 disease | PLOS Genetics / [link](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010129) | v2.5.1 | | Exome sequencing of families from Ghana reveals known and candidate hearing impairment genes | Communications Biology / [link](https://www.nature.com/articles/s42003-022-03326-8) | Germline pipeline v3.2.8 | | Severe Acute Respiratory Syndrome Coronavirus 2 Delta Vaccine Breakthrough Transmissibility in Alachua County, Florida | Clinical Infectious Diseases / [link](https://doi.org/10.1093/cid/ciac197) | | | In Vitro Activity of Sulbactam–Durlobactam against Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates: A Multicentre Report from Italy | Antibiotics / [link](https://www.mdpi.com/2079-6382/11/8/1136) | | | A novel STING agonist-adjuvanted pan-sarbecovirus vaccine elicits potent and durable neutralizing antibody and T cell responses in mice, rabbits and NHPs | Cell Research / [link](https://www.nature.com/articles/s41422-022-00612-2) | alignment | | Helicobacter pylori actively suppresses innate immune nucleic acid receptors | Gut Microbes / [link](https://doi.org/10.1080/19490976.2022.2105102) | v3.6.3 | | Interferon pathway lupus risk alleles modulate risk of death from acute COVID-19 | Translational Research / [link](https://www.sciencedirect.com/science/article/pii/S1931524422000202) | onboard | | Oncogenic RAS commandeers amino acid sensing machinery to aberrantly activate mTORC1 in multiple myeloma | Nature Communications / [link](https://www.nature.com/articles/s41467-022-33142-x) | demultiplexing; v3.7.4 | | Presumptive positive with the Cepheid Xpert Xpress SARS-CoV-2 assay due to N mutations in the Delta variant | Diagnostic Microbiology and Infectious Disease / [link](https://www.sciencedirect.com/science/article/pii/S0732889322000633) | COVID Lineage App | | A novel protein truncating mutation in L2HGDH causes L-2-hydroxyglutaric aciduria in a consanguineous Pakistani family | Metabolic Brain Disease / [link](https://doi.org/10.1007/s11011-021-00832-2) | BSSH; Germline Pipeline v3.2.8 | | Culture and identification of a “Deltamicron” SARS-CoV-2 in a three cases cluster in southern France | Journal of Medical Virology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.27789) | | | External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories | Journal of Clinical Microbiology / [link](https://journals.asm.org/doi/full/10.1128/jcm.01698-21) | BSSH; COVID Lineage | | Three SARS-CoV-2 recombinants identified in Brazilian childre | -- / [link](https://europepmc.org/article/PPR/PPR491787) | COVID Lineage App | | NEDDylated Cullin 3 mediates the adaptive response to topoisomerase 1 inhibitors | Science Advances / [link](https://www.science.org/doi/full/10.1126/sciadv.abq0648) | v3.9.3 | | Novel subtype of mucopolysaccharidosis caused by arylsulfatase K (ARSK) deficiency | Journal of Medical Genetics / [link](https://jmg.bmj.com/content/59/10/957) | Germline pipeline v3.2.8 | | A novel map of human p53 response elements uncovers evidence of selection pressures and variants similar to Li-Fraumeni Syndrome mutations | -- / [link](https://www.medrxiv.org/content/10.1101/2022.09.28.22280453v1) | alignment | | Biallelic truncating variants in ATP9A cause a novel neurodevelopmental disorder involving postnatal microcephaly and failure to thrive | Journal of Medical Genetics / [link](https://jmg.bmj.com/content/59/7/662) | BSSH; Germline pipeline v3.2.8 | | Integrated analyses of growth differentiation factor-15 concentration and cardiometabolic diseases in humans | eLife / [link](https://doi.org/10.7554/eLife.76272) | AWS; Germline pipeline v3.0.7 | | Broadening the phenotype of *LRRK1* mutations - Features of malignant osteopetrosis and optic nerve atrophy with intrafamilial variable expressivity | European Journal of Medical Genetics / [link](https://www.sciencedirect.com/science/article/pii/S1769721221002494) | alignment; v3.6.3 | | Protocol for unbiased, consolidated variant calling from whole exome sequencing data | STAR Protocols / [link](https://www.sciencedirect.com/science/article/pii/S2666166722002982) | | | Genomic surveillance: Circulating lineages and genomic variation of SARS-CoV-2 in early pandemic in Ceará state, Northeast Brazil | Virus Research / [link](https://www.sciencedirect.com/science/article/pii/S0168170222002362) | COVID Lineage App; BSSH | | The rate of secondary genomic findings in the Saudi population | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.62491) | v3.7 | | Analyzing the Korean reference genome with meta-imputation increased the imputation accuracy and spectrum of rare variants in the Korean population | Frontiers in Genetics / [link](https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.1008646/full) | Variant calling | | A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands | Frontiers in Microbiology / [link](https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.803827/full) | COVID Lineage App | | Pharmacogenetic Gene-Drug Associations in Pediatric Burn and Surgery Patients | Journal of Burn Care & Research: Official Publication of the American Burn Association / [link](https://doi.org/10.1093/jbcr/irac062) | | | Kinetics and persistence of cellular and humoral immune responses to SARS-CoV-2 vaccine in healthcare workers with or without prior COVID-19 | Journal of Cellular and Molecular Medicine / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/jcmm.17186) | COVID Lineage App | | A 21L/BA.2-21K/BA.1 “MixOmicron” SARS-CoV-2 hybrid undetected by qPCR that screen for variant in routine diagnosis | Infection, Genetics and Evolution / [link](https://www.sciencedirect.com/science/article/pii/S1567134822001575) | BCL convert | | First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France | Journal of Medical Virology / [link](https://onlinelibrary.wiley.com/doi/10.1002/jmv.27695) | | | Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study | Cell Reports Medicine / [link](https://www.sciencedirect.com/science/article/pii/S2666379122001690) | Germline pipeline; v3 | | Clinical and Virological Features of Patients Hospitalized with Different Types of COVID-19 Vaccination in Mexico City | Vaccines / [link](https://www.mdpi.com/2076-393X/10/8/1181) | COVIDSeq Test pipeline; BSSH | | The Easy-to-Use SARS-CoV-2 Assembler for Genome Sequencing: Development Study | JMIR Bioinformatics and Biotechnology / [link](https://bioinform.jmir.org/2022/1/e31536) | RNA pathogen detection; BSSH | | Evidence of co-infections during Delta and Omicron SARS-CoV-2 variants co-circulation through prospective screening and sequencing | Clinical Microbiology and Infection / [link](https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X\(22\)00345-7/fulltext#supplementaryMaterial) | | | Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study | eLife / [link](https://doi.org/10.7554/eLife.81849) | BSSH; COVID Lineage Pipeline | | Optimized conditions for Listeria, Salmonella and Escherichia whole genome sequencing using the Illumina iSeq100 platform with point-and-click bioinformatic analysis | PLOS ONE / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9710801/) | | | Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies | Genome Biology / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9746098/) | | | Ataxia-Telangiectasia Mutated Loss of Heterozygosity in Melanoma | International Journal of Molecular Sciences / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9786167/) | Germline pipeline; Somatic pipeline | | Truvari: refined structural variant comparison preserves allelic diversity | Genome Biology / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9793516/) | | | COVIDSeq as Laboratory Developed Test (LDT) for Diagnosis of SARS-CoV-2 Variants of Concern (VOC) | Archives of clinical and biomedical research / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9802674/) | BSSH | | A Novel CRISPR Interference Effector Enabling Functional Gene Characterization with Synthetic Guide RNAs | The CRISPR Journal / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9805873/) | RNA pipeline v3.7.5 | | Approaches to long-read sequencing in a clinical setting to improve diagnostic rate | Scientific Reports / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9548499/) | | | First Detection of the SARS-CoV-2 Omicron BA.5/22B in Monaco | Microorganisms / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9607325/) | BCL convert | | Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features | Nature Genetics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9649442/) | RNA pipeline | | Strategies to inhibit FGFR4 V550L-driven rhabdomyosarcoma | British Journal of Cancer / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9681859/) | RNA pipeline; Somatic pipeline | | The landscape of cancer-associated fibroblasts in colorectal cancer liver metastases | Theranostics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9691344/) | v3.8.4 | | Resequencing worldwide spinach germplasm for identification of field resistance QTLs to downy mildew and assessment of genomic selection methods | Horticulture Research / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9715576/) | v3.8.4 | | Comprehensive single-cell transcriptional profiling defines shared and unique epithelial injury responses during kidney fibrosis | Cell metabolism / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9742301/) | v3.9.3 | | Defective binding of ETS1 and STAT4 due to a mutation in the promoter region of THPO as a novel mechanism of congenital amegakaryocytic thrombocytopenia | Haematologica / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10153527/) | v3.8 | | Loss of FOCAD, operating via the SKI messenger RNA surveillance pathway, causes a pediatric syndrome with liver cirrhosis | Nature genetics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7615854/) | | | Genomic architecture of fetal central nervous system anomalies using whole-genome sequencing | NPJ Genomic Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9106651/) | | | An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases | Nature Communications / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9325884/) | v3.7 | | Assessing clinical utility of preconception expanded carrier screening regarding residual risk for neurodevelopmental disorders | NPJ Genomic Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9338263/) | v3.7.5 | | Whole-genome sequencing reveals complex genomic features underlying anti-CD19 CAR T-cell treatment failures in lymphoma | Blood / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9353150/) | Somatic pipeline | | Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis | Nature Genetics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9355874/) | Germline pipeline | | SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings | Nature Communications / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9366802/) | | | Candidate Genes in Testing Strategies for Linkage Analysis and Bioinformatic Sorting of Whole Genome Sequencing Data in Three Small Japanese Families with Idiopathic Superior Oblique Muscle Palsy | International Journal of Molecular Sciences / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9369257/) | v3.7.5 | | Ultra-deep sequencing validates safety of CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells | Nature Communications / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372057/) | Enrichment pipeline; Germline pipeline | | Expansion and mechanistic insights into de novo DEAF1 variants in DEAF1-associated neurodevelopmental disorders | Human Molecular Genetics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10310974/) | alignment | | Adult-onset CblC deficiency: a challenging diagnosis involving different adult clinical specialists | Orphanet Journal of Rare Diseases / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8812048/) | Enrichment app v3.8.4 | | Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA | Cell Reports Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8913280/) | BSSH; COVID Lineage App | | Emergence of Q493R mutation in SARS-CoV-2 spike protein during bamlanivimab/etesevimab treatment and resistance to viral clearance | The Journal of Infection / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8381628/) | COVIDSeq Test pipeline | | Transient regulation of focal adhesion via Tensin3 is required for nascent oligodendrocyte differentiation | eLife / [link](https://doi.org/10.7554/eLife.80273) | v3.6.3 | | Two-Period Study Results from a Large Italian Hospital Laboratory Attesting SARS-CoV-2 Variant PCR Assay Evolution | Microbiology Spectrum / [link](https://journals.asm.org/doi/10.1128/spectrum.02922-22) | COVIDSeq pipeline | | SARS-CoV-2 Lineage Tracking, and Evolving Trends Seen during Three Consecutive Peaks of Infection in Delhi, India: a Clinico-Genomic Study | Microbiology Spectrum / [link](https://journals.asm.org/doi/10.1128/spectrum.02729-21) | | | Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells | Science Advances / [link](https://www.science.org/doi/10.1126/sciadv.abl5621) | | | A novel human monogenic obesity trait: severe early-onset childhood obesity caused by aberrant expression of agouti-signaling protein (ASIP): a case report | -- / [link](https://www.researchsquare.com/article/rs-1459517/v1) | v3.7.5 | | Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement | eLife / [link](https://doi.org/10.7554/eLife.73010) | |
2021 | Title | Publisher / Link | Tags | | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------- | | Biallelic Variants in KIF17 Associated with Microphthalmia and Coloboma Spectrum | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/22/9/4471) | Germline pipeline v3.3.7 | | Clonal dynamics in a composite chronic lymphocytic leukemia and hairy cell leukemia-variant | Genes, Chromosomes and Cancer / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/gcc.22925) | Somatic pipeline; Enrichment pipeline; BSSH; CNV Baseline Builder | | Role of chimeric transcript formation in the pathogenesis of birth defects | Congenital Anomalies / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/cga.12400) | | | A novel de novo intronic variant in ITPR1 causes Gillespie syndrome | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.62232) | | | Genome Sequence of a SARS-CoV-2 Strain from a COVID-19 Clinical Sample from the Khagrachari District of Bangladesh | Microbiology Resource Announcements / [link](https://journals.asm.org/doi/10.1128/mra.00189-21) | RNA pathogen detection | | Whole genome sequencing for revealing the point mutations of SARS-CoV-2 genome in Bangladeshi isolates and their structural effects on viral proteins | RSC Advances / [link](https://pubs.rsc.org/en/content/articlelanding/2021/ra/d1ra05327b) | RNA pathogen detection; RNA pipeline | | Rare Recurrent Variants in Noncoding Regions Impact Attention-Deficit Hyperactivity Disorder (ADHD) Gene Networks in Children of both African American and European American Ancestry | Genes / [link](https://www.mdpi.com/2073-4425/12/2/310) | | | Pan-Cancer Drivers Are Recurrent Transcriptional Regulatory Heterogeneities in Early-Stage Luminal Breast Cancer | Cancer Research / [link](https://doi.org/10.1158/0008-5472.CAN-20-1034) | Somatic mode | | Genome sequencing of 320 Chinese children with epilepsy: a clinical and molecular study | Brain / [link](https://doi.org/10.1093/brain/awab233) | | | Further confirmation of the association of SLC12A2 with non-syndromic autosomal-dominant hearing impairment | Journal of Human Genetics / [link](https://www.nature.com/articles/s10038-021-00954-6) | v3.4.12 | | Monitoring the rise of the SARS-CoV-2 lineage B.1.1.7 in Tenerife (Spain) since mid-December 2020 | Journal of Infection / [link](https://www.sciencedirect.com/science/article/pii/S0163445321001687) | | | Ultra-rapid emergency genomic diagnosis of Donahue syndrome in a preterm infant within 17 hours | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.61917) | DRAGEN server | | High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0247115) | COVIDSeq Test pipeline | | Branching clonal evolution patterns predominate mutational landscape in multiple myeloma | American Journal of Cancer Research / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8640818/) | Somatic pipeline v3.5.7 | | Topoisomerase II alpha inhibition can overcome taxane-resistant prostate cancer through DNA repair pathways | Scientific Reports / [link](https://www.nature.com/articles/s41598-021-01697-2) | | | Rare variant contribution to human disease in 281,104 UK Biobank exomes | Nature / [link](https://www.nature.com/articles/s41586-021-03855-y) | UK Biobank | | Accuracy of somatic variant detection workflows for whole genome sequencing experiments | -- / [link](https://www.biorxiv.org/content/10.1101/2021.06.10.446467v2) | tumor-only; Somatic pipeline v3.7.5; CGP-WGS pipeline v2.0.1 | | Genomic complexity is associated with epigenetic regulator mutations and poor prognosis in diffuse large B-cell lymphoma | OncoImmunology / [link](https://doi.org/10.1080/2162402X.2021.1928365) | Somatic pipeline; tumor-only | | Application of Massive Parallel DNA Sequencing to Diagnose Drug-Resistant Epilepsy in Children | Molecular Genetics, Microbiology and Virology / [link](https://doi.org/10.3103/S0891416821040091) | DRAGEN enrichment app; DRAGEN CNV Baseline builder app | | A founder mutation in the GMPPB gene \[c.1000G > A (p.Asp334Asn)] causes a mild form of limb-girdle muscular dystrophy/congenital myasthenic syndrome (LGMD/CMS) in South Indian patients | Neurogenetics / [link](https://link.springer.com/article/10.1007/s10048-021-00658-1) | | | Nager syndrome in patient lacking acrofacial dysostosis: Expanding the phenotypic spectrum of SF3B4-related disease | American Journal of Medical Genetics. Part A / [link](https://onlinelibrary.wiley.com/doi/10.1002/ajmg.a.62113) | | | Application of WGS Technologies in Disease Diagnostics, Surveillance, Transmission, and Outbreak Investigation in the Food Sector | Sequencing Technologies in Microbial Food Safety and Quality / [link](https://www.researchgate.net/publication/349358216_Application_of_WGS_Technologies_in_Disease_Diagnostics_Surveillance_Transmission_and_Outbreak_Investigation_in_the_Food_Sector) | | | Sickle Cell Hemoglobin Induces Autophagy in Human Macrophages | Blood / [link](https://www.sciencedirect.com/science/article/pii/S0006497121029360) | | | Exome sequencing in high and low fetal haemoglobin Arab-Indian haplotype sickle cell disease | British Journal of Haematology / [link](https://onlinelibrary.wiley.com/doi/10.1111/bjh.17542) | Germline pipeline; Joint genotyping | | Determination of the phylogenetic origins of the Árpád Dynasty based on Y chromosome sequencing of Béla the Third | European Journal of Human Genetics / [link](https://www.nature.com/articles/s41431-020-0683-z) | Variant calling; alignment; v3.2.5 | | Recognition of plausible therapeutic agents to combat COVID-19: An omics data based combined approach | Gene / [link](https://www.sciencedirect.com/science/article/pii/S0378111920310374) | | | Long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders | HGG advances / [link](https://doi.org/10.1016/j.xhgg.2021.100023) | v3.2.8 | | Comparison of multiple imputation algorithms and verification using whole-genome sequencing in the CMUH genetic biobank | BioMedicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8823485/) | v3.6; DNA pipeline | | Genome Sequencing of the SARS-CoV-2 Delta (B.1.617.2) Variant of Concern Detected in Bangladesh | Microbiology Resource Announcements / [link](https://journals.asm.org/doi/full/10.1128/mra.00849-21) | RNA pathogen detection | | High diagnosis rate for nonimmune hydrops fetalis with prenatal clinical exome from the Hydrops-Yielding Diagnostic Results of Prenatal Sequencing (HYDROPS) Study | Genetics in Medicine / [link](https://www.sciencedirect.com/science/article/pii/S1098360021050292) | v2.0.3 | | First Detection and Genome Sequencing of SARS-CoV-2 Lambda (C.37) Variant in Symptomatic Domestic Cats in Lima, Peru | Frontiers in Veterinary Science / [link](https://www.frontiersin.org/articles/10.3389/fvets.2021.737350) | COVID Lineage App; BSSH | | Targeting cancer stem cells in medulloblastoma by inhibiting AMBRA1 dual function in autophagy and STAT3 signalling | Acta Neuropathologica / [link](https://doi.org/10.1007/s00401-021-02347-7) | BSSH; Differential expression; RNA pipeline | | Reducing Sanger confirmation testing through false positive prediction algorithms | Genetics in Medicine / [link](https://www.sciencedirect.com/science/article/pii/S1098360021050498) | Germline pipeline | | Fuzzy set intersection based paired-end short-read alignment | -- / [link](https://www.biorxiv.org/content/10.1101/2021.11.23.469039v1) | v3.8 | | Novel indel mutation in the N gene of SARS-CoV-2 clinical samples that were diagnosed positive in a commercial RT-PCR assay | Virus Research / [link](https://www.sciencedirect.com/science/article/pii/S0168170221001052) | RNA pipeline | | Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases | Genome Medicine / [link](https://doi.org/10.1186/s13073-021-00965-0) | Variant calling; v3.2.8 | | Confirming putative variants at ≤ 5% allele frequency using allele enrichment and Sanger sequencing | Scientific Reports / [link](https://www.nature.com/articles/s41598-021-91142-1) | Somatic pipeline | | Diversity of genetic alterations of primary central nervous system lymphoma in Hispanic versus non-Hispanic patients | Cancer Treatment and Research Communications / [link](https://www.sciencedirect.com/science/article/pii/S2468294221000095) | Somatic pipeline | | A Monoallelic Variant in REST Is Associated with Non-Syndromic Autosomal Dominant Hearing Impairment in a South African Family | Genes / [link](https://www.mdpi.com/2073-4425/12/11/1765) | alignment; v3.4.12; Germline Pipeline v3.2.8 | | Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases | Genetics in Medicine / [link](https://www.nature.com/articles/s41436-020-01084-8) | | | High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses | Viruses / [link](https://www.mdpi.com/1999-4915/13/10/2063) | RNA pathogen detection; BSSH; Metagenomics pipeline; v3.5.16 | | A novel case of an infantile fibrosarcoma-like tumor with *KIAA1549*-*BRAF* translocation and an oncogenic *NF2*p.Q459\* SNV with potential clinical significance | Archives of Pathology and Clinical Research / [link](https://www.pathologyresjournal.com/fulltext/apcr/apcr-aid1023.php) | v3.7.5; alignment; DRAGEN fusion caller | | Whole exome sequencing of a gut-associated lymphoid tissue neoplasm points to precursor or early form of sporadic colon carcinoma | Pathology - Research and Practice / [link](https://www.sciencedirect.com/science/article/pii/S0344033821000674) | v3.5 | | Detection of hypermethylation at *H19*DMR at amniocentesis in a fetus with overgrowth, distended abdomen and Beckwith-Wiedemann syndrome | Taiwanese Journal of Obstetrics and Gynecology / [link](https://www.sciencedirect.com/science/article/pii/S1028455921002655) | Methylation pipeline v3.8 | | Pangenomics enables genotyping of known structural variants in 5202 diverse genomes | Science / [link](https://www.science.org/doi/full/10.1126/science.abg8871) | | | Upregulation of Antiviral Factors That Inhibit HIV-1 Infection in Sickle Cell Disease | Blood / [link](https://www.sciencedirect.com/science/article/pii/S000649712102944X) | Differential Expression pipeline; RNA pipeline | | IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes | Nucleic Acids Research / [link](https://doi.org/10.1093/nar/gkaa923) | v3.4 | | High concordance of mutation patterns in 10 common mutated genes between tumor tissue and cell-free DNA in metastatic colorectal cancer | American Journal of Cancer Research / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8167700/) | BSSH; Somatic mutation pipeline | | Identification of a missense variant in SPDL1 associated with idiopathic pulmonary fibrosis | Communications Biology / [link](https://www.nature.com/articles/s42003-021-01910-y) | AWS; v3.0.7; Germline pipeline | | Making a Difference: Adaptation of the Clinical Laboratory in Response to the Rapidly Evolving COVID-19 Pandemic | Academic Pathology / [link](https://doi.org/10.1177/23742895211023948) | BSSH; Metagenomics pipeline | | Distinct Patterns of Emergence of SARS-CoV-2 Spike Variants including N501Y in Clinical Samples in Columbus Ohio | -- / [link](https://www.biorxiv.org/content/10.1101/2021.01.12.426407v3) | RNA pathogen detection | | Exome Sequencing Analysis of Familial Cases of Multiple Sclerosis and a Monozygotic Discordant Twin | Arabian Journal for Science and Engineering / [link](https://doi.org/10.1007/s13369-020-05242-7) | Variant calling; alignment | | Expanding the genotypic spectrum of ACTG2-related visceral myopathy | Molecular Case Studies / [link](http://molecularcasestudies.cshlp.org/content/7/3/a006085) | DRAGEN server | | Novel Variant Findings and Challenges Associated With the Clinical Integration of Genomic Testing: An Interim Report of the Genomic Medicine for Ill Neonates and Infants (GEMINI) Study | JAMA Pediatrics / [link](https://doi.org/10.1001/jamapediatrics.2020.5906) | v2.6.5 | | Cobimetinib Plus Gemcitabine: An Active Combination in KRAS G12R-Mutated Pancreatic Ductal Adenocarcinoma Patients in Previously Treated and Failed Multiple Chemotherapies | Journal of Pancreatic Cancer / [link](https://www.liebertpub.com/doi/full/10.1089/pancan.2021.0006) | | | Inhibitory activity of medicinal mushroom Ganoderma lucidum on colorectal cancer by attenuating inflammation | Precision Clinical Medicine / [link](https://doi.org/10.1093/pcmedi/pbab023) | | | \[Application of the artificial intelligence-rapid whole-genome sequencing diagnostic system in the neonatal/pediatric intensive care unit] | Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics / [link](https://europepmc.org/articles/PMC8140348) | | | Coding-Complete Genome Sequences and Mutation Profiles of Nine SARS-CoV-2 Strains Detected from COVID-19 Patients in Bangladesh | Microbiology Resource Announcements / [link](https://journals.asm.org/doi/full/10.1128/mra.00124-21) | v3.5 | | Evaluation of two RT-PCR screening assays for identifying SARS-CoV-2 variants | Journal of Clinical Virology / [link](https://www.sciencedirect.com/science/article/pii/S1386653221002365) | COVID Lineage App v3.5.1 | | Estrogen-related Receptor Alpha (ERRα) is Required for PGC-1α-dependent Gene Expression in the Mouse Brain | Neuroscience / [link](https://www.sciencedirect.com/science/article/pii/S0306452221005078) | BCL convert | | Machine learning analysis using 77,044 genomic and transcriptomic profiles to accurately predict tumor type | Translational Oncology / [link](https://www.sciencedirect.com/science/article/pii/S1936523321000085) | demultiplexing | | Whole genome mapping and identification of single nucleotide polymorphisms of four Bangladeshi individuals and their functional significance | BMC Research Notes / [link](https://doi.org/10.1186/s13104-021-05514-x) | Germline; v3.4.5 | | Case Report: Paucisymptomatic College-Age Population as a Reservoir for Potentially Neutralization-Resistant Severe Acute Respiratory Syndrome Coronavirus 2 Variants | The American Journal of Tropical Medicine and Hygiene / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8592217/) | COVIDSeq Test RUO v1.0.0 | | Turnover of SARS-CoV-2 Lineages Shaped the Pandemic and Enabled the Emergence of New Variants in the State of Rio de Janeiro, Brazil | Viruses / [link](https://www.mdpi.com/1999-4915/13/10/2013) | COVID Lineage v3.5.1 | | The LDLR, APOB, and PCSK9 Variants of Index Patients with Familial Hypercholesterolemia in Russia | Genes / [link](https://www.mdpi.com/2073-4425/12/1/66) | | | Influence of age on the spread of SARS-CoV-2 variant B.1.1.7 | Journal of Clinical Virology / [link](https://www.sciencedirect.com/science/article/pii/S1386653221001396) | COVIDSeq Test pipeline | | New SARS-CoV-2 Variant from Jordan | Microbiology Resource Announcements / [link](https://journals.asm.org/doi/full/10.1128/mra.00532-21) | | | Epidemiologically Linked COVID-19 Outbreaks at a Youth Camp and Men’s Conference — Illinois, June–July 2021 | MMWR. Morbidity and Mortality Weekly Report / [link](https://www.cdc.gov/mmwr/volumes/70/wr/mm7035e4.htm) | | | Genome Sequence of a SARS-CoV-2 P.1 Variant of Concern (20J/501Y.V3) from Bangladesh | Microbiology Resource Announcements / [link](https://journals.asm.org/doi/full/10.1128/mra.00524-21) | RNA pathogen detection | | Immune cell residency in the nasal mucosa may partially explain respiratory disease severity across the age range | Scientific Reports / [link](https://www.nature.com/articles/s41598-021-95532-3) | v1.1.15 | | Functional analysis of a *de novo* variant in the neurodevelopment and generalized epilepsy disease gene *NBEA* | Molecular Genetics and Metabolism / [link](https://www.sciencedirect.com/science/article/pii/S1096719221007642) | Variant calling; Joint genotyping; v2.6 | | Virome characterization in serum of healthy show pigs raised in Oklahoma demonstrated great diversity of ssDNA viruses | Virology / [link](https://www.sciencedirect.com/science/article/pii/S0042682221000143) | BSSH; Metagenomics pipeline | | Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela | Infection, Genetics and Evolution / [link](https://www.sciencedirect.com/science/article/pii/S1567134821004470) | | | High performance of a GPU-accelerated variant calling tool in genome data analysis | -- / [link](https://www.biorxiv.org/content/10.1101/2021.12.12.472266v1) | | | Genomic Surveillance of SARS-CoV-2 Viruses Collected during the Ending Phase of the First Wave of the COVID-19 Pandemic in Bangladesh | Microbiology Resource Announcements / [link](https://journals.asm.org/doi/full/10.1128/mra.00496-21) | RNA pathogen detection app | | A ZFYVE19 gene mutation associated with neonatal cholestasis and cilia dysfunction: case report with a novel pathogenic variant | Orphanet Journal of Rare Diseases / [link](https://doi.org/10.1186/s13023-021-01775-8) | Variant calling; v3.2.8 | | Molecular Mechanisms of Skewed X-Chromosome Inactivation in Female Hemophilia Patients—Lessons from Wide Genome Analyses | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/22/16/9074) | v3.8 | | *A ZFHX4* mutation associated with a recognizable neuropsychological and facial phenotype | European Journal of Medical Genetics / [link](https://www.sciencedirect.com/science/article/pii/S1769721221001877) | Variant calling; Germline pipeline | | Low Grade Papillary Sinonasal (Schneiderian) Carcinoma: A Series of Five Cases of a Unique Malignant Neoplasm with Comparison to Inverted Papilloma and Conventional Nonkeratinizing Squamous Cell Carcinoma | Head and Neck Pathology / [link](https://doi.org/10.1007/s12105-021-01335-3) | Enrichment pipeline | | Pan-cancer analysis of RNA expression of ANGIOTENSIN-I-CONVERTING ENZYME 2 reveals high variability and possible impact on COVID-19 clinical outcomes | Scientific Reports / [link](https://www.nature.com/articles/s41598-021-84731-7) | demultiplexing | | Wastewater SARS-CoV-2 monitoring as a community-level COVID-19 trend tracker and variants in Ohio, United States | Science of The Total Environment / [link](https://www.sciencedirect.com/science/article/pii/S0048969721048324) | | | Sub-genic intolerance, ClinVar, and the epilepsies: A whole-exome sequencing study of 29,165 individuals | American Journal of Human Genetics / [link](https://doi.org/10.1016/j.ajhg.2021.04.009) | | | The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City | Viruses / [link](https://www.mdpi.com/1999-4915/13/11/2182) | v3.3 | | Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results | Viruses / [link](https://www.mdpi.com/1999-4915/13/12/2474) | COVIDSeq Test pipeline | | CYP2C9 Variations and Their Pharmacogenetic Implications Among Diverse South Asian Populations | Pharmacogenomics and Personalized Medicine / [link](https://www.tandfonline.com/doi/abs/10.2147/PGPM.S272015) | v3.6.3 | | Genotypic analysis of the female BPH/5 mouse, a model of superimposed preeclampsia | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0253453) | Germline pipeline | | FFPE samples from cavitational ultrasonic surgical aspirates are suitable for RNA profiling of gliomas | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0255168) | RNA pipeline v3.7.5 | | Predicted Immunogenicity of *CDK12* Biallelic Loss-of-Function Tumors Varies across Cancer Types | The Journal of Molecular Diagnostics / [link](https://www.sciencedirect.com/science/article/pii/S1525157821002890) | demultiplexing | | Practical guide for managing large-scale human genome data in research | Journal of Human Genetics / [link](https://www.nature.com/articles/s10038-020-00862-1) | review | | Levodopa-responsive dystonia caused by biallelic PRKN exon inversion invisible to exome sequencing | Brain Communications / [link](https://doi.org/10.1093/braincomms/fcab197) | Variant calling; alignment | | Genomic analysis reveals a rapid spread and predominance of lambda (C.37) SARS-COV-2 lineage in Peru despite circulation of variants of concern | Journal of Medical Virology / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.27261) | | | Novel mutations identified from whole-genome sequencing of SARS-CoV-2 isolated from Noakhali, Bangladesh | -- / [link](https://www.researchsquare.com/article/rs-437228/v1) | RNA pathogen detection app | | Transmission of SARS-CoV-2 in Inpatient and Outpatient Settings in a Veterans Affairs Health Care System | Open Forum Infectious Diseases / [link](https://doi.org/10.1093/ofid/ofab328) | | | Genomic and Molecular Profiling of Human Papillomavirus Associated Head and Neck Squamous Cell Carcinoma Treated with Immune Checkpoint Blockade Compared to Survival Outcomes | Cancers / [link](https://www.mdpi.com/2072-6694/13/24/6309) | BCL convert | | Posterior Lissencephaly Associated with Subcortical Band Heterotopia Due to a Variation in the CEP85L Gene: A Case Report and Refining of the Phenotypic Spectrum | Genes / [link](https://www.mdpi.com/2073-4425/12/8/1208) | BSSH; Enrichment app | | Advances in Genomic Discovery and Implications for Personalized Prevention and Medicine: Estonia as Example | Journal of Personalized Medicine / [link](https://www.mdpi.com/2075-4426/11/5/358) | review | | Genome sequencing and genetic characterization of 17 SARS-CoV-2 viruses and spike protein analyses of isolates from Bangladeshi patients | -- / [link](https://www.researchsquare.com/article/rs-968594/v1) | RNA pathogen detection; BSSH | | Early prenatal presentation of the cartilage-hair hypoplasia / anauxetic dysplasia spectrum of disorders mimicking recurrent thanatophoric dysplasia | European Journal of Medical Genetics / [link](https://www.sciencedirect.com/science/article/pii/S1769721221000288) | | | Mutational burden, MHC-I expression and immune infiltration as limiting factors for *in situ* vaccination by TNFα and IL-12 gene electrotransfer | Bioelectrochemistry / [link](https://www.sciencedirect.com/science/article/pii/S1567539421000943) | Variant calling; alignment | | Whole Exome Sequencing Is the Minimal Technological Approach in Probands Born to Consanguineous Couples | Genes / [link](https://www.mdpi.com/2073-4425/12/7/962) | BSSH; Germline Enrichment app | | Fluoropyrimidine-Induced Severe Toxicities Associated with Rare DPYD Polymorphisms: Case Series from Saudi Arabia and a Review of the Literature | Clinics and Practice / [link](https://www.mdpi.com/2039-7283/11/3/62) | alignment; Variant calling | | Genetic Characterization of a Model Ciliopathy: Bardet–Biedl Syndrome | Journal of Pediatric Genetics / [link](http://www.thieme-connect.de/DOI/DOI?10.1055/s-0040-1708844) | | | The spectrum of mitochondrial DNA (mtDNA) mutations in pediatric CNS tumors | Neuro-oncology Advances / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8320689/) | Genome pipeline v2.3.1 | | Whole genome sequencing identifies rare germline variants enriched in cancer related genes in first degree relatives of familial pancreatic cancer patients | Clinical Genetics / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/cge.14038) | | | Chronic demodicosis in patients with immune dysregulation: An unexpected infectious manifestation of Signal transducer and activator of transcription (STAT)1 gain-of-function | Clinical and Experimental Immunology / [link](https://doi.org/10.1111/cei.13636) | v3.4.9 | | A phase II study of poziotinib in patients with recurrent and/or metastatic head and neck squamous cell carcinoma | Cancer Medicine / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/cam4.4231) | alignment; DNA pipeline; Somatic mutation | | Multi-omic profiling of lung and liver tumor microenvironments of metastatic pancreatic cancer reveals site-specific immune regulatory pathways | Genome Biology / [link](https://doi.org/10.1186/s13059-021-02363-6) | Somatic mode | | Blended phenotype of combination of HERC2 and AP3B2 deficiency and Angelman syndrome caused by paternal isodisomy of chromosome 15 | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.62371) | | | Enabling fast and energy-efficient FM-index exact matching using processing-near-memory | The Journal of Supercomputing / [link](https://doi.org/10.1007/s11227-021-03661-3) | review | | Clinical characteristics of AY.4 infections are similar to B.1.617.2 infections: a preliminary study | Indian Journal of Basic and Applied Medical Research / [link](https://www.ijbamr.com/assets/images/issues/pdf/1Th9jp_5JkE71_21GxL4_xdgw6r_113191.pdf) | COVID Lineage App | | Clinical RNA sequencing confirms compound heterozygous intronic variants in RYR1 in a patient with congenital myopathy, respiratory failure, neonatal brain hemorrhage, and d-transposition of the great arteries | Molecular Genetics & Genomic Medicine / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/mgg3.1804) | | | The Quandary of DNA-Based Treatment Assessment in De Novo Metastatic Prostate Cancer in the Era of Precision Oncology | Journal of Personalized Medicine / [link](https://www.mdpi.com/2075-4426/11/5/330) | Germline | | Applications and challenges of high performance computing in genomics | CCF Transactions on High Performance Computing / [link](https://doi.org/10.1007/s42514-021-00081-w) | review | | Influence of SARS-CoV-2 Variant B.1.1.7, Vaccination, and Public Health Measures on the Spread of SARS-CoV-2 | Viruses / [link](https://www.mdpi.com/1999-4915/13/5/898) | COVIDSeq Test pipeline | | Severe course with lethal hepatocellular injury and skeletal muscular dysgenesis in a neonate with infantile liver failure syndrome type 1 caused by novel LARS1 mutations | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.62012) | | | VCFcontam: A Machine Learning Approach to Estimate Cross-Sample Contamination from Variant Call Data | -- / [link](https://www.biorxiv.org/content/10.1101/2021.03.12.435007v1) | v3.3.4 | | Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L associated with symptoms | Microbial Genomics / [link](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000684) | BSSH | | New variant of PRDM16 gene nucleotide sequence in a family with various phenotypic manifestations of the non-compacted myocardium | Russian Journal of Cardiology / [link](https://russjcardiol.elpub.ru/jour/article/view/4315) | | | Molecular characterization of Kita-Kyushu lung cancer antigen (KK-LC-1) expressing carcinomas | Oncotarget / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8664394/) | demultiplexing | | Loss of KDM1A in GIP-dependent primary bilateral macronodular adrenal hyperplasia with Cushing's syndrome: a multicentre, retrospective, cohort study | The Lancet Diabetes & Endocrinology / [link](https://www.thelancet.com/journals/landia/article/PIIS2213-8587\(21\)00236-9/abstract) | | | TCF12 controls oligodendroglial cell proliferation and regulates signaling pathways conserved in gliomas | -- / [link](https://www.biorxiv.org/content/10.1101/2021.07.26.453859v1) | v3.6.3 | | Genetic mechanisms of critical illness in COVID-19 | Nature / [link](https://www.nature.com/articles/s41586-020-03065-y) | v3.2.22 | | Genomic epidemiology of the first epidemic wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Palestine | Microbial Genomics / [link](https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000584) | RNA pathogen detection | | Postmortem whole-genome sequencing on a dried blood spot identifies a novel homozygous SUOX variant causing isolated sulfite oxidase deficiency | Molecular Case Studies / [link](http://molecularcasestudies.cshlp.org/content/7/3/a006091) | v3.7 | | Rapid Response to SARS-CoV-2 in Aotearoa New Zealand: Implementation of a Diagnostic Test and Characterization of the First COVID-19 Cases in the South Island | Viruses / [link](https://www.mdpi.com/1999-4915/13/11/2222) | | | Exome sequencing in obsessive–compulsive disorder reveals a burden of rare damaging coding variants | Nature Neuroscience / [link](https://www.nature.com/articles/s41593-021-00876-8) | | | COVID-19 RT-PCR diagnostic assay sensitivity and SARS-CoV-2 transmission: A missing link? | -- / [link](https://www.medrxiv.org/content/10.1101/2021.03.24.21254271v1) | BSSH | | Blue Cone Monochromatism with Foveal Hypoplasia Caused by the Concomitant Effect of Variants in OPN1LW/OPN1MW and GPR143 Genes | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/22/16/8617) | BSSH; Enrichment app | | Sex- and Mutation-Specific p53 Gain-of-Function Activity in Gliomagenesis | Cancer Research Communications / [link](https://doi.org/10.1158/2767-9764.CRC-21-0026) | | | Rapid whole genome sequencing impacts care and resource utilization in infants with congenital heart disease | npj Genomic Medicine / [link](https://www.nature.com/articles/s41525-021-00192-x) | | | Newly emerged immunogenic neoantigens in established tumors enable hosts to regain immunosurveillance in a T-cell-dependent manner | International Immunology / [link](https://doi.org/10.1093/intimm/dxaa049) | alignment | | Cloud-based genomics pipelines for ophthalmology: Reviewed from research to clinical practice | Journal for Modeling in Ophthalmology / [link](https://doi.org/10.35119/maio.v3i1.115) | review | | Large-scale analysis of KMT2 mutations defines a distinctive molecular subset with treatment implication in gastric cancer | Oncogene / [link](https://www.nature.com/articles/s41388-021-01840-3) | | | Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions | Nature Communications / [link](https://www.nature.com/articles/s41467-021-26055-8) | COVID Lineage | | Precision modeling of gall bladder cancer patients in mice based on orthotopic implantation of organoid-derived tumor buds | Oncogenesis / [link](https://www.nature.com/articles/s41389-021-00322-1) | v3.6.3 | | SOX9 keeps growth plates and articular cartilage healthy by inhibiting chondrocyte dedifferentiation/osteoblastic redifferentiation | Proceedings of the National Academy of Sciences / [link](https://www.pnas.org/doi/abs/10.1073/pnas.2019152118) | | | Analysis of Whole Genome Sequencing in a Cohort of Individuals with PHACE Syndrome Suggests Dysregulation of RAS/PI3K Signaling | -- / [link](https://www.medrxiv.org/content/10.1101/2021.08.05.21261553v1) | alignment | | ITGB6-Knockout Suppresses Cholangiocarcinoma Cell Migration and Invasion with Declining PODXL2 Expression | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/22/12/6303) | alignment | | Serine biosynthesis defect due to haploinsufficiency of PHGDH causes retinal disease | Nature metabolism / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8084205/) | v2.5.1 | | The Implementation Science for Genomic Health Translation (INSIGHT) Study in Epilepsy: Protocol for a Learning Health Care System | JMIR Research Protocols / [link](https://www.researchprotocols.org/2021/3/e25576) | | | Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States | Cell / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8009040/) | COVIDSeq Test pipeline v1.3 | | Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states | Genome Research / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7849412/) | alignment | | Features of repertoire diversity and gene expression in human cytotoxic T cells following allogeneic hematopoietic cell transplantation | Communications Biology / [link](https://www.nature.com/articles/s42003-021-02709-7) | v3.6.3 | | Tissue-selective alternate promoters guide NLRP6 expression | Life Science Alliance / [link](https://www.life-science-alliance.org/content/4/3/e202000897) | v3.5.7 | | Emergence and Spread of B.1.1.7 Lineage in Primary Care and Clinical Impact in the Morbi-Mortality among Hospitalized Patients in Madrid, Spain | Microorganisms / [link](https://www.mdpi.com/2076-2607/9/7/1517) | COVID Lineage | | Genome-Wide Approach to Identify Quantitative Trait Loci for Drought Tolerance in Tetraploid Potato (Solanum tuberosum L.) | International Journal of Molecular Sciences / [link](https://www.mdpi.com/1422-0067/22/11/6123) | | | Mutation-Specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation | Journal of Clinical Microbiology / [link](https://journals.asm.org/doi/full/10.1128/jcm.00926-21) | | | A study of elective genome sequencing and pharmacogenetic testing in an unselected population | Molecular Genetics & Genomic Medicine / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/mgg3.1766) | Variant calling | | The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil | Frontiers in Public Health / [link](https://www.frontiersin.org/journals/public-health/articles/10.3389/fpubh.2021.745310/full) | | | Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing | Viruses / [link](https://www.mdpi.com/1999-4915/13/12/2544) | | | Next-Generation Sequencing for Congenital Nephrotic Syndrome: A Multi-Center Cross-Sectional Study from India | Indian Pediatrics / [link](https://doi.org/10.1007/s13312-021-2215-5) | | | Potential Diagnostic Value of the Differential Expression of Histone H3 Variants between Low- and High-Grade Gliomas | Cancers / [link](https://www.mdpi.com/2072-6694/13/21/5261) | RNA pipeline v3.7.5 | | A Novel WT1 Mutation Identified in a 46,XX Testicular/Ovotesticular DSD Patient Results in the Retention of Intron 9 | Biology / [link](https://www.mdpi.com/2079-7737/10/12/1248) | BSSH; Germline pipeline v2.3 | | Developmental and temporal characteristics of clonal sperm mosaicism | Cell / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8496133/) | | | A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control | -- / [link](https://www.biorxiv.org/content/10.1101/2021.04.05.438352v1) | BSSH; COVIDSeq Test RUO v1.3.0 | | High-resolution epigenome analysis in nasal samples derived from children with respiratory viral infections reveals striking changes upon SARS-CoV-2 infection | -- / [link](https://www.medrxiv.org/content/10.1101/2021.03.09.21253155v1) | v2.3.6 | | A catalog of associations between rare coding variants and COVID-19 outcomes | -- / [link](https://www.medrxiv.org/content/10.1101/2020.10.28.20221804v2) | alignment | | The Efficacy of Whole Genome Sequencing and RNA-Seq in the Diagnosis of Whole Exome Sequencing Negative Patients with Complex Neurological Phenotypes | Journal of Pediatric Genetics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10421693/) | v2.6 | | Isolation and characterization of fetal nucleated red blood cells from maternal blood as a target for single cell sequencing‐based non‐invasive genetic testing | Reproductive Medicine and Biology / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8254165/) | v3.6.3 | | Human sensorimotor organoids derived from healthy and amyotrophic lateral sclerosis stem cells form neuromuscular junctions | Nature Communications / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8346474/) | | | MutScape: an analytical toolkit for probing the mutational landscape in cancer genomics | NAR Genomics and Bioinformatics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8559159/) | | | Bacteroides spp. promotes branched-chain amino acid catabolism in brown fat and inhibits obesity | iScience / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8586802/) | v3.6.3 |
2020 | Title | Publisher / Link | Tags | | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------ | | Accuracy and efficiency of germline variant calling pipelines for human genome data | Scientific Reports / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7678823/) | comparison of DRAGEN with other technologies; Germline | | An RCT of Rapid Genomic Sequencing among Seriously Ill Infants Results in High Clinical Utility, Changes in Management, and Low Perceived Harm | The American Journal of Human Genetics / [link](https://www.sciencedirect.com/science/article/pii/S000292972030361X) | | | Eltrombopag for patients with moderate aplastic anemia or uni-lineage cytopenias | Blood Advances / [link](https://doi.org/10.1182/bloodadvances.2020001657) | Somatic pipeline | | Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh | Microbiology Resource Announcements / [link](https://journals.asm.org/doi/full/10.1128/mra.00764-20) | RNA pathogen detection; BSSH | | Whole-genome sequencing reveals distinct genetic bases for insulinomas and non-functional pancreatic neuroendocrine tumours: leading to a new classification system | Gut / [link](https://gut.bmj.com/content/69/5/877) | | | Optimized trio genome sequencing (OTGS) as a first-tier genetic test in critically ill infants: practice in China | Human Genetics / [link](https://doi.org/10.1007/s00439-019-02103-8) | v3.2.8; Genome pipeline | | Assessing the NOTCH2NLC GGC expansion in European patients with essential tremor | Brain / [link](https://doi.org/10.1093/brain/awaa291) | alignment | | Analytical performance evaluation of a commercial next generation sequencing liquid biopsy platform using plasma ctDNA, reference standards, and synthetic serial dilution samples derived from normal plasma | BMC Cancer / [link](https://doi.org/10.1186/s12885-020-07445-5) | TSO500 ctDNA; DRAGEN server v3 | | Targeted next-generation sequencing of circulating cell-free DNA vs bone marrow in patients with acute myeloid leukemia | Blood Advances / [link](https://ashpublications.org/bloodadvances/article/4/8/1670/454447/Targeted-next-generation-sequencing-of-circulating) | somatic | | A diploid assembly-based benchmark for variants in the major histocompatibility complex | Nature Communications / [link](https://www.nature.com/articles/s41467-020-18564-9) | v3.3.7; v3.2 | | Partially automated whole-genome sequencing reanalysis of previously undiagnosed pediatric patients can efficiently yield new diagnoses | npj Genomic Medicine / [link](https://www.nature.com/articles/s41525-020-00140-1) | Giraffe comparison | | Discovery of TITIN Gene Truncating Variant Mutations and 5-Year Outcomes in Patients With Nonischemic Dilated Cardiomyopathy | The American Journal of Cardiology / [link](https://www.sciencedirect.com/science/article/pii/S0002914920310018) | v3.2.2 | | Clinical and Genomic Evaluation of 207 Genetic Myopathies in the Indian Subcontinent | Frontiers in Neurology / [link](https://www.frontiersin.org/journals/neurology/articles/10.3389/fneur.2020.559327/full) | v2.03 | | High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs | -- / [link](https://www.medrxiv.org/content/10.1101/2020.07.27.20163147v3) | RNA pathogen detection; BSSH | | Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation | Virus Evolution / [link](https://doi.org/10.1093/ve/veaa075) | v3.5.13 | | Germline and somatic albinism variants in amelanotic/hypomelanotic melanoma: Increased carriage of TYR and OCA2 variants | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0238529) | | | An Indian child with Coats plus syndrome due to mutations in STN1 | American Journal of Medical Genetics Part A / [link](https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.61737) | | | Higher Incidence of Germline Mutations in DNA Damage Response Genes in Lymphoid Than in Myeloid Neoplasms without Significant Increase in the Prevalence of Clonal Hematopoiesis | Blood / [link](https://www.sciencedirect.com/science/article/pii/S0006497118728139) | | | Cerebellar ataxia with normal intellect associated with a homozygous truncating variant in CA8 | Clinical Genetics / [link](https://onlinelibrary.wiley.com/doi/abs/10.1111/cge.13666) | | | Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes | -- / [link](https://www.biorxiv.org/content/10.1101/2020.01.03.894428v1) | Unified genotyper | | Chapter 17 - Industry perspective | Rna-Based Regulation in Human Health and Disease / [link](https://www.sciencedirect.com/science/article/pii/B9780128171936000170) | review | | Genotype‑phenotype analysis in Mowat‑Wilson syndrome associated with two novel and two recurrent *ZEB2* variants | Experimental and Therapeutic Medicine / [link](https://www.spandidos-publications.com/10.3892/etm.2020.9393) | | | Mutations in SARS-CoV-2 viral RNA identified in Eastern India: Possible implications for the ongoing outbreak in India and impact on viral structure and host susceptibility | Journal of Biosciences / [link](https://doi.org/10.1007/s12038-020-00046-1) | RNA pathogen detection; BSSH | | Low-Pass Genome Sequencing: Validation and Diagnostic Utility from 409 Clinical Cases of Low-Pass Genome Sequencing for the Detection of Copy Number Variants to Replace Constitutional Microarray | The Journal of Molecular Diagnostics / [link](https://www.sciencedirect.com/science/article/pii/S152515782030297X) | | | A non-human primate model of familial Alzheimer’s disease | -- / [link](https://www.biorxiv.org/content/10.1101/2020.08.24.264259v1) | mapping; v3.5.7; Variant calling | | High-resolution analyses of human sperm dynamic methylome reveal thousands of novel age-related epigenetic alterations | Clinical Epigenetics / [link](https://doi.org/10.1186/s13148-020-00988-1) | v2.6.3 | | Bi-Allelic Novel Variants in CLIC5 Identified in a Cameroonian Multiplex Family with Non-Syndromic Hearing Impairment | Genes / [link](https://www.mdpi.com/2073-4425/11/11/1249) | Germline pipeline v3.2.8 | | Low-level parental somatic mosaic SNVs in exomes from a large cohort of trios with diverse suspected Mendelian conditions | Genetics in Medicine / [link](https://www.nature.com/articles/s41436-020-0897-z) | | | A de-novo NFIX mutation causes a case of neonatal lethal Marshall–Smith syndrome | Clinical Dysmorphology / [link](https://journals.lww.com/clindysmorphol/citation/2020/10000/a_de_novo_nfix_mutation_causes_a_case_of_neonatal.12.aspx) | | | Biallelic variants in two complex I genes cause abnormal splicing defects in probands with mild Leigh syndrome | Molecular Genetics and Metabolism / [link](https://www.sciencedirect.com/science/article/pii/S1096719220301992) | Variant calling; Joint genotyping; v2.6 | | A broad exome study of the genetic architecture of asthma reveals novel patient subgroups | -- / [link](https://www.biorxiv.org/content/10.1101/2020.12.10.419663v1) | AWS; Germline pipeline v3.0.7 | | Rapid Large-Scale COVID-19 Testing during Shortages | Diagnostics / [link](https://www.mdpi.com/2075-4418/10/7/464) | | | Targeting Epidermal Growth Factor Receptor (EGFR) in Pediatric Colorectal Cancer | Cancers / [link](https://www.mdpi.com/2072-6694/12/2/414) | Somatic pipeline | | Carriership of the rs113883650/rs2287120 haplotype of the *SLC7A5* (*LAT1*) gene increases the risk of obesity in infants with phenylketonuria | Molecular Genetics and Metabolism Reports / [link](https://www.sciencedirect.com/science/article/pii/S2214426920300860) | Enrichment pipeline | | A Comprehensive, Multidisciplinary, Precision Medicine Approach to Discover Effective Therapy for an Undiagnosed, Progressive, Fibro-inflammatory Disease | Translational research : the journal of laboratory and clinical medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6939610/) | | | Mortality in a neonate with molybdenum cofactor deficiency illustrates the need for a comprehensive rapid precision medicine system | Cold Spring Harbor Molecular Case Studies / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6996516/) | | | The potential impact of tumor suppressor genes on human gametogenesis: a case-control study | Journal of Assisted Reproduction and Genetics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7056797/) | | | A framework using topological pathways for deeper analysis of transcriptome data | BMC Genomics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7057456/) | | | A population-specific low-frequency variant of SLC22A12 (p.W258\*) explains nearby genome-wide association signals for serum uric acid concentrations among Koreans | PLoS ONE / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145145/) | | | BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks | Epigenetics & Chromatin / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7175505/) | | | Comprehensive Analysis of CDC27 Related to Peritoneal Metastasis by Whole Exome Sequencing in Gastric Cancer | OncoTargets and therapy / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7183333/) | | | A refined cell-of-origin classifier with targeted NGS and artificial intelligence shows robust predictive value in DLBCL | Blood Advances / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7391158/) | Somatic pipeline | | A Pilot Study for the Feasibility of Exome-Sequencing in Circulating Tumor Cells Versus Single Metastatic Biopsies in Breast Cancer | International Journal of Molecular Sciences / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7402350/) | BSSH; Enrichment app | | Novel homozygous variant in WISP3 in a family with unrecognized progressive pseudorheumatoid dysplasia | Clinical Case Reports / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7455413/) | Germline pipeline | | Clinical utility of ultra-rapid whole-genome sequencing in an infant with atypical presentation of WT1-associated nephrotic syndrome type 4 | Cold Spring Harbor Molecular Case Studies / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7476414/) | | | Autophagy mitigates ethanol-induced mitochondrial dysfunction and oxidative stress in esophageal keratinocytes | PLoS ONE / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7510980/) | demultiplexing | | Postmortem diagnosis of PPA2-associated sudden cardiac death from dried blood spot in a neonate presenting with vocal cord paralysis | Cold Spring Harbor Molecular Case Studies / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7552926/) | | | Evaluation of the RAS signaling network in response to MEK inhibition using organoids derived from a familial adenomatous polyposis patient | Scientific Reports / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7567075/) | | | Integrative immunogenomic analysis of gastric cancer dictates novel immunological classification and the functional status of tumor‐infiltrating cells | Clinical & Translational Immunology / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7568758/) | v3.5.7 | | Chromosomal translocation disrupting the SMAD4 gene resulting in the combined phenotype of Juvenile polyposis syndrome and Hereditary Hemorrhagic Telangiectasia | Molecular Genetics & Genomic Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7667351/) | | | A Bioinformatics Crash Course for Interpreting Genomics Data | Chest / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8176646/) | review |
2019 | Title | Publisher / Link | Tags | | ------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------ | | Early diagnosis of Pearson syndrome in neonatal intensive care following rapid mitochondrial genome sequencing in tandem with exome sequencing | European Journal of Human Genetics / [link](https://www.nature.com/articles/s41431-019-0477-3) | | | The Association of Fibroblast Growth Factor 5 (FGF5), Fibroblast Growth Factor Receptor 1 (FGFR1), and Prolactin (PRL) with Hair Length in Scottish Highland Cattle | The FASEB Journal / [link](https://faseb.onlinelibrary.wiley.com/doi/10.1096/fasebj.2019.33.1_supplement.474.9) | | | Higher Stability of Mutant mRNA As Compared to Wild-Type mRNA in Diffuse Large B-Cell Lymphoma | Blood / [link](https://www.sciencedirect.com/science/article/pii/S0006497118594167) | | | Genetics of intellectual disability in consanguineous families | Molecular Psychiatry / [link](https://www.nature.com/articles/s41380-017-0012-2) | Variant calling; alignment | | IREB2-associated neurodegeneration | Brain / [link](https://doi.org/10.1093/brain/awz183) | Variant calling; alignment | | Resistance to autosomal dominant Alzheimer’s disease in an APOE3 Christchurch homozygote: a case report | Nature Medicine / [link](https://www.nature.com/articles/s41591-019-0611-3) | Genome pipeline | | Clinical genome sequencing in an unbiased pediatric cohort | Genetics in Medicine / [link](https://www.sciencedirect.com/science/article/pii/S1098360021046402) | v2.0.4-v2.1.3 | | Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics | Frontiers in Genetics / [link](https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2019.00049/full) | DRAGEN comparison to other technologies; review | | Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation | Science Translational Medicine / [link](https://www.science.org/doi/10.1126/scitranslmed.aat6177) | | | A semiautomated whole-exome sequencing workflow leads to increased diagnostic yield and identification of novel candidate variants | Molecular Case Studies / [link](http://molecularcasestudies.cshlp.org/content/5/2/a003756) | Variant calling | | A Randomized, Controlled Trial of the Analytic and Diagnostic Performance of Singleton and Trio, Rapid Genome and Exome Sequencing in Ill Infants | The American Journal of Human Genetics / [link](https://www.sciencedirect.com/science/article/pii/S0002929719303131) | Variant calling | | Effect of parental origin of damaging variants in pro-angiogenic genes on fetal growth in patients with congenital heart defects: Data and analyses | Data in Brief / [link](https://www.sciencedirect.com/science/article/pii/S2352340919306651) | | | Landscape of Germline and Somatic Mitochondrial DNA Mutations in Pediatric Malignancies | Cancer Research / [link](https://doi.org/10.1158/0008-5472.CAN-18-2220) | Genome pipeline; Somatic variant calling; v2.3.1 | | Higher Stability of Mutant IDH1/2 mRNA As Compared to Wild-Type mRNA in Patients with Acute Myeloid Leukemia | Blood / [link](https://www.sciencedirect.com/science/article/pii/S0006497118606597) | | | Reliable variant calling during runtime of Illumina sequencing | Scientific Reports / [link](https://www.nature.com/articles/s41598-019-52991-z) | | | Rapid Genome Sequencing in the Critically Ill | Clinical Chemistry / [link](https://doi.org/10.1373/clinchem.2018.293506) | | | Review of applications of high-throughput sequencing in personalized medicine: barriers and facilitators of future progress in research and clinical application | Briefings in Bioinformatics / [link](https://doi.org/10.1093/bib/bby051) | review | | NARD: whole-genome reference panel of 1779 Northeast Asians improves imputation accuracy of rare and low-frequency variants | Genome Medicine / [link](https://doi.org/10.1186/s13073-019-0677-z) | | | Virtual Grid Engine: a simulated grid engine environment for large-scale supercomputers | BMC Bioinformatics / [link](https://doi.org/10.1186/s12859-019-3085-x) | | | Damaging Variants in Pro-Angiogenic Genes Impair Growth in Fetuses with Cardiac Defects | The Journal of pediatrics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6765419/) | | | Neonatal diabetes mellitus due to a novel variant in the INS gene | Cold Spring Harbor Molecular Case Studies / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6672029/) | | | Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil | Nature Communications / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6744486/) | | | Molecular Profiles and Metastasis Markers in Chinese Patients with Gastric Carcinoma | Scientific Reports / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769015/) | | | Recommendations for performance optimizations when using GATK3.8 and GATK4 | BMC Bioinformatics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6842142/) | | | A Comprehensive Survey of Genomic Alterations in Gastric Cancer Reveals Recurrent Neoantigens as Potential Therapeutic Targets | BioMed Research International / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874998/) | | | Mutations in PDLIM5 are rare in dilated cardiomyopathy but are emerging as potential disease modifiers | Molecular Genetics & Genomic Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7005607/) | | | A Comprehensive Iterative Approach is Highly Effective in Diagnosing Individuals who are Exome Negative | Genetics in medicine : official journal of the American College of Medical Genetics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6295275/) | alignment |
2018 | Title | Publisher / Link | Tags | | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------- | ----------------- | | On the verge of diagnosis: Detection, reporting, and investigation of de novo variants in novel genes identified by clinical sequencing | Human Mutation / [link](https://onlinelibrary.wiley.com/doi/10.1002/humu.23646) | v2 | | Improving classification of melanocytic nevi: Association of BRAF V600E expression with distinct histomorphologic features | Journal of the American Academy of Dermatology / [link](https://www.sciencedirect.com/science/article/pii/S0190962218305140) | DRAGEN server | | NGSOne: Cloud-based NGS data analysis tool | Journal of Platform Technology / [link](https://koreascience.kr/article/JAKO201829862637963.page) | | | Comprehensive genetic testing for female and male infertility using next-generation sequencing | Journal of Assisted Reproduction and Genetics / [link](https://doi.org/10.1007/s10815-018-1204-7) | Germline pipeline | | The case for early use of rapid whole-genome sequencing in management of critically ill infants: late diagnosis of Coffin–Siris syndrome in an infant with left congenital diaphragmatic hernia, congenital heart disease, and recurrent infections | Cold Spring Harbor Molecular Case Studies / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5983173/) | | | Rapid whole-genome sequencing identifies a novel AIRE variant associated with autoimmune polyendocrine syndrome type 1 | Cold Spring Harbor Molecular Case Studies / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5983174/) | | | Whole‐exome sequencing in 20,197 persons for rare variants in Alzheimer's disease | Annals of Clinical and Translational Neurology / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6043775/) | | | Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures | Cell / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6225773/) | | | Integrated genome sizing (IGS) approach for the parallelization of whole genome analysis | BMC Bioinformatics / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276166/) | | | Concomitant diagnosis of immune deficiency and Pseudomonas sepsis in a 19 month old with ecthyma gangrenosum by host whole-genome sequencing | Cold Spring Harbor Molecular Case Studies / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318772/) | | | Novel Factor XIII variant identified through whole-genome sequencing in a child with intracranial hemorrhage | Cold Spring Harbor Molecular Case Studies / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6318776/) | |
2017 | Title | Publisher / Link | Tags | | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------- | --------- | | Genome-Wide Exome Analysis of Cmv5-Disparate Mouse Strains that Differ in Host Resistance to Murine Cytomegalovirus Infection | G3 Genes\|Genomes\|Genetics / [link](https://doi.org/10.1534/g3.117.042531) | | | Ultra-Fast Next Generation Human Genome Sequencing Data Processing Using DRAGENTM Bio-IT Processor for Precision Medicine | Open Journal of Genetics / [link](https://www.scirp.org/journal/paperinformation.aspx?paperid=74603) | | | A high-throughput molecular data resource for cutaneous neurofibromas | Scientific Data / [link](https://www.nature.com/articles/sdata201745) | alignment | | Next-generation sequencing: big data meets high performance computing | Drug Discovery Today / [link](https://www.sciencedirect.com/science/article/pii/S1359644617300582) | | | Rapid whole-genome sequencing identifies a novel GABRA1 variant associated with West syndrome | Cold Spring Harbor Molecular Case Studies / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5593154/) | | | Need for speed in accurate whole-genome data analysis: GENALICE MAP challenges BWA/GATK more than PEMapper/PECaller and Isaac | Proceedings of the National Academy of Sciences / [link](https://www.pnas.org/doi/abs/10.1073/pnas.1713830114) | | | Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics | PLOS ONE / [link](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0181604) | alignment | | Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility | PLoS ONE / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289527/) | | | An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations | Genome Research / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411782/) | | | Rapid whole-genome sequencing identifies a novel homozygous NPC1 variant associated with Niemann–Pick type C1 disease in a 7-week-old male with cholestasis | Cold Spring Harbor Molecular Case Studies / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5593156/) | |
2015 | Title | Publisher / Link | Tags | | --------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------- | ------ | | A 26-hour system of highly sensitive whole genome sequencing for emergency management of genetic diseases | Genome Medicine / [link](https://doi.org/10.1186/s13073-015-0221-8) | | | DNA methylation and epigenomics: new technologies and emerging concepts | Genome Biology / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438343/) | | | Emergency medical genomes: a breakthrough application of precision medicine | Genome Medicine / [link](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4520148/) | review |