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
Comprehensive investigation of gene mutations in canine large cell gastrointestinal lymphoma
Frontiers in Veterinary Science / link
Oncology
Comparisons of performances of structural variants detection algorithms in solitary or combination strategy
PLOS ONE / link
Population Genomics
Comparative genomics reveals phylogenetic intermixing of Stomoxys fly, manure, and bovine mastitis-associated bacteria in dairy settings
biorxiv / link
Population Genomics
Comparative analysis of the Mexico City Prospective Study and the UK Biobank identifies ancestry-specific effects on clonal hematopoiesis
nature genetics / link
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
Genetic Disease
Classification of acute myeloid leukemia based on multi-omics and prognosis prediction value
Molecular Oncology / link
Oncology
CIROZ is dispensable in ancestral vertebrates but essential for left-right patterning in humans
The American Journal of Human Genetics / link
Genetic Disease
Case Report: Importance of high-throughput genetic investigations in the differential diagnosis of unexplained erythrocytosis
National Library of Medicine / link
Genetic Disease
Building a growing genomic repository for maternal and fetal health through the PING Consortium
Nature / link
Genetic Disease
Blood DNA virome associates with autoimmune diseases and COVID-19
nature genetics / link
Population Genomics
Bi-Allelic MARVELD2 Variant Identified with Exome Sequencing in a Consanguineous Multiplex Ghanaian Family Segregating Non-Syndromic Hearing Loss
MDPI / link
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
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
Genomic Factory
Benchmarking of germline copy number variant callers from whole genome sequencing data for clinical applications
Bioinformatics Advances / link
Genomic Factory
Bacteriophage Treatment Induces Phenotype Switching and Alters Antibiotic Resistance of ESBL Escherichia coli
MDPI / link
Genomic Factory
BACH2 regulates T cell lineage states to overcome dysfunction driven by tonic CAR signaling
Research Square / link
Oncology
Assessment of candidate high-grade serous ovarian carcinoma predisposition genes through integrated germline and tumour sequencing
npj Genomic Medicine / link
Genetic Disease
Assessing the Impact of Cell Isolation Method on B cell Gene Expression using Next-Generation Sequencing
Experimental Hematology / link
Genomic Factory
Assessing the contribution of rare protein-coding germline variants to prostate cancer risk and severity in 37,184 cases
Nature Communications / link
Genetic Disease
APOBEC3A drives ovarian cancer metastasis by altering epithelial-mesenchymal transition
JCI Insight / link
Oncology
Analysis of Population-Level Avirulence and Virulence Genetic Frequencies Provides Insight Into Resistance Gene Rotation and Plant Disease Epidemiology
Plant Pathology / link
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
Genomic Factory
An Exploratory Genomic and Transcriptomic Analysis Between Choloepus didactylus and Homo sapiens
Genes / link
Genomic Factory
AMPed up immunity: 418 whole genomes reveal intraspecific diversity of koala antimicrobial peptides
Immunogenetics / link
Population Genomics
Adrenal mixed corticomedullary tumors: report of a case with molecular characterization and systematic review
Virchows Archiv / link
Oncology
Activated cardiac fibroblasts are a primary source of high-molecular-weight hyaluronan production
American Journal of Physiology-Cell Physiology / link
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
Genetic Disease
A triad of somatic mutagenesis converges in self-reactive B cells to cause a virus-induced autoimmune disease
Immunity / link
Genetic Disease
A phase II trial of mTORC1/2 inhibition in STK11 deficient non small cell lung cancer
npj Precision Oncology / link
Oncology
A nationwide comprehensive genomic profiling and molecular tumor board platform for patients with advanced cancer
npj Precision Oncology / link
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
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
P260: Enhancing copy number variant analysis in exome sequencing with backbone probe optimization
-- / link
Identification of technically challenging variants: Whole-genome sequencing improves diagnostic yield in patients with high clinical suspicion of rare diseases
HGG Advances / link
Genetic Disease
Benchmarking of variant calling software for whole-exome sequencing using gold standard datasets
Nature / link
Evaluating Discordant Somatic Calls Across Mutation Discovery Approaches to Minimize False-Negative Drug-Resistant Findings
The Journals of Molecular Diagnostics / link
2024
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
v3.10; TMB
Whole genome sequencing in paediatric channelopathy and cardiomyopathy
Frontiers in Cardiovascular Medicine / link
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
ExpansionHunter; Germline Pipeline
High fusion and cytopathy of SARS-CoV-2 variant B.1.640.1
Journal of Virology / link
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
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
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
BSSH; Enrichment pipeline
PKHD1L1, a gene involved in the stereocilia coat, causes autosomal recessive nonsyndromic hearing loss
Human Genetics / link
CNV pipeline
LncRNAs expression profile in a family household cluster of COVID ‐19 patients
Journal of Cellular and Molecular Medicine / link
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
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
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
v4.2.4
Genetics of psycho-emotional well-being: genome-wide association study and polygenic risk score analysis
Frontiers in Psychiatry / link
Claudin-10 Expression and the Gene Expression Pattern of Thick Ascending Limb Cells
International Journal of Molecular Sciences / link
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
alignment
Whole-genome sequencing of tetraploid potato varieties reveals different strategies for drought tolerance
Scientific Reports / link
DRAGEN-GATK
Prospective cohort study of genomic newborn screening: BabyScreen+ pilot study protocol
BMJ open / link
SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation?
Frontiers in Microbiology / link
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
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
Somatic variant calling
Chronic stress alters hepatic metabolism and thermodynamic respiratory efficiency affecting epigenetics in C57BL/6 mice
iScience / link
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
Immune infiltration, aggressive pathology, and poor survival outcomes in RECQL helicase deficient breast cancers
Neoplasia / link
Somatic pipeline; v4.0.3
Extending DeepTrio for sensitive detection of complex de novo mutation patterns
NAR Genomics and Bioinformatics / link
v3.6
Spatial Mapping of Hematopoietic Clones in Human Bone Marrow
Blood Cancer Discovery / link
alignment; v3.10.4
The contributions of deleterious rare alleles in NLRP12 and inflammasome-related genes to polymyalgia rheumatica
Scientific Reports / link
Myxoid liposarcoma with nuclear pleomorphism: a clinicopathological and molecular study
Virchows Archiv / link
RNA app
Targeting cell-type-specific, choroid-peripheral immune signaling to treat age-related macular degeneration
Cell Reports Medicine / link
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
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
iPSC-Derived Endothelial Cells Reveal LDLR Dysfunction and Dysregulated Gene Expression Profiles in Familial Hypercholesterolemia
International Journal of Molecular Sciences / link
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
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
BSSH; Germline Pipeline; v3.4.5
Changes in DNA methylation associated with a specific mode of delivery: a pilot study
Frontiers in Medicine / link
Methylation pipeline
Directing the migration of serum-free, ex vivo-expanded Vγ9Vδ2 T cells
Frontiers in Immunology / link
AWS; v3.10.4a
Targeting TRIP13 in favorable histology Wilms tumor with nuclear export inhibitors synergizes with doxorubicin
Communications Biology / link
v3.5.7
Immune evasion, infectivity, and fusogenicity of SARS-CoV-2 BA.2.86 and FLip variants
Cell / link
COVID Lineage App
Single-cell multi-omic analysis of the vestibular schwannoma ecosystem uncovers a nerve injury-like state
Nature Communications / link
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
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
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
v4.0.3; joint genotyper
Utility of polygenic scores across diverse diseases in a hospital cohort for predictive modeling
Nature Communications / link
Genome pipeline
SALL4 deletion and kidney and cardiac defects associated with VACTERL association
Pediatric Nephrology / link
v3.5
Functional variants in a TTTG microsatellite on 15q26.1 cause familial nonautoimmune thyroid abnormalities
Nature Genetics / link
v3.9.5
Narrowing the diagnostic gap: Genomes, episignatures, long-read sequencing, and health economic analyses in an exome-negative intellectual disability cohort
Genetics in Medicine / link
DNA identification of monozygotic twins
Forensic Science International: Genetics / link
Somatic pipeline v4.0.3
Sequencing technologies and hardware-accelerated parallel computing transform computational genomics research
Frontiers in Bioinformatics / link
review
Genome sequencing as a generic diagnostic strategy for rare disease
Genome Medicine / link
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
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
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
Novel hemizygous single-nucleotide duplication in RPGR in a patient with retinal dystrophy and sensorineural hearing loss
Molecular Genetics & Genomic Medicine / link
CNV caller; Haplotype variant calling
Simultaneous detection and characterization of common respiratory pathogens in wastewater through genomic sequencing
Water Research / link
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
BSSH; Enrichment app
Inherited defects of piRNA biogenesis cause transposon de-repression, impaired spermatogenesis, and human male infertility
-- / link
v4.2
CpG methylation changes associated with hyperglycemia in type 1 diabetes occur at angiogenic glomerular and retinal gene loci
-- / link
Epigenome pipeline
Mpox Viral Lineage Analysis and Technique Development Using Next-generation Sequencing Approach
The Journal of Infectious Diseases / link
Large-scale DNA sequencing identifies rare variants associated with Systemic Lupus Erythematosus susceptibility in known risk genes
Gene / link
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
v3.9
Rare De Novo and Inherited Genes in Familial and Nonfamilial Pediatric Attention-Deficit/Hyperactivity Disorder
JAMA pediatrics / link
Treatment and prognostic implications of strong PD-L1 expression in primary hepatic sarcomatoid carcinoma
Immunotherapy / link
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
Cost-effectiveness of genetic testing of endocrine tumor patients using a comprehensive hereditary cancer gene panel
The Journal of Clinical Endocrinology & Metabolism / link
v4.0.3; Germline pipeline
Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives
Cells / link
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
Germline
Photoperiod associated late flowering reaction norm: Dissecting loci and genomic-enviromic associated prediction in maize
Field Crops Research / link
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
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
v3.9.3
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
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
v3.3.1
DPF2-related Coffin-Siris syndrome type 7 in two generations
European Journal of Medical Genetics / link
v3.9
Beyond Single Diagnosis: Exploring Multidiagnostic Realities in Pediatric Patients through Genome Sequencing
Human Mutation / link
Variant calling; alignment
Whole-genome sequencing of Chromobacterium subtsugae strains exhibiting toxicity to Drosophila melanogaster
Microbiology Resource Announcements / link
v3.10.12
Gut microbiome composition: link between sports performance and protein absorption?
Journal of the International Society of Sports Nutrition / link
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
PRKD1-related telangiectasia-ectodermal dysplasia-brachydactyly-cardiac anomaly syndrome: Case report and review of the literature
European Journal of Medical Genetics / link
Good Manufacturing Practice–compliant human induced pluripotent stem cells: from bench to putative clinical products
Cytotherapy / link
PPP2R5D heterozygous pathogenic variant causes early-onset parkinsonism and treatment implications: A case report
Parkinsonism & Related Disorders / link
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
BCL convert
Strategies for diagnosis and management of CMMRD in low-resource countries: report of a Tunisian family
Familial Cancer / link
Enrichment tool
Sudden unexpected postnatal collapse and BUB1B mutation: first forensic case report
International Journal of Legal Medicine / link
Germline
Novel mutation of COG5 in a Taiwanese girl with congenital disorders of glycosylation manifesting as developmental delay
Molecular Genetics and Metabolism Reports / link
alignment
Intraarticular Nodular Fasciitis of the Elbow Confirmed by USP6-MYH9 Gene Fusion.
-- / link
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
Identification of a novel GNAS mutation in a family with pseudohypoparathyroidism type 1A
BMC Pediatrics / link
Germline pipeline
Biallelic NDUFA4 Deletion Causes Mitochondrial Complex IV Deficiency in a Patient with Leigh Syndrome
Genes / link
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
Introducing Exome Sequencing as Part of the Diagnostic Algorithm for Pediatric Nephrology Patients in Bulgaria: A Single-Center Experience
Nephron / link
Leveraging Off-Target Reads in Panel Sequencing for Homologous Recombination Repair Deficiency Screening in Tumor
The Journal of Molecular Diagnostics / link
v3.10.9
Development and validation of a pharmacogenomics reporting workflow based on the illumina global screening array chip
Frontiers in Pharmacology / link
v3.7.6
Management of SARS-CoV-2 and Persistent Viral Detection in Solid Organ Transplant Recipients
Current Pulmonology Reports / link
COVID Lineage App
Evolution of a Distinct SARS-CoV-2 Lineage Identified during an Investigation of a Hospital Outbreak
Viruses / link
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
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
Mapping Whole Exome Sequencing to In Vivo Imaging with Stereotactic Localization and Deep Learning
-- / link
The Scalable Variant Call Representation: Enabling Genetic Analysis Beyond One Million Genomes
-- / link
A deep intronic variant in MME causes autosomal recessive Charcot-Marie-Tooth neuropathy through aberrant splicing
-- / link
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
Clinical application of Complete Long Read genome sequencing identifies a 16kb intragenic duplication in EHMT1 in a patient with suspected Kleefstra syndrome
-- / link
BSSH; ICLR WGS pipeline app v2.0.6
Comprehensive analysis of the genetic variation in the LPA gene from short-read sequencing
-- / link
LPA caller
Functional Analysis of G6PD Variants Associated With Low G6PD Activity in the All of Us Research Program
-- / link
Genome-wide study of gene-by-sex interactions identifies risks for cleft palate
-- / link
Germline pipeline v3.7.5
Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
-- / link
Pan-Cancer Interrogation of B7-H3 (CD276) as an Actionable Therapeutic Target across Human Malignancies
Cancer Research Communications / link
A 39 kb structural variant causing Lynch Syndrome detected by optical genome mapping and nanopore sequencing
European Journal of Human Genetics / link
SV caller
A framework for the evaluation and reporting of incidental findings in clinical genomic testing
European Journal of Human Genetics / link
Natural Killer Cell Infiltration in Prostate Cancers Predict Improved Patient Outcomes
Prostate Cancer and Prostatic Diseases / link
demultiplexing
Antimicrobial susceptibility and resistome of Actinobacillus pleuropneumoniae in Taiwan: a next-generation sequencing analysis
Veterinary Quarterly / link
Clinical exome sequencing by general pediatricians: high clinical utility and no evidence of inappropriate testing
Frontiers in Pediatrics / link
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
Unveiling the impact of temperature shift on microbial community dynamics and metabolic pathways in anaerobic digestion
Process Safety and Environmental Protection / link
Metagenomics pipeline
Two Cases of Sporadic Amyotrophic Lateral Sclerosis With Contrasting Clinical Phenotypes: Genetic Insights
Cureus / link
Variant calling
Molecular profiling and the impact of treatment on outcomes in adenoid cystic carcinoma (ACC) type-I and II
Clinical Cancer Research / link
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
v3.5.13
Repair of leukemia-associated single nucleotide variants via interallelic gene conversion
-- / link
Somatic pipeline
Expanding the Phenotype of the CACNA1C-Associated Neurological Disorders in Children: Systematic Literature Review and Description of a Novel Mutation
Children / link
Symptomatology and IgG Levels Before and After SARS-CoV-2 Omicron Breakthrough Infections in Vaccinated Individuals
-- / link
CCR5 and CCL5 gene expression in colorectal cancer: comprehensive profiling and clinical value
Journal for Immunotherapy of Cancer / link
Nuclear Factor κB Signaling Deficiency in CD11c-Expressing Phagocytes Mediates Early Inflammatory Responses and Enhances Mycobacterium tuberculosis Control
The Journal of Infectious Diseases / link
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
High Comorbidity of Pediatric Cancers in Patients with Birth Defects: Insights from Whole Genome Sequencing Analysis of Copy Number Variations
Translational Research / link
Another case of nuclear speckleopathy due to a novel NKAP pathogenic variant
Clinical Dysmorphology / link
Multiomics Analysis of PCB126’s Effect on a Mouse Chronic-Binge Alcohol Feeding Model
Environmental Health Perspectives / link
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
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
Evidence from 2100 index cases supports genome sequencing as a first-tier genetic test
Genetics in Medicine / link
Natural Killer Cells Do Not Attenuate a Mouse-Adapted SARS-CoV-2-Induced Disease in Rag2−/− Mice
Viruses / link
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
Exome Sequencing Reveals Biallelic Mutations in MBTPS1 Gene in a Girl with a Very Rare Skeletal Dysplasia
Diagnostics / link
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
BCL convert
Spectrum of PHEX Mutations and FGF23 Profiles in a Taiwanese Cohort With X-Linked Hypophosphatemia Including 102 Patients
In Vivo / link
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
CNV pipeline
Establishing mesothelioma patient-derived organoid models from malignant pleural effusions
Lung Cancer / link
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
COVIDSeq Test pipeline; BSSH
Whole genome sequencing of a family with autosomal dominant features within the oculoauriculovertebral spectrum
-- / link
Systematic molecular analyses for 115 karyotypically normal men with isolated non-obstructive azoospermia
Human Reproduction / link
Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses
-- / link
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
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
alignment; RNA pipeline
The complement regulator CD55 modulates TLR9 signaling and supports survival in marginal zone B cells
-- / link
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
Surveillance Outcome and Genetic Findings in Individuals at High Risk of Pancreatic Cancer
Clinical and Translational Gastroenterology / link
SV caller
Functional evaluation of a novel nonsense variant of the calcium-sensing receptor gene leading to hypocalcemia
European Journal of Endocrinology / link
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
Genomic Characterization of SARS-CoV-2 Variants from Clinical Isolates during the COVID-19 Epidemic in Mauritania
Genes / link
BCL convert
Ex vivo modeling of acquired drug resistance in BRAF - mutated pancreatic cancer organoids uncovers individual therapeutic vulnerabilities
Cancer Letters / link
RNA pipeline
Genomic and Phylogenetic Characterisation of SARS-CoV-2 Genomes Isolated in Patients from Lambayeque Region, Peru
Tropical Medicine and Infectious Disease / link
BSSH
Consanguineous marriages increase the incidence of recurrent tuberculosis: Evidence from whole exome sequencing
Infection, Genetics and Evolution / link
alignment
Brain injury drives optic glioma formation through neuron-glia signaling
Acta Neuropathologica Communications / link
Antiviral response and HIV-1 inhibition in sickle cell disease
Iscience / link
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
v3.6.4
Chapter 6 - Assessing microbiota composition in the context of aging
Methods in Cell Biology / link
BSSH; Metagenomics pipeline
Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics
Frontiers in Microbiology / link
Intellectual disability syndrome associated with a homozygous founder variant in SGSM3 in Ashkenazi Jews
Journal of Medical Genetics / link
Molecular analysis and transfusion management in a rare case of cis-AB blood group: A report from India
Transfusion Clinique et Biologique / link
v3.4
Immune transcriptomic profile in adult female pigs: dominance status has more influence than environmental enrichment
-- / link
v3.8.4; RNA
Differential Responses to Immune Checkpoint Inhibitors are Governed by Diverse Mismatch Repair Gene Alterations
Clinical Cancer Research / link
Comparative molecular profiling of pancreatic ductal adenocarcinoma of the head versus body and tail
npj Precision Oncology / link
BCL convert
Beyond the kidney biopsy: genomic approach to undetermined kidney diseases
Clinical Kidney Journal / link
BCL convert
Myocardial Matrix Hydrogels Mitigate Negative Remodeling and Improve Function in Right Heart Failure Model
JACC: Basic to Translational Science / link
RNA pipeline; v3.10.12
Despite Recovery from Necrotizing Enterocolitis Infants Retain a Hyperinflammatory Response to Injury
Journal of Inflammation Research / link
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
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
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
alignment; v4.0.3
Genetic Markers Among the Israeli Druze Minority Population With End-Stage Kidney Disease
American Journal of Kidney Diseases / link
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
High Frequencies of Genetic Variants in Patients with Atypical Femoral Fractures
International Journal of Molecular Sciences / link
Loss of function in NSD2 causes DNA methylation signature similar to that in Wolf-Hirschhorn syndrome
Genetics in Medicine Open / link
Concordance between an FDA-approved companion diagnostic and an alternative assay kit for assessing homologous recombination deficiency in ovarian cancer
Gynecologic Oncology / link
A Cataract-Causing Mutation in the TRPM3 Cation Channel Disrupts Calcium Dynamics in the Lens
Cells / link
v3.9
Homozygous variant in TKFC abolishing triokinase activities is associated with isolated immunodeficiency
Journal of Medical Genetics / link
Renal transcriptome analysis of uninephrectomized db/db mice identified a mechanism for the transition to severe diabetic nephropathy
Experimental Animals / link
The diversity and clinical implications of genetic variants influencing clopidogrel bioactivation and response in the Emirati population
Human Genomics / link
v4
A new potential therapeutic approach for ALS: A case report with NGS analysis
Medicine / link
Germline app v3.9.5
Conditionally replicative adenovirus as a therapy for malignant peripheral nerve sheath tumors
Molecular Therapy Oncology / link
Somatic mode
Embigin Is Highly Expressed on CD4+ and CD8+ T Cells but Is Dispensable for Several T Cell Effector Responses
ImmunoHorizons / link
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
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
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
In ovo delivery of oregano essential oil activated xenobiotic detoxification and lipid metabolism at hatch in broiler chickens
Poultry Science / link
Interrogating Pharmacogenetics Using Next-Generation Sequencing
The Journal of Applied Laboratory Medicine / link
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
alignment
Seasonality of respiratory, enteric, and urinary viruses revealed by wastewater genomic surveillance
mSphere / link
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
v3.6.3; RNA Seq pipeline; BSSH
Developing a genetic testing panel for evaluation of morbidities in kidney transplant recipients
Kidney International / link
Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater
Environmental Science & Technology / link
Microbial Enrichment pipeline
Synthetic Lethality between Cohesin and WNT Signaling Pathways in Diverse Cancer Contexts
Cells / link
Somatic pipeline
Skin Cancer Risk Is Increased by Somatic Mutations Detected Noninvasively in Healthy-Appearing Sun-Exposed Skin
Journal of Investigative Dermatology / link
Somatic app
Generative Haplotype Prediction Outperforms Statistical Methods for Small Variant Detection in NGS Data
-- / link
Coexistence of blaNDM-5, blaCTX-M-15, blaOXA-232, blaSHV-182 genes in multidrug-resistant K. pneumoniae ST437-carrying OmpK36 and OmpK37 porin mutations: First report in Italy
Journal of Global Antimicrobial Resistance / link
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
RNASeq pipeline
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc
Genome Biology / link
v3
Multimodal data fusion using sparse canonical correlation analysis and cooperative learning: a COVID-19 cohort study
npj Digital Medicine / link
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
v3.8
Late-life dietary folate restriction reduces biosynthetic processes without compromising healthspan in mice
-- / link
RNA Seq pipeline
Clinical Diversity and Outcomes of Progressive Familial Intrahepatic Cholestasis Diagnosed by Whole Genome Sequencing in Pakistani Children
-- / link
v3.10.4; SV; Indels
Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review
npj Genomic Medicine / link
review
Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer
-- / link
alignment; BSSH
Replicative senescence and high glucose induce the accrual of self-derived cytosolic nucleic acids in human endothelial cells
Cell Death Discovery / link
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
v3.10
Identification of spatially-resolved markers of malignant transformation in Intraductal Papillary Mucinous Neoplasms
Nature Communications / link
BSSH
Structural rearrangements as a recurrent pathogenic mechanism for SETBP1 haploinsufficiency
Human Genomics / link
Comparative analysis of 136,401 Admixed Americans and 419,228 Europeans reveals ancestry-specific genetic determinants of clonal haematopoiesis
-- / link
Germline pipeline v3.0.7
From GPUs to AI and quantum: three waves of acceleration in bioinformatics
Drug Discovery Today / link
review
Orthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing
-- / link
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
Somatic pipeline
Genome-Wide Association Study Reveals a QTL Region for Ashy Stem Blight Resistance in PRA154 Andean Common Bean
Plant Disease / link
Childhood-related neural genotype-phenotype in ATP1A3 mutations: comprehensive analysis
Genes & Genomics / link
v3.4.12
Molecular Heterogeneity of Osteopetrosis in India: Report of 17 Novel Variants
Indian Journal of Hematology and Blood Transfusion / link
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
DNMTs-mediated SOCS3 methylation promotes the occurrence and development of AML
European Journal of Haematology / link
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
Targeting prostate tumor low–molecular weight tyrosine phosphatase for oxidation-sensitizing therapy
Science Advances / link
demultiplexing
HiHo-AID2: boosting homozygous knock-in efficiency enables robust generation of human auxin-inducible degron cells
Genome Biology / link
v4.2.4
Self-reactive B cells traverse a perfect storm of somatic mutagenesis to cause a virus-induced autoimmune disease
-- / link
Nasopharyngeal metatranscriptomics reveals host-pathogen signatures of pediatric sinusitis
-- / link
onboard; demultiplexing
Multi-Tissue Network Analysis Reveals the Effect of JNK Inhibition on Dietary Sucrose-Induced Metabolic Dysfunction in Rats
-- / link
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
Damaging mutations in LXRα uncouple lipogenesis from hepatotoxicity and implicate hepatic cholesterol sensing in human liver health
-- / link
Germline pipeline v3.7.8
2P-NucTag: on-demand phototagging for molecular analysis of functionally identified cortical neurons
-- / link
De-multiplexing
Congenital Heart Defects in Patients with Molecularly Confirmed Sotos Syndrome
Diagnostics / link
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
v3.8.4
Proteogenomic analysis reveals adaptive strategies to alleviate the consequences of aneuploidy in cancer
-- / link
Engineered interleukin-6-derived cytokines recruit artificial receptor complexes and disclose CNTF signaling via the OSMR
Journal of Biological Chemistry / link
BCL convert
A novel T cell-redirecting anti-GPRC5D × CD3 bispecific antibody with potent antitumor activity in multiple myeloma preclinical models
Scientific Reports / link
alignment
Protocol for isolating single species of bacteria with swarming ability from human feces
STAR Protocols / link
v3.10.12; onboard
Mutational rescue of the activity of high-fidelity Cas9 enzymes
Cell Reports Methods / link
BCL convert
Clinical application of tumour-in-normal contamination assessment from whole genome sequencing
Nature Communications / link
alignment; v3.2.22
Roles for RERE in lymphatic endothelial cell proliferation and survival, and human cystic lymphatic malformations
-- / link
alignment
Epigenetic regulation by TET1 in gene-environmental interactions influencing susceptibility to congenital malformations
-- / link
Haplotype variant calling
Transcriptomic characterization of recombinant Clostridium beijerinckii NCIMB 8052 expressing methylglyoxal synthase and glyoxal reductase from Clostridium pasteurianum ATCC 6013
-- / link
onboard; v3.10.12
Simultaneous blastic plasmacytoid dendritic cell neoplasm and myelofibrosis: A case report
Oncology Letters / link
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
DMHPpp1r17 neurons regulate aging and lifespan in mice through hypothalamic-adipose inter-tissue communication
Cell Metabolism / link
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
BCL convert
ATM-deficiency-induced microglial activation promotes neurodegeneration in ataxia-telangiectasia
Cell reports / link
DRAGEN-GATK; Germline pipeline
Pangenome graph construction from genome alignments with Minigraph-Cactus
Nature Biotechnology / link
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
BCL convert
Assessing Genomic Mutations in SARS-CoV-2: Potential Resistance to Antiviral Drugs in Viral Populations from Untreated COVID-19 Patients
Microorganisms / link
BSSH; COVID Lineage App v3.5.2
Deployment of a Vibrio cholerae ordered transposon mutant library in a quorum-competent genetic background
-- / link
v3.10.11; NextSeq2000; DRAGEN onboard
Cleave and Rescue gamete killers create conditions for gene drive in plants
-- / link
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
CNV caller; Small variant caller
Detection of Mpox Virus Using a Wastewater Surveillance Approach in Brazil
-- / link
BSSH; Microbial Enrichment pipeline
Metagenomics or Metataxonomics: Best Practice Methods to Uncover the Sinus Microbiome
-- / link
BCL convert
Immunocompetent murine model of Ewing sarcoma reveals role for TGFβ inhibition to enhance immune infiltrates in Ewing tumors during radiation
-- / link
v3.10.12; onboard; demultiplexing
Toward clinical exomes in diagnostics and management of male infertility
American Journal of Human Genetics / link
CCR2+ monocytes promote white matter injury and cognitive dysfunction after myocardial infarction
Brain, Behavior, and Immunity / link
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
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
fusion caller
A case of T-cell acute lymphoblastic leukemia in retroviral gene therapy for ADA-SCID
Nature Communications / link
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
RNA
Early-life house dust mite aeroallergen exposure augments cigarette smoke-induced myeloid inflammation and emphysema in mice
Respiratory Research / link
BCL convert
Altered Osteoblast Metabolism with Aging Results in Lipid Accumulation and Oxidative Stress Mediated Bone Loss
Aging and Disease / link
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
v3.9.5
SARS-CoV-2 variant with the spike protein mutation F306L in the southern border provinces of Thailand
Scientific Reports / link
Craniofacial chondrogenesis in organoids from human stem cell-derived neural crest cells
iScience / link
onboard
Protein-truncating variants in BSN are associated with severe adult-onset obesity, type 2 diabetes and fatty liver disease
Nature Genetics / link
AWS
De novo variants in the non-coding spliceosomal snRNA gene RNU4-2 are a frequent cause of syndromic neurodevelopmental disorders
medRxiv / link
alignment
Targeting DNMT3A-mediated oxidative phosphorylation to overcome ibrutinib resistance in mantle cell lymphoma
Cell Reports Medicine / link
v3.10
11p13 microduplication: a differential diagnosis of Silver–Russell syndrome?
Molecular Cytogenetics / link
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
BSSH; RNA pipeline
Impact of media supplements FGF2, LIF and IGF1 on the genome activity of porcine embryos produced in vitro
Scientific Reports / link
Immunophenotypic and Gene Expression Analyses of the Inflammatory Microenvironment in High-Grade Oral Epithelial Dysplasia and Oral Lichen Planus
Head and Neck Pathology / link
v3.8.4
A microfluidic platform integrating functional vascularized organoids-on-chip
Nature Communications / link
BSSH; RNA app
Pangenome graphs improve the analysis of structural variants in rare genetic diseases
Nature Communications / link
alignment
Autoimmune demyelination alters hypothalamic transcriptome and endocrine function
Journal of Neuroinflammation / link
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
v2.03
Spatiotemporal dynamics and epidemiological impact of SARS-CoV-2 XBB lineage dissemination in Brazil in 2023
Microbiology Spectrum / link
Evidence of SARS-CoV-2 Antibody in Mississippi White-Tailed Deer
Vector-Borne and Zoonotic Diseases / link
Transcriptional features of low-grade neuroepithelial tumors with the BRAF V600E mutation associated with epileptogenicity
Genes to Cells / link
Integrative multi-region molecular profiling of primary prostate cancer in men with synchronous lymph node metastasis
Nature Communications / link
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
v3.8.4
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
Diabetes mellitus in Kabuki syndrome 1 on a background of post-transplant diabetes mellitus
Endocrinology, Diabetes & Metabolism Case Reports / link
Novel variants in TECRL leading to catecholaminergic polymorphic ventricular tachycardia
Life Science Alliance / link
Type 1 diabetes human enteroid studies reveal major changes in the intestinal epithelial compartment
Scientific Reports / link
v3.10
Limb-girdle muscular dystrophy: A rare clinical case report
Demiroğlu Bilim University Florence Nightingale Journal of Medicine / link
v3.6
Resolving unsolved whole-genome sequencing data in paediatric neurological disorders: a cohort study
Archives of Disease in Childhood / link
v4.0
Efficient wastewater sample filtration improves the detection of SARS-CoV-2 variants: An extensive analysis based on sequencing parameters
PLOS ONE / link
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
v3.9
Clinician-Driven Reanalysis of Exome Sequencing Data From Patients With Inherited Retinal Diseases
JAMA Network Open / link
2023
Reliability of panel-based mutational signatures for immune-checkpoint-inhibition efficacy prediction in non-small cell lung cancer
Lung Cancer / link
DRAGEN server; TSO 500 Analysis software v2.1
Viral kinetics of sequential SARS-CoV-2 infections
Nature Communications / link
BSSH; COVID Lineage App
Optimization of the Illumina COVIDSeq™ protocol for decentralized, cost-effective genomic surveillance
Practical Laboratory Medicine / link
COVID Lineage App; v3.5.4
Mechanism of KMT5B haploinsufficiency in neurodevelopment in humans and mice
Science Advances / link
v3.6.3
De novo MCM6 variants in neurodevelopmental disorders: a recognizable phenotype related to zinc binding residues
Human Genetics / link
[11C]metomidate PET-CT versus adrenal vein sampling for diagnosing surgically curable primary aldosteronism: a prospective, within-patient trial
Nature Medicine / link
Somatic mode
Persistent Molecular Disease in Adult Patients With AML Evaluated With Whole-Exome and Targeted Error-Corrected DNA Sequencing
JCO Precision Oncology / link
v3.9.3
Improvement in neoantigen prediction via integration of RNA sequencing data for variant calling
Frontiers in Immunology / link
tumor-normal mode
Unravelling homologous recombination repair deficiency and therapeutic opportunities in soft tissue and bone sarcoma
EMBO Molecular Medicine / link
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
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
Increased clonal hematopoiesis involving DNA damage response genes in patients undergoing lung transplantation
JCI Insight / link
Molecular and phenotypic characteristics influencing the degree of cytoreduction in high‐grade serous ovarian carcinomas
Cancer Medicine / link
DRAGEN server; v3.8
Integrated multi-omics for rapid rare disease diagnosis on a national scale
Nature Medicine / link
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
v3.5.7
Androgens show sex-dependent differences in myelination in immune and non-immune murine models of CNS demyelination
Nature Communications / link
v3.6.3
SLC26A1 is a major determinant of sulfate homeostasis in humans
Journal of Clinical Investigation / link
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
Mapping
Case Report: A new case of YARS1-associated autosomal recessive disorder with compound heterozygous and concurrent 47, XXY
Frontiers in Pediatrics / link
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
BSSH; RNA pathogen detection; v3.5.1
The genetic determinants of recurrent somatic mutations in 43,693 blood genomes
Science Advances / link
MiR-4521 perturbs FOXM1-mediated DNA damage response in breast cancer
Frontiers in Molecular Biosciences / link
RNA Seq pipeline
Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer
Nature Communications / link
COVID Lineage App; v3.5.6
The pharmacogenomic landscape of an Indigenous Australian population
Frontiers in Pharmacology / link
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
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
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
COVID Lineage App; Somatic caller
Biallellic variants in CACNA1S cause fetal akinesia sequence, progressive hydrops and stillbirth
Prenatal Diagnosis / link
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
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
alignment; Variant calling
Evaluation of an optimized germline exomes pipeline using BWA-MEM2 and Dragen-GATK tools
PLOS ONE / link
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
CNV
First sequenced cases of Omicron BA.2 sublineage in Ecuador
Virus Research / link
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
Comparative Analysis of Structural Variant Callers on Short-Read Whole-Genome Sequencing Data
Russian Journal of Genetics / link
v3.5.7
Identification of allele-specific KIV-2 repeats and impact on Lp (a) measurements for cardiovascular disease risk
bioRxiv / link
KIV2 CN caller; LPA caller; v4.2
Whole genome sequencing in ROHHAD trios proved inconclusive: what’s beyond?
Frontiers in Genetics / link
Rapid identification of SARS-CoV-2 variants: Validation of the simplexa SARS-CoV-2 variant direct assay
Journal of Virological Methods / link
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
Detection of ATXN2 Expansions in an Exome Dataset: An Underdiagnosed Cause of Parkinsonism
Movement Disorders Clinical Practice / link
ExpansionHunter; v3.9
An absolute approach to using whole exome DNA and RNA workflow for cancer biomarker testing
Frontiers in Oncology / link
RNA pipeline; Somatic pipeline; v3.6
Emergence of SARS-CoV-2 variant of interest B. 1.525 (Eta) in Bangladesh
Biologicals / link
RNA pathogen detection
Clinical Implementation of MetaFusion for Accurate Cancer-Driving Fusion Detection from RNA Sequencing
The Journal of Molecular Diagnostics / link
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
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
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
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
COVIDSeq Test pipeline; DRAGEN server
Genomic Surveillance of SARS-CoV-2 Sequence Variants at Universities in Southwest Idaho
COVID / link
BSSH; COVID Lineage App; v3.5.12
Midline brain hamartomatous lesions in fibrodysplasia ossificans progressiva with ACVR1 mutations
Neuropathology / link
Biphenotypic Immunohistochemical Features and NTRK1 Amplification in Intermediate Cell Carcinoma of the Liver
International Journal of Surgical Pathology / link
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
Novel association of Dandy–Walker malformation with CAPN15 variants expands the phenotype of oculogastrointestinal neurodevelopmental syndrome
American Journal of Medical Genetics Part A / link
Nicotine, THC, and Dolutegravir Modulate E-Cigarette-Induced Changes in Addiction-and Inflammation-Associated Genes in Rat Brains and Astrocytes
Brain Sciences / link
epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data
GigaScience / link
v3.9.5; Methylation pipeline
Clinical Validation of Tagmentation-Based Genome Sequencing for Germline Disorders
The Journal of Molecular Diagnostics / link
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
tumor-only liquid-biopsy variant calling pipeline; v3.5.7
The clinical characteristics of pediatric patients infected by SARS-CoV-2 Omicron variant and whole viral genome sequencing analysis
Plos one / link
COVID Lineage
Scalable, high quality, whole genome sequencing from archived, newborn, dried blood spots
NPJ Genomic Medicine / link
Effects of protein-coding variants on blood metabolite measurements and clinical biomarkers in the UK Biobank
The American Journal of Human Genetics / link
Germline Pipeline v3.0.7
Monogenic diabetes clinic (MDC): 3-year experience
Acta Diabetologica / link
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
Evaluation of Breast Implant–Associated Anaplastic Large Cell Lymphoma With Whole Exome and Genome Sequencing
Aesthetic Surgery Journal / link
v3.8
Flavored E-cigarette product aerosols induce transformation of human bronchial epithelial cells
Lung Cancer / link
RNA pipeline; Differential Expression App
Design and implementation of a hybrid cloud system for large-scale human genomic research
Human Genome Variation / link
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
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
BSSH
Fibroblast-expressed LRRC15 is a receptor for SARS-CoV-2 spike and controls antiviral and antifibrotic transcriptional programs
PLOS Biology / link
Differential Expression
Combined low-pass whole genome and targeted sequencing in liquid biopsies for pediatric solid tumors
npj Precision Oncology / link
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
Genomic perspectives of SARS CoV-2 in liver disease patients with its clinical correlation: A single centre retrospective study
-- / link
COVID Lineage App
An accessible patient-derived xenograft model of low-risk myelodysplastic syndromes
Haematologica / link
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
BCL convert
Experimental Evaluation of the Possibility to Detect Cross-Contaminated DNA Samples Based on Genetic Data
Russian Journal of Genetics / link
alignment
Identification of copy number variants with genome sequencing: Clinical experiences from the NYCKidSeq program
Clinical Genetics / link
RNA Sequencing Reveals Novel Oncogenic Fusions and Depicts Detailed Fusion Transcripts of FN1-FGFR1 in Phosphaturic Mesenchymal Tumors
Modern Pathology / link
BSSH; RNA pipeline v3.3.7
Fast and reliable detection of repeat expansions in spinocerebellar ataxia using exomes
Journal of Medical Genetics / link
KMT2A-rearranged sarcoma with unusual fusion gene CBX6::KMT2A::PYGO1
Virchows Archiv / link
fusion analysis; RNA app v3.10.4
An SPG7 mutation as a novel cause of monogenic progressive muscular atrophy
Neurological Sciences / link
Variant annotation
A short-term three dimensional culture-based drug sensitivity test is feasible for malignant bone tumors
Human Cell / link
BSSH; RNA pipeline
Variants in CLDN5 cause a syndrome characterized by seizures, microcephaly and brain calcifications
Brain / link
Transcriptomic Profiling of Placental Cells in Preeclampsia as an Effective Tool for Personalized Medicine
Russian Journal of Genetics / link
SARS-CoV-2 Sequencing for Variant Surveillance
Clinical Applications of Nucleic Acid Amplification / link
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
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
SNV/indel hypermutator phenotype in biallelic RAD51C variant: Fanconi anemia
Human Genetics / link
v3.4.15
Hyperinsulinemia acts via acinar insulin receptors to initiate pancreatic cancer by increasing digestive enzyme production and inflammation
Cell Metabolism / link
alignment; BCL convert; BSSH; RNA app
Respective roles of Pik3ca mutations and cyproterone acetate impregnation in mouse meningioma tumorigenesis
Cancer Gene Therapy / link
An autosomal-dominant childhood-onset disorder associated with pathogenic variants in VCP
American Journal of Human Genetics / link
alignment; Germline pipeline v3.2.8
Identification of human exTreg cells as CD16+CD56+ cytotoxic CD4+ T cells
Nature Immunology / link
FASTQ toolkit; read trimming
Generation of quality-controlled SARS-CoV-2 variant stocks
Nature Protocols / link
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
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
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
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
Differential Expression v3.6.3
Accurate tumor purity determination is critical for the analysis of homologous recombination deficiency (HRD)
Translational Oncology / link
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
Somatic mode
Effects of S-Adenosylhomocysteine Hydrolase Downregulation on Wnt Signaling Pathway in SW480 Cells
International Journal of Molecular Sciences / link
BSSH; RNA Pipeline v3.9.5; Differential Expression App
Rapid Genome Sequencing Diagnosis in Pediatric Patients with Liver Dysfunction
The Journal of Pediatrics / link
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
Chronic stress targets mitochondrial respiratory efficiency in the skeletal muscle of C57BL/6 mice
Cellular and Molecular Life Sciences / link
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
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
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
haplotype caller
Distinct Molecular Profiles and Drug Vulnerabilities in Pancreatic Metastases of Renal Cell Carcinoma
-- / link
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
A Panel-Agnostic Strategy ‘HiPPo’ Improves Diagnostic Efficiency in the UK Genomic Medicine Service
Healthcare / link
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
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
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
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
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
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
Population genetic testing and SERPINA1 sequencing identifies unidentified alpha-1 antitrypsin deficiency alleles and gene-environment interaction with hepatitis C infection
PLOS ONE / link
BSSH; Germline small variant caller
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
[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
Investigation of SNP markers for the melatonin production trait in the Hu sheep with bulked segregant analysis
BMC Genomics / link
Genome pipeline
Combining cell-free RNA with cell-free DNA in liquid biopsy for hematologic and solid tumors
Heliyon / link
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
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
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
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
Somatic pipeline; v3.6
Limitations in next-generation sequencing-based genotyping of breast cancer polygenic risk score loci
-- / link
STIM1 signals through NFAT1 independently of Orai1 and SOCE to regulate breast cancer cell migration
Cell Calcium / link
Differential Expression; BSSH; RNA-Seq
Analysis of a hit-and-run tumor model by HPV in oropharyngeal cancers
Journal of Medical Virology / link
v3.9.3; Somatic small variant calling
Wastewater Genomic Surveillance Captures Early Detection of Omicron in Utah
Microbiology Spectrum / link
COVIDSeq Test pipeline
Evaluation of an automated genome interpretation model for rare disease routinely used in a clinical genetic laboratory
Genetics in Medicine / link
v3.1.5
Whole genome and RNA sequencing analyses for 254 Taiwanese hepatocellular carcinomas
Biomarker Research / link
Newborn screening for X-linked adrenoleukodystrophy in Italy: Diagnostic algorithm and disease monitoring
Frontiers in Neurology / link
v3.0
Homozygous CDH2 variant may be associated with hypopituitarism without neurological disorders
Endocrine Connections / link
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
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
RNA pipeline; BSSH
Rapid Whole-Genomic Sequencing and a Targeted Neonatal Gene Panel in Infants With a Suspected Genetic Disorder
JAMA / link
v3.7
Applications of artificial intelligence in clinical laboratory genomics
American Journal of Medical Genetics Part C: Seminars in Medical Genetics / link
review
Intermediate repeat expansions of TBP and STUB1: Genetic modifier or pure digenic inheritance in spinocerebellar ataxias?
Genetics in Medicine / link
Variant calling; alignment
Genomic surveillance identifies SARS-CoV-2 transmission patterns in local university populations, Wisconsin, USA, 2020–2022
Microbial Genomics / link
COVID Lineage Pipeline
SCN1A Gene Mutations in Indian Children With Epilepsy: Single Center Experience
Indian Pediatrics / link
Immune evasion and membrane fusion of SARS-CoV-2 XBB subvariants EG.5.1 and XBB.2.3
Emerging Microbes & Infections / link
COVID Lineage
Capicua (CIC) mutations in gliomas in association with MAPK activation for exposing a potential therapeutic target
Medical Oncology / link
BCL convert
Clinical characteristics and outcomes of laboratory-confirmed SARS-CoV-2 cases infected with omicron subvariants and the XBB recombinant variant
Cureus / link
alignment; COVID Lineage App
Whole genome sequencing provides comprehensive genetic testing in childhood B-cell acute lymphoblastic leukaemia
Leukemia / link
Report of two cases of Schaaf‐Yang syndrome: Same genotype and different phenotype
Clinical Case Reports / link
SNV
Balanced Translocation Disrupting JAG1 Identified by Optical Genomic Mapping in Suspected Alagille Syndrome
Human Mutation / link
v3.2.8
Disentangling archaic introgression and genomic signatures of selection at human immunity genes
Infection, Genetics and Evolution / link
v3.6.4
Intracranial mesenchymal tumor with (novel) COX14::PTEN rearrangement
Acta Neuropathologica Communications / link
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
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
Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs
Journal of Computational Biology / link
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
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
Somatic pipeline v3.8.4
Metastatic insulinoma: exploration from clinicopathological signatures and genetic characteristics
Frontiers in Oncology / link
Preliminary analysis of oral and gut microbiome of an elderly patient with late-diagnosed phenylketonuria
Annals of Agricultural and Environmental Medicine / link
Hypolipidemic treatment increases lipoprotein(a) levels in patients with mixed hyperlipidemia
Atherosclerosis / link
An overview of SARS-CoV-2 variants circulating in the 2020–2022 period in Lombardy
Diagnostic Microbiology and Infectious Disease / link
COVID Lineage App
Insights into the Rare cis-AB Blood Group: In Silico Genotyping and Analysis in the Indian Subcontinent
-- / link
v3.4
Novel STAT3 variant causing infantile-onset autoimmune disease
Frontiers in Medicine / link
BSSH; Germline pipeline
Adipose tissue insulin resistance exacerbates liver inflammation and fibrosis in a diet-induced NASH model
Hepatology Communications / link
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
Variant calling; alignment
Personalized neoantigen-based T cell therapy triggers cytotoxic lymphocytes expressing polyclonal TCR against metastatic ovarian cancer
Biomedicine & Pharmacotherapy / link
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
COVID Lineage App
Myosin Mutations and Sudden Sensorineural Hearing Loss: Results of Whole Exome Sequencing
Otology & Neurotology / link
Genomic alterations in chronic myeloid leukaemia patients who failed second generation tyrosine kinase inhibitor
Pathology / link
Exome-First Strategy in Adult Patients With CKD: A Cohort Study
Kidney International Reports / link
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
COVID Lineage
Development of a somatic variant registry in a National Cancer Center: towards Molecular Real World Data preparedness
Journal of Biomedical Informatics / link
The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub
Viruses / link
Success and Pitfalls of Genetic Testing in Undiagnosed Diseases: Whole Exome Sequencing and Beyond
Genes / link
FUS-ERG induces late-onset azacitidine resistance in acute myeloid leukaemia cells
Scientific Reports / link
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
Genetic insights into childhood-onset schizophrenia: The yield of clinical exome sequencing
Schizophrenia Research / link
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
DNA amplicon app
Clinical and molecular features of four Brazilian families with multiple endocrine neoplasia type 1
Frontiers in Endocrinology / link
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
CNV pipeline
Concurrent predictors of an immune responsive tumor microenvironment within tumor mutational burden-high breast cancer
Frontiers in Oncology / link
Genetic heterogeneity and enrichment of variants in DNA-repair genes in ameloblastoma
Journal of Oral Pathology & Medicine / link
v3.2.8; alignment
Functional and Molecular Heterogeneity in Glioma Stem Cells Derived from Multiregional Sampling
Cancers / link
Complex Microphthalmia due to a Homozygous Novel Variant in SIX Homeobox 6 Gene
Delhi Journal of Ophthalmology / link
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
Kohlschutter-Tonz syndrome (amelo-cerebro-hypohidrotic syndrome) in an Indian family with a novel ROGD1 mutation
Clinical Dysmorphology / link
GAMT Deficiency Among Pediatric Population: Clinical and Molecular Characteristics and Management
Child Neurology Open / link
v3.4.12
Loss of Nudt15 thiopurine detoxification increases direct DNA damage in hematopoietic stem cells
Scientific Reports / link
v3.7.5
Fetal de novo heterozygous variant in the isocitrate dehydrogenase 1 gene associated with growth restriction, skeletal, cerebral and vascular anomalies
Prenatal Diagnosis / link
Diagnosis of Kidney Diseases of Unknown Etiology Through Biopsy-Genetic Analysis
Kidney International Reports / link
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
v3.4.12
Comprehensive Analysis and Drug Modulation of Human Endogenous Retrovirus in Hepatocellular Carcinomas
Cancers / link
Impact of High-to-Moderate Penetrance Genes on Genetic Testing: Looking over Breast Cancer
Genes / link
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
Germline pipeline
Circulating Variants of SARS-CoV-2 Among Macedonian COVID - 19 Patients in the First Year of Pandemic
PRILOZI / link
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
alignment; BSSH
3′ UTR Deletion of FBXO28 in a Patient with Brain Abnormalities and Developmental Delay
Genes / link
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
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
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
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
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
Germline Pipeline
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
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
v2.1
A New Case of Autosomal-Dominant POLR3B-Related Disorder: Widening Genotypic and Phenotypic Spectrum
Brain Sciences / link
BSSH; Enrichment app
Limitations of gene editing assessments in human preimplantation embryos
Nature Communications / link
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
A novel de novo pathogenic variant in TBL1XR1 as a new proposed cause of Pierpont syndrome
American Journal of Medical Genetics Part A / link
Technical feasibility of newborn screening for spinal muscular atrophy by next-generation DNA sequencing
Frontiers in Genetics / link
BCL convert
Clinical Performance of BD Veritor™ Assay Across SARS-CoV-2 Variants
-- / link
COVID Lineage App v3.5.9
Deep Intronic LINE-1 Insertions in NF1: Expanding the Spectrum of Neurofibromatosis Type 1-Associated Rearrangements
Biomolecules / link
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
alignment
The current benefit of genome sequencing compared to exome sequencing in patients with developmental or epileptic encephalopathies
Molecular Genetics & Genomic Medicine / link
Comprehensive genomic profiling of penile squamous cell carcinoma and the impact of human papillomavirus status on immune-checkpoint inhibitor-related biomarkers
Cancer / link
Chromosomal instability and a deregulated cell cycle are intrinsic features of high-risk gastrointestinal stromal tumours with a metastatic potential
Molecular Oncology / link
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
v3
Genomic Strategies in Mitochondrial Diagnostics
Mitochondrial DNA: Methods and Protocols / link
protocol
EndoC-βH5 cells are storable and ready-to-use human pancreatic beta cells with physiological insulin secretion
Molecular Metabolism / link
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
BCL convert
Breaking Barriers to Rapid Whole Genome Sequencing in Pediatrics: Michigan’s Project Baby Deer
Children / link
CNV
The Effect of Long-Term Inorganic Iodine on Intrathyroidal Iodothyronine Content and Gene Expression in Mice with Graves' Hyperthyroidism
Thyroid® / link
v3.6.3
Mucopolysaccharidosis Type I Presenting with Persistent Neonatal Respiratory Distress: A Case Report
Diseases / link
v3.4.12
Anti-inflammatory effects of cold atmospheric plasma irradiation on the THP-1 human acute monocytic leukemia cell line
PLOS ONE / link
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
BSSH
DNA methylation signature in NSD2 loss-of-function variants appeared similar to that in Wolf-Hirschhorn syndrome
-- / link
Combined sequence and copy number analysis improves diagnosis of limb girdle and other myopathies
Annals of Clinical and Translational Neurology / link
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
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
Whole Exome Sequence Analysis for Inborn Errors of IL-12/IFN-γ Axis in Patient with Recurrent Typhoid Fever
BioMed Research International / link
Genome pipeline
Long-Term Culturing of FreeStyle 293-F Cells Affects Immunoglobulin G Glycome Composition
Biomolecules / link
Differential Expression tool
Commercially available SARS-CoV-2 RT-qPCR diagnostic tests need obligatory internal validation
Scientific Reports / link
COVID Lineage Pipeline
Expanding the spectrum of neonatal-onset AIFM1-associated disorders
Annals of Clinical and Translational Neurology / link
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
Diagnostic Utility of Exome Sequencing Among Israeli Children With Kidney Failure
Kidney International Reports / link
CNV
In-Depth Comparison of Genetic Variants Demonstrates a Close Relationship Between Invasive and Intraductal Components of Prostate Cancer
Modern Pathology / link
Mutation in Chek2 triggers von Hippel-Lindau hemangioblastoma growth
Acta Neurochirurgica / link
v3.6.3
Genomic analysis of a Palestinian family with inherited cancer syndrome: a next-generation sequencing study
Frontiers in Genetics / link
Non-invasive harvesting of conjunctival cells for whole transcriptome sequencing
Experimental Eye Research / link
BCL convert
RNA Sequencing in Hypoxia-Adapted T98G Glioblastoma Cells Provides Supportive Evidence for IRE1 as a Potential Therapeutic Target
Genes / link
v3.3.7
Systematic lung ultrasound in Omicron-type vs. wild-type COVID-19
European Heart Journal - Cardiovascular Imaging / link
Genome characterization, phylogenomic assessment and spatio-temporal dynamics study of highly mutated BA variants from India
Indian Journal of Medical Microbiology / link
BSSH; COVID Lineage
Interplay between Nrf2 and αB-crystallin in the lens and heart of zebrafish under proteostatic stress
Frontiers in Molecular Biosciences / link
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
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
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
Germline pipeline
Mutational Analysis of Circulating Omicron SARS-CoV-2 Lineages in the Al-Baha Region of Saudi Arabia
Journal of Multidisciplinary Healthcare / link
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
BSSH; COVID Lineage
High incidence of occult familial SDHD cases amongst Czech patients with head and neck paragangliomas
Frontiers in Endocrinology / link
The emergence of Omicron VOC and its rapid spread and persistence in the Western Amazon
PLOS ONE / link
BSSH; COVID Lineage
Pharmacogenetics of tuberculosis treatment toxicity and effectiveness in a large Brazilian cohort
-- / link
BSSH; Joint genotyping pipeline; Germline app
Productive infection of primary human hepatocytes with SARS-CoV-2 induces antiviral and proinflammatory responses
Gut / link
Genomic variants exclusively identified in children with birth defects and concurrent malignant tumors predispose to cancer development
Molecular Cancer / link
Timeline of SARS-CoV-2 Transmission in Sabah, Malaysia: Tracking the Molecular Evolution
Pathogens / link
Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial
-- / link
Blood transcriptome responses in patients correlate with severity of COVID-19 disease
Frontiers in Immunology / link
BCL convert
Precision Medicine in a Community Cancer Center: Pan-Cancer DNA/RNA Sequencing of Tumors Reveals Clinically Relevant Gene Fusions
Biologics / link
demultiplexing
High Throughput SARS-CoV-2 Genome Sequencing from 384 Respiratory Samples Using the Illumina COVIDSeq Protocol
Genes / link
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
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
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
DRAGEN server; BCL convert
The clinical utility of rapid exome sequencing in a consanguineous population
Genome Medicine / link
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
COVID Lineage App v3.5.7
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
mRNA quantification pipeline
Prenatal diagnosis of lanosterol synthase deficiency: Fetal ultrasound findings as a window on family genetics
European Journal of Medical Genetics / link
SNV; CNV
Amp(1q) and tetraploidy are commonly acquired chromosomal abnormalities in relapsed multiple myeloma
European Journal of Haematology / link
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
CoVEx: SARS-CoV-2 Mutation Explorer for genomic surveillance
Infection, Genetics and Evolution / link
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
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
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
Prevalence of familial BRCA1/2 mutation in four cancer types in the United Arab Emirates and of Arab Nationals
-- / link
BSSH; Enrichment app
Strong protective effect of the APOL1 p.N264K variant against G2-associated focal segmental glomerulosclerosis and kidney disease
Nature Communications / link
Improving the response to oxaliplatin by targeting chemotherapy-induced CLDN1 in resistant metastatic colorectal cancer cells
Cell & Bioscience / link
v3.8.4
Epidermal differentiation complex genetic variation in atopic dermatitis and peanut allergy
Journal of Allergy and Clinical Immunology / link
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
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
v3.6
Genomic and Epidemiologic Surveillance of SARS-CoV-2 in the Pandemic Period: Sequencing Network of the Lazio Region, Italy
Viruses / link
BSSH
PTPA variants and impaired PP2A activity in early-onset parkinsonism with intellectual disability
Brain / link
Sensitive Detection of Cell-Free Tumour DNA Using Optimised Targeted Sequencing Can Predict Prognosis in Gastro-Oesophageal Cancer
Cancers / link
BCL convert
Biallelic loss of function variants in WBP4, encoding a spliceosome protein, result in a variable neurodevelopmental delay syndrome
-- / link
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
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
Emergence and Persistent Dominance of Omicron BA.2.3.7 Variant in Community Outbreaks in Taiwan
-- / link
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
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
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
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
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
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
Genomic epidemiology of SARS-CoV-2 in large university hospital cohort: the UnCoVER-Brazil project
Epidemiology & Infection / link
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
Genomic epidemiology reveals the dominance of Hennepin County in the transmission of SARS-CoV-2 in Minnesota from 2020 to 2022
mSphere / link
COVID Lineage
Genomic Landscape Comparison of Cardiac versus Extra-Cardiac Angiosarcomas
Biomedicines / link
RNA app
Spinal cord extracts of amyotrophic lateral sclerosis spread TDP-43 pathology in cerebral organoids
PLOS Genetics / link
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
alignment
Data Analysis Pipeline for Detection and Quantification of Pseudouridine (ψ) in RNA by HydraPsiSeq
Computational Epigenomics and Epitranscriptomics / link
BCL convert
Muscle spasms as presenting feature of Nivelon-Nivelon-Mabile syndrome
American Journal of Medical Genetics Part A / link
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
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
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
DRAGEN server
The Impact of Phase-Specific Macrophage Depletion on Intestinal Anastomotic Healing
Cells / link
demultiplexing
Rapid genome diagnosis of alveolar capillary dysplasia leading to treatment in a child with respiratory and cardiac failure
Molecular Case Studies / link
Role of Royal Jelly Treated Adipose-Derived Stem Cell-Extracellular Vesicles on Fibroblast Proliferation, Migration, and Collagen Production
Dermatologic Therapy / link
v3.6.3; Differential Expression
Clinical predominance of whole-exome sequencing to evaluate microsatellite instability status
Cancer Science / link
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
v3.5.13
Koala Genome Survey: An Open Data Resource to Improve Conservation Planning
Genes / link
v3.8.4; alignment; Koala reference genome
Biallelic NEXN variants and fetal onset dilated cardiomyopathy: two independent case reports and revision of literature.
-- / link
BSSH; Enrichment app
NGS method for parallel processing of high quality, damaged or fragmented input material using target enrichment
-- / link
BCL convert
Detection of mosaic variants using genome sequencing in a large pediatric cohort
American Journal of Medical Genetics. Part A / link
Systematic identification of disease-causing promoter and untranslated region variants in 8,040 undiagnosed individuals with rare disease
-- / link
Enhanced microglial dynamics and paucity of tau seeding in the amyloid plaque microenvironment contributes to cognitive resilience in Alzheimer’s disease
-- / link
DRAGEN server v4
Immuno-oncologic profiling of pediatric CNS tumors reveals major clinical significance of the tumor immune microenvironment
-- / link
BSSH
SARS-CoV-2 variants-associated outbreaks of COVID-19 in a tertiary institution, North-Central Nigeria: Implications for epidemic control
PLOS ONE / link
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
v4.0.3; tumor-only
Reclassification of the Etiology of Infant Mortality With Whole-Genome Sequencing
JAMA Network Open / link
The Impact of Muscarinic Antagonism on Psychosis-Relevant Behaviors and Striatal [11C] Raclopride Binding in Tau Mouse Models of Alzheimer’s Disease
Biomedicines / link
v3.9.0
Assessment of Apolipoprotein(a) Isoform Size Using Phenotypic and Genotypic Methods
International Journal of Molecular Sciences / link
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
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
DRAGEN-GATK
Severe NAD(P)HX Dehydratase (NAXD) Neurometabolic Syndrome May Present in Adulthood after Mild Head Trauma
International Journal of Molecular Sciences / link
Germline- and Somatic-Inactivating FLCN Variants in Parathyroid Cancer and Atypical Parathyroid Tumors
The Journal of Clinical Endocrinology & Metabolism / link
FLAIRR-Seq: A Method for Single-Molecule Resolution of Near Full-Length Antibody H Chain Repertoires
The Journal of Immunology / link
Elucidating the Proximal Tubule HNF4A Gene Regulatory Network in Human Kidney Organoids
Journal of the American Society of Nephrology / link
Advanced Age in Humans and Mouse Models of Glioblastoma Show Decreased Survival from Extratumoral Influence
Clinical Cancer Research / link
BCL convert
Determining the impact of vaccination on SARS-CoV-2 RT-PCR cycle threshold values and infectious viral titres
Access Microbiology / link
BSSH; COVID Lineage App v3.5.2
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
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
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
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
Enrichment pipeline v3.7.5
A Breast Cancer Polygenic Risk Score Is Feasible for Risk Stratification in the Norwegian Population
Cancers / link
DRAGEN-GATK
A “Two-in-One Hit” Model of Shortcut Carcinogenesis in MLH1 Lynch Syndrome Carriers
Gastroenterology / link
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
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
RNA pathogen detection
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
Interplay of gene expression and regulators under salinity stress in gill of Labeo rohita
BMC Genomics / link
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
Phase II trial of CDK4/6 inhibitor palbociclib in advanced sarcoma based on mRNA expression of CDK4/CDKN2A
Signal Transduction and Targeted Therapy / link
Variant calling
Deep genomic characterization highlights complexities and prognostic markers of pediatric acute myeloid leukemia
Communications Biology / link
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
BCL convert
Human Induced Pluripotent Stem Cell based Hepatic-Modeling of Lipid metabolism associated TM6SF2 E167K variant
-- / link
RNA; v3.10.12
De novo TRPM3 missense variant associated with neurodevelopmental delay and manifestations of cerebral palsy
Molecular Case Studies / link
Germline pipeline v3.9.5
A Novel RUNX1 Genetic Variant Identified in a Young Male with Severe Osteoporosis
JBMR Plus / link
Variant calling; alignment; Enrichment pipeline
Placental Infection Associated with SARS-CoV-2 Wildtype Variant and Variants of Concern
Viruses / link
COVID Lineage App
Genetic landscape of homologous recombination repair genes in early-onset/familial prostate cancer patients
Genes, Chromosomes and Cancer / link
Next-Generation sequencing transforming clinical practice and precision medicine
Clinica Chimica Acta / link
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
Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort
Nature Communications / link
alignment
Congenital heart defects in CTNNB1 syndrome: Raising clinical awareness
Clinical Genetics / link
Germline pipeline
Multi-omic profiling reveals discrepant immunogenic properties and a unique tumor microenvironment among melanoma brain metastases
npj Precision Oncology / link
The importance of genome sequencing: unraveling SSBP1 variant missed by exome sequencing
Ophthalmic Genetics / link
Skim resequencing finely maps the downy mildew resistance loci RPF2 and RPF3 in spinach cultivars whale and Lazio
Horticulture Research / link
v3.8.4
A confinable female-lethal population suppression system in the malaria vector, Anopheles gambiae
Science Advances / link
v3.8.4; BCL convert
Characterization of an in vitro steatosis model simulating activated de novo lipogenesis in MAFLD patients
iScience / link
v3.9.5; BCL convert
Semaphorin 4B is an ADAM17-cleaved adipokine that inhibits adipocyte differentiation and thermogenesis
Molecular Metabolism / link
Secondary findings in a large Pakistani cohort tested with whole genome sequencing
Life Science Alliance / link
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
The Quebec Dental Anomalies Registry: Identifying genes for rare disorders
PNAS Nexus / link
Enrichment pipeline v3.9.5
Codon affinity in mitochondrial DNA shapes evolutionary and somatic fitness
-- / link
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
Identification of 13 Novel Loci in a Genome-Wide Association Study on Taiwanese with Hepatocellular Carcinoma
International Journal of Molecular Sciences / link
RNA; v3.7
Streptococcus mutans inhibits the growth of Enterococcus via the non-ribosomal cyclic peptide mutanobactin
-- / link
v3.10.12
Efficient sex separation by exploiting differential alternative splicing of a dominant marker in Aedes aegypti
PLOS Genetics / link
v3.8.4; BCL convert
Genetic architecture of telomere length in 462,675 UK Biobank whole-genome sequences
-- / link
Germline pipeline
Sequencing 4.3 million mutations in wheat promoters to understand and modify gene expression
Proceedings of the National Academy of Sciences / link
Sex and molecular differences in cardiovascular parameters at peak influenza disease in mice
Physiological Genomics / link
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
DRAGEN server; v3.9.3
Pharmacological inhibition of TBK1/IKKε blunts immunopathology in a murine model of SARS-CoV-2 infection
Nature Communications / link
BCL convert
IRF7 and UNC93B1 variants in an infant with recurrent herpes simplex virus infection
The Journal of Clinical Investigation / link
v3.6.3
Structural basis of spike RBM-specific human antibodies counteracting broad SARS-CoV-2 variants
Communications Biology / link
COVID Lineage
Syngap1 Disruption Induced by Recombination between Inverted loxP Sites Is Associated with Hippocampal Interneuron Dysfunction
eNeuro / link
ApoE isoform– and microbiota-dependent progression of neurodegeneration in a mouse model of tauopathy
Science / link
abstract; DRAGEN server; remove; v3.9.3
Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation
Nature Communications / link
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
v4.0; Variant calling
Functional assessment of homozygous ALDH18A1 variants reveals alterations in amino acid and antioxidant metabolism
Human Molecular Genetics / link
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
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
BCL convert
25-hydroxycholesterol mediates brain cytokine production and neutrophil infiltration in a mouse model of lipopolysaccharide-induced neuroinflammation
-- / link
DRAGEN server; alignment; v3.9.3; RNA quantification
Non-invasive mapping of systemic neutrophil dynamics upon cardiovascular injury
Nature Cardiovascular Research / link
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
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
Genotypic and phenotypic homogeneity of vaginal and rectal yeast isolates from recurrent vulvovaginal candidiasis
-- / link
The Landscape of Clinical Whole Genome Sequencing and the Emergence of Rapid Genetic Diagnosis in Critical Care
Advances in Molecular Pathology / link
review
Advances in the discovery and analyses of human tandem repeats
Emerging topics in life sciences / link
review
iPSC–derived retinal pigmented epithelial cells from patients with macular telangiectasia show decreased mitochondrial function
The Journal of Clinical Investigation / link
alignment; v2.5.1
Selective adaptation of SARS-CoV-2 Omicron under booster vaccine pressure: a multicentre observational study
eBioMedicine / link
Functional analysis of recurrent CDC20 promoter variants in human melanoma
Communications Biology / link
DRAGEN server; v3.9.3
Real-Time Analysis of SARS-CoV-2-Induced Cytolysis Reveals Distinct Variant-Specific Replication Profiles
Viruses / link
Investigation into the genetics of fetal congenital lymphatic anomalies
Prenatal Diagnosis / link
alignment
APC-Related Phenotypes and Intellectual Disability in 5q Interstitial Deletions: A New Case and Review of the Literature
Genes / link
NLRP3 inflammasome activation and symptom burden in KRAS-mutated CMML patients is reverted by IL-1 blocking therapy
Cell Reports Medicine / link
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
Whole-Exome Sequencing and cfDNA Analysis Uncover Genetic Determinants of Melanoma Therapy Response in a Real-World Setting
International Journal of Molecular Sciences / link
Germline pipeline; Somatic pipeline
Luminal-Type Invasive Carcinoma in Association With Microglandular Adenosis/Atypical Microglandular Adenosis: A Case Report and Molecular Comparison
Cureus / link
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
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
Generation of anti-GD2 CAR macrophages from human pluripotent stem cells for cancer immunotherapies
Stem Cell Reports / link
A genetic mosaic mouse model illuminates the pre-malignant progression of basal-like breast cancer
Disease Models & Mechanisms / link
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
DNA pipeline; GBA caller; v4
Prenatal BRCA1 epimutations contribute significantly to triple-negative breast cancer development
Genome Medicine / link
v3.6.3
vcfdist: accurately benchmarking phased small variant calls in human genomes
Nature Communications / link
Performance analysis of conventional and AI-based variant callers using short and long reads
BMC Bioinformatics / link
DRAGEN-GATK
Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases
Genome Research / link
DRAGMAP
Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases
Scientific Data / link
Talniflumate abrogates mucin immune suppressive barrier improving efficacy of gemcitabine and nab-paclitaxel treatment in pancreatic cancer
Journal of Translational Medicine / link
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
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
Rare variant analyses validate known ALS genes in a multi-ethnic population and identifies ANTXR2 as a candidate in PLS
medRxiv / link
alignment
Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1
-- / link
BCL convert
Fibrolamellar hepatocellular carcinoma: a case report and gene analysis
Surgical Case Reports / link
RNA pipeline v3.5.7
Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets
Nature Communications / link
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
v4.2
PALB2 Variants Extend the Mutational Profile of Hungarian Patients with Breast and Ovarian Cancer
Cancers / link
Enrichment pipeline
Integrative miRNA-mRNA network analysis to identify crucial pathways of salinity adaptation in brain transcriptome of Labeo rohita
Frontiers in Genetics / link
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
Germline; Joint genotyping
The choroidal nervous system: a link between mineralocorticoid receptor and pachychoroid
Acta Neuropathologica / link
v3.8.4
LINE-1 regulates cortical development by acting as long non-coding RNAs
Nature Communications / link
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
Germline pipeline
Challenging interpretation of germline TP53 variants based on the experience of a national comprehensive cancer centre
Scientific Reports / link
BSSH; Germline pipeline
Antigen concentration, viral load, and test performance for SARS-CoV-2 in multiple specimen types
PLOS ONE / link
BSSH; COVID Lineage App
Tumor biology and immune infiltration define primary liver cancer subsets linked to overall survival after immunotherapy
Cell Reports Medicine / link
tumor-only mode
Comparative epidemic expansion of SARS-CoV-2 variants Delta and Omicron in the Brazilian State of Amazonas
Nature Communications / link
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
RNA
Resilience to autosomal dominant Alzheimer’s disease in a Reelin-COLBOS heterozygous man
Nature Medicine / link
Neutrophil extracellular traps formed during chemotherapy confer treatment resistance via TGFβ activation
Cancer cell / link
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
Enrichment
Comparison of the mutation patterns between tumor tissue and cell-free DNA in stage IV gastric cancer
Aging (Albany NY) / link
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
COVIDSeq
From gene to dose: Long-read sequencing and *-allele tools to refine phenotype predictions of CYP2C19
Frontiers in Pharmacology / link
Overview of the SARS-CoV-2 genotypes circulating in Latin America during 2021
Frontiers in Public Health / link
SEQUIN is an R/Shiny framework for rapid and reproducible analysis of RNA-seq data
Cell Reports Methods / link
Genetic Variants Associated with Bronchial Asthma Specific to the Population of the Russian Federation
Acta Naturae / link
Long-term risk associated with clonal hematopoiesis in patients with severe aortic valve stenosis undergoing TAVR
Clinical Research in Cardiology / link
Enrichment app
Classification and genetics of pediatric B-other acute lymphoblastic leukemia by targeted RNA sequencing
Blood Advances / link
RNA pipeline
A pathological autopsy of a case dying from omicron variant of COVID-19
Open Journal of Clinical & Medical Case Reports / link
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
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
v4.1.5
An Integrated Pipeline for Trio‐Rapid Genome Sequencing in Critically Ill Infants
Current Protocols / link
Comparative molecular profiling of pancreatic ductal adenocarcinoma of the head versus body/tail reveals differences in the tumor immune microenvironment (TIME)
-- / link
Genetic landscape of homologous recombination repair genes in early-onset/familial prostate cancer patients
-- / link
2022
Analysis of the Plastid Genome Sequence During Maize Seedling Development
Frontiers in Genetics / link
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
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
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
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
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
v3.5
Whole‐exome sequencing of a Saudi epilepsy cohort reveals association signals in known and potentially novel loci
Human Genomics / link
Acute stress induces severe neural inflammation and overactivation of glucocorticoid signaling in interleukin-18-deficient mice
Translational Psychiatry / link
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
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
Inherited and De Novo Variation in Lithuanian Genomes: Introduction to the Analysis of the Generational Shift
Genes / link
Genome Analysis in Sick Neonates and Infants: High-yield Phenotypes and Contribution of Small Copy Number Variations
The Journal of Pediatrics / link
v3.4
Differentially methylated CpGs in response to growth hormone administration in children with idiopathic short stature
Clinical Epigenetics / link
Concurrent inhibition of CDK2 adds to the anti-tumour activity of CDK4/6 inhibition in GIST
British Journal of Cancer / link
Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample
Genome Biology / link
DRAGEN comparison to other technologies
Cutting-Edge AI Technologies Meet Precision Medicine to Improve Cancer Care
Biomolecules / link
review
A Splice Variant of the MYH7 Gene Is Causative in a Family with Isolated Left Ventricular Noncompaction Cardiomyopathy
Genes / link
SNP calling
Lymphocytes Utilize Somatic Mutations, Epigenetic Silencing, and the Proteasome to Escape Truncated WASP Expression
Journal of Clinical Immunology / link
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
Identification of SARS-CoV-2 variants using viral sequencing for the Centers for Disease Control and Prevention genomic surveillance program
BMC Infectious Diseases / link
Cardiovascular Involvement in Pediatric FLNC Variants: A Case Series of Fourteen Patients
Journal of Cardiovascular Development and Disease / link
BSSH; Enrichment app
Comparison of calling pipelines for whole genome sequencing: an empirical study demonstrating the importance of mapping and alignment
Scientific Reports / link
comparison of DRAGEN with other technologies; v3.8.4
Molecular Epidemiological Investigations of Localized SARS-CoV-2 Outbreaks-Utility of Public Algorithms
Epidemiologia / link
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
Whole genome sequencing identifies candidate genes for familial essential tremor and reveals biological pathways implicated in essential tremor aetiology
eBioMedicine / link
DNA pipeline; SV caller
The Brazilian Rare Genomes Project: Validation of Whole Genome Sequencing for Rare Diseases Diagnosis
Frontiers in Molecular Biosciences / link
Genetic Dissection of TLR9 Reveals Complex Regulatory and Cryptic Pro-inflammatory Roles in Murine Lupus
Nature immunology / link
BCL convert
Whole-genome sequencing analysis of clozapine-induced myocarditis
The Pharmacogenomics Journal / link
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
COVID Lineage App; BSSH
Molecular Profiling of Liquid Biopsies for Precision Oncology
Advances in Experimental Medicine and Biology / link
review
Frequent HLA-DR loss on hematopoietic stem progenitor cells in patients with cyclosporine-dependent aplastic anemia carrying HLA-DR15
Leukemia / link
Congenital heart defects in molecularly confirmed KBG syndrome patients
American Journal of Medical Genetics Part A / link
Low rate of RNAemia in blood donations collected during the first wave of COVID-19 in France
Transfusion / link
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
RNA-seq Fusion Detection in Clinical Oncology
Computational Methods for Precision Oncology / link
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
v3.8.4
PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions
Cell Genomics / link
PrecisionFDA
Characteristics of Amelanotic Acantholytic-Like Melanoma Resembling Squamous Cell Carcinoma
Journal of cutaneous pathology / link
v3.8
Novel mutation of IFT140 in an infant with Mainzer-Saldino syndrome presenting with retinal dystrophy
Molecular Genetics and Metabolism Reports / link
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
BSSH; COVID Lineage App v3.5.10
A complete pedigree-based graph workflow for rare candidate variant analysis
Genome Research / link
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
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
COVID Lineage App; BSSH
Genome sequencing as a first-line diagnostic test for hospitalized infants
Genetics in Medicine / link
SARS-CoV-2 BA.1 and BA.2 coinfection detected by genomic surveillance in Brazil, January 2022
Archives of Virology / link
Whole-exome sequencing of BRCA-negative breast cancer patients and case–control analyses identify variants associated with breast cancer susceptibility
Human Genomics / link
BSSH; v3.5.7
Evaluating use of changing technologies for rapid next-generation sequencing in pediatrics
Pediatric Research / link
CNV
Chronic Myeloid Leukemia Failed Second Generation Tyrosine Kinase Inhibitor Patients' Molecular Interrogation Using Next Generation Sequencing
Blood / link
alignment; Variant calling
Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity
Human Genetics / link
v3.5.7; v3.6.3
Successful Laparoscopic Oviductal Artificial Insemination in the Endangered Tsushima Leopard Cat (Prionailurus bengalensis euptilurus)
Animals / link
CYP2C8, CYP2C9, and CYP2C19 Characterization Using Next-Generation Sequencing and Haplotype Analysis
The Journal of Molecular Diagnostics / link
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
RNA pipeline; miRNA expression
Fetal pharmacogenomics: A promising addition to complex neonatal care
Molecular Genetics and Metabolism / link
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
Bioinformatic Challenges Detecting Genetic Variation in Precision Medicine Programs
Frontiers in Medicine / link
review
CRAM compression: practical across-technologies considerations for large-scale sequencing projects
-- / link
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
alignment; Germline pipeline v3.2.8
Clonal Myeloid Heterogeneity in Older Autopsy Patients Determined By Multiple Bone Marrow Site Sequencing
Blood / link
ISGylation is increased in the peripheral blood mononuclear cells derived from symptomatic COVID-19 patients
Experimental Biology and Medicine / link
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
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
SV caller
Secure secondary utilization system of genomic data using quantum secure cloud
Scientific Reports / link
Genotyping of Circulating Free DNA Enables Monitoring of Tumor Dynamics in Synovial Sarcomas
Cancers / link
Somatic pipeline; Enrichment pipeline; BSSH
Evaluating the analytical validity of mutation calling pipeline for tumor whole exome sequencing
-- / link
DRAGEN comparison to other technologies
HiCUP-Plus: a fast open-source pipeline for accurately processing large scale Hi-C sequence data
-- / link
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
Assessing the risk stratification of breast cancer polygenic risk scores in two Brazilian samples
-- / link
DRAGEN-GATK; DNA pipeline; v3.6.4
Germline Variants Associated with Nasopharyngeal Carcinoma Predisposition Identified through Whole-Exome Sequencing
Cancers / link
v3.8.4
1029 genomes of self-declared healthy individuals from India reveal prevalent and clinically relevant cardiac ion channelopathy variants
Human Genomics / link
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
Forensic Application of Snp-Targeted Next-Generation Sequencing on Korean Kinship Analysis
-- / link
BSSH; Germline pipeline
Somatic and Germline Variant Calling from Next-Generation Sequencing Data
Computational Methods for Precision Oncology / link
Chronic reduction of store operated Ca2+ entry is viable therapeutically but is associated with cardiovascular complications
The Journal of Physiology / link
Differential expression pipeline v3.6.3; RNA pipeline v3.6.3
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
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
protocol
Refining the Camelus dromedarius Myostatin Gene Polymorphism through Worldwide Whole-Genome Sequencing
Animals / link
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
RNA pipeline v3.6.3
Assessing reproducibility of inherited variants detected with short-read whole genome sequencing
Genome Biology / link
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
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
Inhibition of the Phosphatidylinositol-3 Kinase Pathway Using Bimiralisib in Loss-of-Function NOTCH1-Mutant Head and Neck Cancer
The Oncologist / link
v3
Whole-genome Sequencing of SARS-CoV-2: Using Phylogeny and Structural Modeling to Contextualize Local Viral Evolution
Military Medicine / link
A guide for the diagnosis of rare and undiagnosed disease: beyond the exome
Genome Medicine / link
review
CD19 expression is maintained in DLBCL patients after treatment with tafasitamab plus lenalidomide in the L-MIND study
Leukemia & Lymphoma / link
v3.4
A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of “Genetic Purging” and Genomic Stability
Genes / link
BSSH; Germline pipeline v3.7.5
Emergence and spreading of the largest SARS-CoV-2 deletion in the Delta AY.20 lineage from Uruguay
Gene Reports / link
BSSH
Genomic and epidemiologic surveillance of SARS-CoV-2 in Southern Brazil and identification of a new Omicron-L452R sublineage
Virus Research / link
BSSH
Similarity Index–Probabilistic Confidence Estimation of SARS-CoV-2 Strain Relatedness in Localized Outbreaks
Epidemiologia / link
COVID Lineage
Clinical phenotypes and outcomes associated with SARS-CoV-2 variant Omicron in critically ill French patients with COVID-19
Nature Communications / link
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
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
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
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
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
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
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
COVIDSeq Test pipeline
Immediate reinfection with Omicron variant after clearance of a previous SARS-CoV-2 infection
Journal of Infection and Public Health / link
Next generation sequencing data analysis pipeline of Children's Hospital of Fudan University and its clinical application
Chinese Journal of Evidence-Based Pediatrics / link
Questioning the Association of the STMN2 Dinucleotide Repeat With Amyotrophic Lateral Sclerosis
Neurology Genetics / link
v3.8
Mapping and selection of downy mildew resistance in spinach cv. whale by low coverage whole genome sequencing
Frontiers in Plant Science / link
v3.8.4; SNP
Molecular dissection of a hyper-aggressive CBFB-MYH11/FLT3-ITD–positive acute myeloid leukemia
Journal of Translational Medicine / link
Germline Pipeline; v3.6.3; Somatic pipeline; BSSH
Premature aging in mice with error-prone protein synthesis
Science Advances / link
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
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
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
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
v3.3.7
Curated variation benchmarks for challenging medically relevant autosomal genes
Nature Biotechnology / link
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
RNA pathogen detection
TRAPPC9-CDG: A novel congenital disorder of glycosylation with dysmorphic features and intellectual disability
Genetics in Medicine / link
v3.8.4
Early Genomic, Epidemiological, and Clinical Description of the SARS-CoV-2 Omicron Variant in Mexico City
Viruses / link
COVID-19 & differential effects in twins: Insights from Placenta Pathology
Placenta / link
BSSH; COVID Lineage Pipeline
Recurrent switch 2 domain RAC2 mutations in intravascular large B-cell lymphoma
Blood Advances / link
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
v3.6.3
Whole exome sequencing reveals potentially pathogenic variants in a small subset of premenopausal women with idiopathic osteoporosis
Bone / link
alignment
Immunoinformatics approach to epitope-based vaccine design against the SARS-CoV-2 in Bangladeshi patients
Journal of Genetic Engineering and Biotechnology / link
RNA pathogen detection; BSSH; v3.5.14
Breakthrough Covid‐19 infections in vaccinated recipients of allogeneic stem cell transplantation
EJHaem / link
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
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
CNV caller
Clinical and Molecular Spectrum of Sporadic Vascular Malformations: A Single-Center Study
Biomedicines / link
mosaicism; Somatic pipeline v3.6.3
Human genetics uncovers MAP3K15 as an obesity-independent therapeutic target for diabetes
Science Advances / link
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
Variant calling; v3.6.3
Molecular characterization of ESR1 variants in breast cancer
Breast Cancer Research and Treatment / link
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
v2.03
Antibody titers and neutralizing activity in cases of COVID-19 after a single dose of vaccination
Journal of Infection and Chemotherapy / link
COVID Lineage App v3.5.9
Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2
eBioMedicine / link
COVIDSeq Test pipeline; DRAGEN server
Understanding the mechanism of the SARS CoV-2 coinfection with other respiratory viruses
-- / link
Pathogen detection app
Identification of risk variants related to malignant tumors in children with birth defects by whole genome sequencing
Biomarker Research / link
Genome Sequences of 408 SARS-CoV-2 Strains Obtained from Nasopharyngeal Swabs in La Araucanía Region, Southern Chile
Microbiology Resource Announcements / link
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
COVID Lineage Pipeline v3.5.0
Genomic surveillance of SARS-CoV-2 in the state of Delaware reveals tremendous genomic diversity
PLOS ONE / link
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
A novel autosomal dominant GREB1L variant associated with non-syndromic hearing impairment in Ghana
BMC Medical Genomics / link
alignment; Germline pipeline v3.4.12
Genetic Appraisal of Hereditary Muscle Disorders In A Cohort From Mumbai, India
Journal of Neuromuscular Diseases / link
Gene-SCOUT: identifying genes with similar continuous trait fingerprints from phenome-wide association analyses
Nucleic Acids Research / link
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
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
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
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
Germline pipeline v3.2.8
Intragenic inversions in NF1 gene as pathogenic mechanism in neurofibromatosis type 1
European Journal of Human Genetics / link
Gene fusions and oncogenic mutations in MLH1 deficient and BRAFV600E wild-type colorectal cancers
Virchows Archiv / link
v3.8.4
Syndromic Microphthalmia 9: Role of rapid genome sequencing and novel mutations in STRA6 gene
Progress in Pediatric Cardiology / link
Syrian hamsters as a model of lung injury with SARS-CoV-2 infection: Pathologic, physiologic, and detailed molecular profiling
Translational Research / link
Whole exome sequencing reveals novel risk genes of pituitary neuroendocrine tumors
PLOS ONE / link
Somatic pipeline
SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic
Viruses / link
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
Whole Exome Sequencing of Patients With Heritable and Idiopathic Pulmonary Arterial Hypertension in Central Taiwan
Frontiers in Cardiovascular Medicine / link
Case report: Genomic screening for inherited cardiac conditions in Ecuadorian mestizo relatives: Improving familial diagnose
Frontiers in Cardiovascular Medicine / link
Enrichment pipeline v3.9.5
Identification of genomic signatures and multiple lineage markers from the second and third wave samples of COVID-19 in Western Rajasthan, India
-- / link
COVID Lineage App
Pathogenic Variants in ZSWIM7 Cause Primary Ovarian Insufficiency
The Journal of Clinical Endocrinology & Metabolism / link
v3.8.4
GATA2 Deficiency in Adult Life Is Characterized by Phenotypic Diversity and Delayed Diagnosis
Frontiers in Immunology / link
v3.8
A patient with mosaic USP9X gene variant
European Journal of Medical Genetics / link
BSSH; Enrichment app; Variant annotation; Variant calling
Local genomic sequencing enhances COVID-19 surveillance in the Northern Territory of Australia
Pathology / link
BSSH; COVID Lineage Pipeline
Rapid genome sequencing identifies novel variants in complement factor I
Molecular Case Studies / link
SNV
Increased prevalence of clonal hematopoiesis of indeterminate potential in hospitalized patients with COVID-19
Frontiers in Immunology / link
Enrichment app
A Multi-Disciplinary Team Approach to Genomic Testing for Drug-Resistant Epilepsy Patients—The GENIE Study
Journal of Clinical Medicine / link
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
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
Characteristics of 24 SARS-CoV-2-Sequenced Reinfection Cases in a Tertiary Hospital in Spain
Frontiers in Microbiology / link
COVID Lineage App
Blockade of the protease ADAM17 ameliorates experimental pancreatitis
Proceedings of the National Academy of Sciences / link
BCL convert
Transcriptional Profiling of Malignant Melanoma Reveals Novel and Potentially Targetable Gene Fusions
Cancers / link
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
Identical IFT140 Variants Cause Variable Skeletal Ciliopathy Phenotypes—Challenges for the Accurate Diagnosis
Frontiers in Genetics / link
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
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
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
BSSH; Enrichment
Establishment of Novel Neuroendocrine Carcinoma Patient-Derived Xenograft Models for Receptor Peptide-Targeted Therapy
Cancers / link
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
SNP calling
Genetic analysis for type 1 diabetes genes in juvenile dermatomyositis unveils genetic disease overlap
Rheumatology / link
v3.3.7
Muscle Biopsy: A Requirement for Precision Medicine in Adult-Onset Myopathy
Journal of Clinical Medicine / link
v3.7.5
Comparison of different sequencing techniques for identification of SARS-CoV-2 variants of concern with multiplex real-time PCR
PLOS ONE / link
Somatic pipeline; BSSH
Phylogenetic and amino acid signature analysis of the SARS-CoV-2s lineages circulating in Tunisia
Infection, Genetics and Evolution / link
RNA pathogen detection pipeline
A patient with Beta-Propeller Protein-Associated Neurodegeneration: a new missense mutation of the gene
Journal of Epileptology / link
alignment; Variant calling
TBX3 and EFNA4 Variant in a Family with Ulnar-Mammary Syndrome and Sagittal Craniosynostosis
Genes / link
Germline; v3.9
Characterization of RNF43 frameshift mutations that drive Wnt ligand- and R-spondin-dependent colon cancer
The Journal of Pathology / link
The study of cancer cell in stromal environment through induced pluripotent stem cell–derived mesenchymal stem cells
Journal of the Chinese Medical Association / link
Convergence between germline and somatic mutations in pancreatic neuroendocrine tumors
European Journal of Endocrinology / link
A genome sequencing system for universal newborn screening, diagnosis, and precision medicine for severe genetic diseases
American Journal of Human Genetics / link
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
Germline pipeline v3.4.5
Genetic Characterization in High-Risk Individuals from a Low-Resource City of Peru
Cancers / link
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
v3.9
The Identification of Novel CYP2D6 Variants in US Hmong: Results From Genome Sequencing and Clinical Genotyping
Frontiers in Pharmacology / link
v2.5.3
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
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
Human Papillomavirus Integration Strictly Correlates with Global Genome Instability in Head and Neck Cancer
Molecular Cancer Research / link
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
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
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
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
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
From molecules to genomic variations: Accelerating genome analysis via intelligent algorithms and architectures
Computational and Structural Biotechnology Journal / link
review
Case Report: Bi-allelic missense variant in the desmocollin 3 gene causes hypotrichosis and recurrent skin vesicles
Frontiers in Genetics / link
BSSH; SV caller
Capsicum hypocotyls mycobiome diversity is unaffected by Phytophthora capsici inoculation
Physiological and Molecular Plant Pathology / link
BSSH
Longitudinal Characterization of a Neutralizing and Total Antibody Response in Patients with Severe COVID-19 and Fatal Outcomes
Vaccines / link
COVIDSeq Test pipeline; BSSH
SARS-CoV-2 Omicron Variant in Croatia—Rapid Detection of the First Case and Cross-Border Spread
Pathogens / link
Whole genome sequencing identifies rare genetic variants in familial pancreatic cancer patients
Annals of Human Genetics / link
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
alignment
GATA1 controls numbers of hematopoietic progenitors and their response to autoimmune neuroinflammation
Blood Advances / link
Genome pipeline
Validation of reduced S-gene target performance and failure for rapid surveillance of SARS-CoV-2 variants
PLOS ONE / link
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
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
v3.3.4
Preliminary Experience of Liquid Biopsy in Lung Cancer Compared to Conventional Assessment: Light and Shadows
Journal of Personalized Medicine / link
DRAGEN server; TSO app
Artificial-Intelligence-Assisted Discovery of Genetic Factors for Precision Medicine of Antiplatelet Therapy in Diabetic Peripheral Artery Disease
Biomedicines / link
v3.6.3; Germline pipeline
STRipy: A graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data
Human Mutation / link
ExpansionHunter
Simple Saliva Sample Collection for the Detection of SARS-CoV-2 Variants Compared With Nasopharyngeal Swab Sample
Archives of Pathology & Laboratory Medicine / link
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
Somatic pipeline; tumor-only
Low-frequency variants in mildly symptomatic vaccine breakthrough infections presents a doubled-edged sword
Journal of Medical Virology / link
SARS-CoV-2 Lineage P.4 Detection in Southeast Brazil: A Retrospective Genomic and Clinical Overview
COVID / link
The SARS-CoV-2 Delta (B.1.617.2) variant with spike N501Y mutation in the shadow of Omicron emergence
Heliyon / link
COVID Lineage Pipeline
Seminal Microbiota of Idiopathic Infertile Patients and Its Relationship With Sperm DNA Integrity
Frontiers in Cell and Developmental Biology / link
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
alignment
A thermostable Cas12b from Brevibacillus leverages one-pot discrimination of SARS-CoV-2 variants of concern
eBioMedicine / link
Sclerostin ablation prevents aortic valve stenosis in mice
American Journal of Physiology-Heart and Circulatory Physiology / link
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
v3.7.5
The variant catalogue pipeline: A workflow to generate a background variant library from Whole Genome Sequences
-- / link
Inhibition of KRAS, MEK and PI3K Demonstrate Synergistic Anti-Tumor Effects in Pancreatic Ductal Adenocarcinoma Cell Lines
Cancers / link
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
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
SARS-CoV-2 and post-donation information: a one-year experience of the French haemovigilance network
Blood Transfusion = Trasfusione Del Sangue / link
Disruption of the HIF-1 pathway in individuals with Ollier disease and Maffucci syndrome
PLOS Genetics / link
Variant calling; alignment
Cancer-driving mutations are enriched in genic regions intolerant to germline variation
Science Advances / link
Effectiveness and protection duration of Covid-19 vaccines and previous infection against any SARS-CoV-2 infection in young adults
Nature Communications / link
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
BCL convert
Genomic Snapshot of SARS-CoV-2 in Migrants Entering Through Mediterranean Sea Routes
Frontiers in Public Health / link
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
TruSight Software Suite
A Mesenchymal Tumor Cell State Confers Increased Dependency on the BCL-XL Antiapoptotic Protein in Kidney Cancer
Clinical Cancer Research / link
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
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
DNA pipeline
Modeling colorectal cancer: A bio-resource of 50 patient-derived organoid lines
Journal of Gastroenterology and Hepatology / link
alignment; v2.4.5
HLA-associated outcomes in peanut oral immunotherapy trials identify mechanistic and clinical determinants of therapeutic success
Frontiers in Immunology / link
Germline small variant caller
Cost Efficacy of Rapid Whole Genome Sequencing in the Pediatric Intensive Care Unit
Frontiers in Pediatrics / link
Variant calling; alignment
RNA sequence analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic patients with COVID-19
International Journal of Infectious Diseases / link
Targeting MLL Methyltransferases Enhances the Antitumor Effects of PI3K Inhibition in Hormone Receptor–positive Breast Cancer
Cancer Research Communications / link
Distinct diagnostic trajectories in NBAS-associated acute liver failure highlights the need for timely functional studies
JIMD Reports / link
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
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
COVID Lineage App v3.3.4
Candidate Modifier Genes for the Penetrance of Leber’s Hereditary Optic Neuropathy
International Journal of Molecular Sciences / link
v3.7.5
Stratum Corneum Ceramide Profiles Provide Reliable Indicators of Remission and Potential Flares in Atopic Dermatitis
Journal of Investigative Dermatology / link
Endocannabinoid dysfunction in neurological disease: neuro-ocular DAGLA-related syndrome
Brain / link
v3.8
SWAN pathway-network identification of common aneuploidy-based oncogenic drivers
Nucleic Acids Research / link
From Alpha to Delta—Genetic Epidemiology of SARS-CoV-2 (hCoV-19) in Southern Poland
Pathogens / link
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
Enrichment pipeline
Adaptive immune responses in vaccinated patients with symptomatic SARS-CoV-2 Alpha infection
JCI Insight / link
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
v3.10; ICA
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
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
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
Pharmacogenomic study of heart failure and candesartan response from the CHARM programme
ESC Heart Failure / link
AWS; Germline pipeline
LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays
Briefings in Bioinformatics / link
Variant calling
A systems biology approach identifies candidate drugs to reduce mortality in severely ill patients with COVID-19
Science Advances / link
alignment; Epigenome pipeline v3.4.5
Balanced chromosomal rearrangements offer insights into coding and noncoding genomic features associated with developmental disorders
-- / link
Ethylmalonic encephalopathy masquerading as meningococcemia
Cold Spring Harbor Molecular Case Studies / link
Individualized Mini-Panel Sequencing of ctDNA Allows Tumor Monitoring in Complex Karyotype Sarcomas
International Journal of Molecular Sciences / link
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
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
Methylation pipeline; BSSH
Identifying SARS-CoV-2 Variants of Concern through Saliva-Based RT-qPCR by Targeting Recurrent Mutation Sites
Microbiology Spectrum / link
v3.5.3
Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota
Communications Biology / link
COVID Lineage App; BSSH
Massively parallel identification of functionally consequential noncoding genetic variants in undiagnosed rare disease patients
Scientific Reports / link
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
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
Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function
International Journal of Molecular Sciences / link
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
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
Aberrant expression of agouti signaling protein (ASIP) as a cause of monogenic severe childhood obesity
Nature Metabolism / link
v3.7.5
Whole-Genome Sequencing of ST2 A. baumannii Causing Bloodstream Infections in COVID-19 Patients
Antibiotics / link
Rare and common variants in ROM1 and PRPH2 genes trans-modify Stargardt/ABCA4 disease
PLOS Genetics / link
v2.5.1
Exome sequencing of families from Ghana reveals known and candidate hearing impairment genes
Communications Biology / link
Germline pipeline v3.2.8
Severe Acute Respiratory Syndrome Coronavirus 2 Delta Vaccine Breakthrough Transmissibility in Alachua County, Florida
Clinical Infectious Diseases / link
In Vitro Activity of Sulbactam–Durlobactam against Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates: A Multicentre Report from Italy
Antibiotics / link
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
alignment
Helicobacter pylori actively suppresses innate immune nucleic acid receptors
Gut Microbes / link
v3.6.3
Interferon pathway lupus risk alleles modulate risk of death from acute COVID-19
Translational Research / link
onboard
Oncogenic RAS commandeers amino acid sensing machinery to aberrantly activate mTORC1 in multiple myeloma
Nature Communications / link
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
COVID Lineage App
A novel protein truncating mutation in L2HGDH causes L-2-hydroxyglutaric aciduria in a consanguineous Pakistani family
Metabolic Brain Disease / link
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
External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories
Journal of Clinical Microbiology / link
BSSH; COVID Lineage
NEDDylated Cullin 3 mediates the adaptive response to topoisomerase 1 inhibitors
Science Advances / link
v3.9.3
Novel subtype of mucopolysaccharidosis caused by arylsulfatase K (ARSK) deficiency
Journal of Medical Genetics / link
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
alignment
Biallelic truncating variants in ATP9A cause a novel neurodevelopmental disorder involving postnatal microcephaly and failure to thrive
Journal of Medical Genetics / link
BSSH; Germline pipeline v3.2.8
Integrated analyses of growth differentiation factor-15 concentration and cardiometabolic diseases in humans
eLife / link
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
alignment; v3.6.3
Protocol for unbiased, consolidated variant calling from whole exome sequencing data
STAR Protocols / link
Genomic surveillance: Circulating lineages and genomic variation of SARS-CoV-2 in early pandemic in Ceará state, Northeast Brazil
Virus Research / link
COVID Lineage App; BSSH
The rate of secondary genomic findings in the Saudi population
American Journal of Medical Genetics Part A / link
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
Variant calling
A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands
Frontiers in Microbiology / link
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
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
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
BCL convert
First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France
Journal of Medical Virology / link
Genetic changes associated with relapse in favorable histology Wilms tumor: A Children’s Oncology Group AREN03B2 study
Cell Reports Medicine / link
Germline pipeline; v3
Clinical and Virological Features of Patients Hospitalized with Different Types of COVID-19 Vaccination in Mexico City
Vaccines / link
COVIDSeq Test pipeline; BSSH
The Easy-to-Use SARS-CoV-2 Assembler for Genome Sequencing: Development Study
JMIR Bioinformatics and Biotechnology / link
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
Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study
eLife / link
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
Structural variant analysis of a cancer reference cell line sample using multiple sequencing technologies
Genome Biology / link
Ataxia-Telangiectasia Mutated Loss of Heterozygosity in Melanoma
International Journal of Molecular Sciences / link
Germline pipeline; Somatic pipeline
COVIDSeq as Laboratory Developed Test (LDT) for Diagnosis of SARS-CoV-2 Variants of Concern (VOC)
Archives of clinical and biomedical research / link
BSSH
A Novel CRISPR Interference Effector Enabling Functional Gene Characterization with Synthetic Guide RNAs
The CRISPR Journal / link
RNA pipeline v3.7.5
Approaches to long-read sequencing in a clinical setting to improve diagnostic rate
Scientific Reports / link
Whole-genome sequencing of chronic lymphocytic leukemia identifies subgroups with distinct biological and clinical features
Nature Genetics / link
RNA pipeline
Strategies to inhibit FGFR4 V550L-driven rhabdomyosarcoma
British Journal of Cancer / link
RNA pipeline; Somatic pipeline
The landscape of cancer-associated fibroblasts in colorectal cancer liver metastases
Theranostics / link
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
v3.8.4
Comprehensive single-cell transcriptional profiling defines shared and unique epithelial injury responses during kidney fibrosis
Cell metabolism / link
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
v3.8
Loss of FOCAD, operating via the SKI messenger RNA surveillance pathway, causes a pediatric syndrome with liver cirrhosis
Nature genetics / link
Genomic architecture of fetal central nervous system anomalies using whole-genome sequencing
NPJ Genomic Medicine / link
An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases
Nature Communications / link
v3.7
Assessing clinical utility of preconception expanded carrier screening regarding residual risk for neurodevelopmental disorders
NPJ Genomic Medicine / link
v3.7.5
Whole-genome sequencing reveals complex genomic features underlying anti-CD19 CAR T-cell treatment failures in lymphoma
Blood / link
Somatic pipeline
Genome-wide analyses of 200,453 individuals yield new insights into the causes and consequences of clonal hematopoiesis
Nature Genetics / link
Germline pipeline
SARS-CoV-2 and other respiratory pathogens are detected in continuous air samples from congregate settings
Nature Communications / link
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
v3.7.5
Ultra-deep sequencing validates safety of CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells
Nature Communications / link
Enrichment pipeline; Germline pipeline
Expansion and mechanistic insights into de novo DEAF1 variants in DEAF1-associated neurodevelopmental disorders
Human Molecular Genetics / link
alignment
Adult-onset CblC deficiency: a challenging diagnosis involving different adult clinical specialists
Orphanet Journal of Rare Diseases / link
Enrichment app v3.8.4
Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA
Cell Reports Medicine / link
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
COVIDSeq Test pipeline
Transient regulation of focal adhesion via Tensin3 is required for nascent oligodendrocyte differentiation
eLife / link
v3.6.3
Two-Period Study Results from a Large Italian Hospital Laboratory Attesting SARS-CoV-2 Variant PCR Assay Evolution
Microbiology Spectrum / link
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
Oncogenic lncRNAs alter epigenetic memory at a fragile chromosomal site in human cancer cells
Science Advances / link
A novel human monogenic obesity trait: severe early-onset childhood obesity caused by aberrant expression of agouti-signaling protein (ASIP): a case report
-- / link
v3.7.5
Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement
eLife / link
2021
Biallelic Variants in KIF17 Associated with Microphthalmia and Coloboma Spectrum
International Journal of Molecular Sciences / link
Germline pipeline v3.3.7
Clonal dynamics in a composite chronic lymphocytic leukemia and hairy cell leukemia-variant
Genes, Chromosomes and Cancer / link
Somatic pipeline; Enrichment pipeline; BSSH; CNV Baseline Builder
Role of chimeric transcript formation in the pathogenesis of birth defects
Congenital Anomalies / link
A novel de novo intronic variant in ITPR1 causes Gillespie syndrome
American Journal of Medical Genetics Part A / link
Genome Sequence of a SARS-CoV-2 Strain from a COVID-19 Clinical Sample from the Khagrachari District of Bangladesh
Microbiology Resource Announcements / link
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
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
Pan-Cancer Drivers Are Recurrent Transcriptional Regulatory Heterogeneities in Early-Stage Luminal Breast Cancer
Cancer Research / link
Somatic mode
Further confirmation of the association of SLC12A2 with non-syndromic autosomal-dominant hearing impairment
Journal of Human Genetics / link
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
Ultra-rapid emergency genomic diagnosis of Donahue syndrome in a preterm infant within 17 hours
American Journal of Medical Genetics Part A / link
DRAGEN server
High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing
PLOS ONE / link
COVIDSeq Test pipeline
Branching clonal evolution patterns predominate mutational landscape in multiple myeloma
American Journal of Cancer Research / link
Somatic pipeline v3.5.7
Topoisomerase II alpha inhibition can overcome taxane-resistant prostate cancer through DNA repair pathways
Scientific Reports / link
Accuracy of somatic variant detection workflows for whole genome sequencing experiments
-- / link
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
Somatic pipeline; tumor-only
Application of Massive Parallel DNA Sequencing to Diagnose Drug-Resistant Epilepsy in Children
Molecular Genetics, Microbiology and Virology / link
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
Nager syndrome in patient lacking acrofacial dysostosis: Expanding the phenotypic spectrum of SF3B4-related disease
American Journal of Medical Genetics. Part A / link
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
Exome sequencing in high and low fetal haemoglobin Arab-Indian haplotype sickle cell disease
British Journal of Haematology / link
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
Variant calling; alignment; v3.2.5
Recognition of plausible therapeutic agents to combat COVID-19: An omics data based combined approach
Gene / link
Long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders
HGG advances / link
v3.2.8
Comparison of multiple imputation algorithms and verification using whole-genome sequencing in the CMUH genetic biobank
BioMedicine / link
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
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
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
COVID Lineage App; BSSH
Targeting cancer stem cells in medulloblastoma by inhibiting AMBRA1 dual function in autophagy and STAT3 signalling
Acta Neuropathologica / link
BSSH; Differential expression; RNA pipeline
Reducing Sanger confirmation testing through false positive prediction algorithms
Genetics in Medicine / link
Germline pipeline
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
RNA pipeline
Artificial intelligence enables comprehensive genome interpretation and nomination of candidate diagnoses for rare genetic diseases
Genome Medicine / link
Variant calling; v3.2.8
Confirming putative variants at ≤ 5% allele frequency using allele enrichment and Sanger sequencing
Scientific Reports / link
Somatic pipeline
Diversity of genetic alterations of primary central nervous system lymphoma in Hispanic versus non-Hispanic patients
Cancer Treatment and Research Communications / link
Somatic pipeline
A Monoallelic Variant in REST Is Associated with Non-Syndromic Autosomal Dominant Hearing Impairment in a South African Family
Genes / link
alignment; v3.4.12; Germline Pipeline v3.2.8
Commonalities across computational workflows for uncovering explanatory variants in undiagnosed cases
Genetics in Medicine / link
High-Throughput Next-Generation Sequencing Respiratory Viral Panel: A Diagnostic and Epidemiologic Tool for SARS-CoV-2 and Other Viruses
Viruses / link
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 NF2p.Q459* SNV with potential clinical significance
Archives of Pathology and Clinical Research / link
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
v3.5
Detection of hypermethylation at H19DMR at amniocentesis in a fetus with overgrowth, distended abdomen and Beckwith-Wiedemann syndrome
Taiwanese Journal of Obstetrics and Gynecology / link
Methylation pipeline v3.8
Upregulation of Antiviral Factors That Inhibit HIV-1 Infection in Sickle Cell Disease
Blood / link
Differential Expression pipeline; RNA pipeline
IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes
Nucleic Acids Research / link
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
BSSH; Somatic mutation pipeline
Identification of a missense variant in SPDL1 associated with idiopathic pulmonary fibrosis
Communications Biology / link
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
BSSH; Metagenomics pipeline
Distinct Patterns of Emergence of SARS-CoV-2 Spike Variants including N501Y in Clinical Samples in Columbus Ohio
-- / link
RNA pathogen detection
Exome Sequencing Analysis of Familial Cases of Multiple Sclerosis and a Monozygotic Discordant Twin
Arabian Journal for Science and Engineering / link
Variant calling; alignment
Expanding the genotypic spectrum of ACTG2-related visceral myopathy
Molecular Case Studies / link
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
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
Inhibitory activity of medicinal mushroom Ganoderma lucidum on colorectal cancer by attenuating inflammation
Precision Clinical Medicine / link
[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
Coding-Complete Genome Sequences and Mutation Profiles of Nine SARS-CoV-2 Strains Detected from COVID-19 Patients in Bangladesh
Microbiology Resource Announcements / link
v3.5
Evaluation of two RT-PCR screening assays for identifying SARS-CoV-2 variants
Journal of Clinical Virology / link
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
BCL convert
Machine learning analysis using 77,044 genomic and transcriptomic profiles to accurately predict tumor type
Translational Oncology / link
demultiplexing
Whole genome mapping and identification of single nucleotide polymorphisms of four Bangladeshi individuals and their functional significance
BMC Research Notes / link
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
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
COVID Lineage v3.5.1
The LDLR, APOB, and PCSK9 Variants of Index Patients with Familial Hypercholesterolemia in Russia
Genes / link
Influence of age on the spread of SARS-CoV-2 variant B.1.1.7
Journal of Clinical Virology / link
COVIDSeq Test pipeline
Epidemiologically Linked COVID-19 Outbreaks at a Youth Camp and Men’s Conference — Illinois, June–July 2021
MMWR. Morbidity and Mortality Weekly Report / link
Genome Sequence of a SARS-CoV-2 P.1 Variant of Concern (20J/501Y.V3) from Bangladesh
Microbiology Resource Announcements / link
RNA pathogen detection
Immune cell residency in the nasal mucosa may partially explain respiratory disease severity across the age range
Scientific Reports / link
v1.1.15
Functional analysis of a de novo variant in the neurodevelopment and generalized epilepsy disease gene NBEA
Molecular Genetics and Metabolism / link
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
BSSH; Metagenomics pipeline
Introduction and rapid dissemination of SARS-CoV-2 Gamma Variant of Concern in Venezuela
Infection, Genetics and Evolution / link
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
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
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
v3.8
A ZFHX4 mutation associated with a recognizable neuropsychological and facial phenotype
European Journal of Medical Genetics / link
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
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
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
Sub-genic intolerance, ClinVar, and the epilepsies: A whole-exome sequencing study of 29,165 individuals
American Journal of Human Genetics / link
The Evolutionary Landscape of SARS-CoV-2 Variant B.1.1.519 and Its Clinical Impact in Mexico City
Viruses / link
v3.3
Nucleocapsid (N) Gene Mutations of SARS-CoV-2 Can Affect Real-Time RT-PCR Diagnostic and Impact False-Negative Results
Viruses / link
COVIDSeq Test pipeline
CYP2C9 Variations and Their Pharmacogenetic Implications Among Diverse South Asian Populations
Pharmacogenomics and Personalized Medicine / link
v3.6.3
Genotypic analysis of the female BPH/5 mouse, a model of superimposed preeclampsia
PLOS ONE / link
Germline pipeline
FFPE samples from cavitational ultrasonic surgical aspirates are suitable for RNA profiling of gliomas
PLOS ONE / link
RNA pipeline v3.7.5
Predicted Immunogenicity of CDK12 Biallelic Loss-of-Function Tumors Varies across Cancer Types
The Journal of Molecular Diagnostics / link
demultiplexing
Practical guide for managing large-scale human genome data in research
Journal of Human Genetics / link
review
Levodopa-responsive dystonia caused by biallelic PRKN exon inversion invisible to exome sequencing
Brain Communications / link
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
Novel mutations identified from whole-genome sequencing of SARS-CoV-2 isolated from Noakhali, Bangladesh
-- / link
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
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
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
BSSH; Enrichment app
Advances in Genomic Discovery and Implications for Personalized Prevention and Medicine: Estonia as Example
Journal of Personalized Medicine / link
review
Genome sequencing and genetic characterization of 17 SARS-CoV-2 viruses and spike protein analyses of isolates from Bangladeshi patients
-- / link
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
Mutational burden, MHC-I expression and immune infiltration as limiting factors for in situ vaccination by TNFα and IL-12 gene electrotransfer
Bioelectrochemistry / link
Variant calling; alignment
Whole Exome Sequencing Is the Minimal Technological Approach in Probands Born to Consanguineous Couples
Genes / link
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
alignment; Variant calling
Genetic Characterization of a Model Ciliopathy: Bardet–Biedl Syndrome
Journal of Pediatric Genetics / link
The spectrum of mitochondrial DNA (mtDNA) mutations in pediatric CNS tumors
Neuro-oncology Advances / link
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
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
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
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
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
Enabling fast and energy-efficient FM-index exact matching using processing-near-memory
The Journal of Supercomputing / link
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
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
The Quandary of DNA-Based Treatment Assessment in De Novo Metastatic Prostate Cancer in the Era of Precision Oncology
Journal of Personalized Medicine / link
Germline
Applications and challenges of high performance computing in genomics
CCF Transactions on High Performance Computing / link
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
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
VCFcontam: A Machine Learning Approach to Estimate Cross-Sample Contamination from Variant Call Data
-- / link
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
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
Molecular characterization of Kita-Kyushu lung cancer antigen (KK-LC-1) expressing carcinomas
Oncotarget / link
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
TCF12 controls oligodendroglial cell proliferation and regulates signaling pathways conserved in gliomas
-- / link
v3.6.3
Genomic epidemiology of the first epidemic wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Palestine
Microbial Genomics / link
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
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
Exome sequencing in obsessive–compulsive disorder reveals a burden of rare damaging coding variants
Nature Neuroscience / link
COVID-19 RT-PCR diagnostic assay sensitivity and SARS-CoV-2 transmission: A missing link?
-- / link
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
BSSH; Enrichment app
Sex- and Mutation-Specific p53 Gain-of-Function Activity in Gliomagenesis
Cancer Research Communications / link
Rapid whole genome sequencing impacts care and resource utilization in infants with congenital heart disease
npj Genomic Medicine / link
Newly emerged immunogenic neoantigens in established tumors enable hosts to regain immunosurveillance in a T-cell-dependent manner
International Immunology / link
alignment
Cloud-based genomics pipelines for ophthalmology: Reviewed from research to clinical practice
Journal for Modeling in Ophthalmology / link
review
Large-scale analysis of KMT2 mutations defines a distinctive molecular subset with treatment implication in gastric cancer
Oncogene / link
Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions
Nature Communications / link
COVID Lineage
Precision modeling of gall bladder cancer patients in mice based on orthotopic implantation of organoid-derived tumor buds
Oncogenesis / link
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
Analysis of Whole Genome Sequencing in a Cohort of Individuals with PHACE Syndrome Suggests Dysregulation of RAS/PI3K Signaling
-- / link
alignment
ITGB6-Knockout Suppresses Cholangiocarcinoma Cell Migration and Invasion with Declining PODXL2 Expression
International Journal of Molecular Sciences / link
alignment
Serine biosynthesis defect due to haploinsufficiency of PHGDH causes retinal disease
Nature metabolism / link
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
Emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States
Cell / link
COVIDSeq Test pipeline v1.3
Post-transcriptional circadian regulation in macrophages organizes temporally distinct immunometabolic states
Genome Research / link
alignment
Features of repertoire diversity and gene expression in human cytotoxic T cells following allogeneic hematopoietic cell transplantation
Communications Biology / link
v3.6.3
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
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
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
A study of elective genome sequencing and pharmacogenetic testing in an unselected population
Molecular Genetics & Genomic Medicine / link
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
Prediction of SARS-CoV-2 Variant Lineages Using the S1-Encoding Region Sequence Obtained by PacBio Single-Molecule Real-Time Sequencing
Viruses / link
Next-Generation Sequencing for Congenital Nephrotic Syndrome: A Multi-Center Cross-Sectional Study from India
Indian Pediatrics / link
Potential Diagnostic Value of the Differential Expression of Histone H3 Variants between Low- and High-Grade Gliomas
Cancers / link
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
BSSH; Germline pipeline v2.3
A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control
-- / link
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
v2.3.6
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
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
v3.6.3
Human sensorimotor organoids derived from healthy and amyotrophic lateral sclerosis stem cells form neuromuscular junctions
Nature Communications / link
MutScape: an analytical toolkit for probing the mutational landscape in cancer genomics
NAR Genomics and Bioinformatics / link
Bacteroides spp. promotes branched-chain amino acid catabolism in brown fat and inhibits obesity
iScience / link
v3.6.3
2020
Accuracy and efficiency of germline variant calling pipelines for human genome data
Scientific Reports / link
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
Eltrombopag for patients with moderate aplastic anemia or uni-lineage cytopenias
Blood Advances / link
Somatic pipeline
Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh
Microbiology Resource Announcements / link
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
Optimized trio genome sequencing (OTGS) as a first-tier genetic test in critically ill infants: practice in China
Human Genetics / link
v3.2.8; Genome pipeline
Assessing the NOTCH2NLC GGC expansion in European patients with essential tremor
Brain / link
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
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
somatic
A diploid assembly-based benchmark for variants in the major histocompatibility complex
Nature Communications / link
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
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
v3.2.2
Clinical and Genomic Evaluation of 207 Genetic Myopathies in the Indian Subcontinent
Frontiers in Neurology / link
v2.03
High-throughput SARS-CoV-2 and host genome sequencing from single nasopharyngeal swabs
-- / link
RNA pathogen detection; BSSH
Evaluation of NGS-based approaches for SARS-CoV-2 whole genome characterisation
Virus Evolution / link
v3.5.13
Germline and somatic albinism variants in amelanotic/hypomelanotic melanoma: Increased carriage of TYR and OCA2 variants
PLOS ONE / link
An Indian child with Coats plus syndrome due to mutations in STN1
American Journal of Medical Genetics Part A / link
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
Cerebellar ataxia with normal intellect associated with a homozygous truncating variant in CA8
Clinical Genetics / link
Sequence and annotation of 42 cannabis genomes reveals extensive copy number variation in cannabinoid synthesis and pathogen resistance genes
-- / link
Unified genotyper
Genotype‑phenotype analysis in Mowat‑Wilson syndrome associated with two novel and two recurrent ZEB2 variants
Experimental and Therapeutic Medicine / link
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
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
High-resolution analyses of human sperm dynamic methylome reveal thousands of novel age-related epigenetic alterations
Clinical Epigenetics / link
v2.6.3
Bi-Allelic Novel Variants in CLIC5 Identified in a Cameroonian Multiplex Family with Non-Syndromic Hearing Impairment
Genes / link
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
A de-novo NFIX mutation causes a case of neonatal lethal Marshall–Smith syndrome
Clinical Dysmorphology / link
Biallelic variants in two complex I genes cause abnormal splicing defects in probands with mild Leigh syndrome
Molecular Genetics and Metabolism / link
Variant calling; Joint genotyping; v2.6
A broad exome study of the genetic architecture of asthma reveals novel patient subgroups
-- / link
AWS; Germline pipeline v3.0.7
Targeting Epidermal Growth Factor Receptor (EGFR) in Pediatric Colorectal Cancer
Cancers / link
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
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
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
The potential impact of tumor suppressor genes on human gametogenesis: a case-control study
Journal of Assisted Reproduction and Genetics / link
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
BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks
Epigenetics & Chromatin / link
Comprehensive Analysis of CDC27 Related to Peritoneal Metastasis by Whole Exome Sequencing in Gastric Cancer
OncoTargets and therapy / link
A refined cell-of-origin classifier with targeted NGS and artificial intelligence shows robust predictive value in DLBCL
Blood Advances / link
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
BSSH; Enrichment app
Novel homozygous variant in WISP3 in a family with unrecognized progressive pseudorheumatoid dysplasia
Clinical Case Reports / link
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
Autophagy mitigates ethanol-induced mitochondrial dysfunction and oxidative stress in esophageal keratinocytes
PLoS ONE / link
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
Evaluation of the RAS signaling network in response to MEK inhibition using organoids derived from a familial adenomatous polyposis patient
Scientific Reports / link
Integrative immunogenomic analysis of gastric cancer dictates novel immunological classification and the functional status of tumor‐infiltrating cells
Clinical & Translational Immunology / link
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
2019
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
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
Higher Stability of Mutant mRNA As Compared to Wild-Type mRNA in Diffuse Large B-Cell Lymphoma
Blood / link
Genetics of intellectual disability in consanguineous families
Molecular Psychiatry / link
Variant calling; alignment
Resistance to autosomal dominant Alzheimer’s disease in an APOE3 Christchurch homozygote: a case report
Nature Medicine / link
Genome pipeline
Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics
Frontiers in Genetics / link
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
A semiautomated whole-exome sequencing workflow leads to increased diagnostic yield and identification of novel candidate variants
Molecular Case Studies / link
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
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
Landscape of Germline and Somatic Mitochondrial DNA Mutations in Pediatric Malignancies
Cancer Research / link
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
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
review
NARD: whole-genome reference panel of 1779 Northeast Asians improves imputation accuracy of rare and low-frequency variants
Genome Medicine / link
Virtual Grid Engine: a simulated grid engine environment for large-scale supercomputers
BMC Bioinformatics / link
Damaging Variants in Pro-Angiogenic Genes Impair Growth in Fetuses with Cardiac Defects
The Journal of pediatrics / link
Neonatal diabetes mellitus due to a novel variant in the INS gene
Cold Spring Harbor Molecular Case Studies / link
Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil
Nature Communications / link
Molecular Profiles and Metastasis Markers in Chinese Patients with Gastric Carcinoma
Scientific Reports / link
A Comprehensive Survey of Genomic Alterations in Gastric Cancer Reveals Recurrent Neoantigens as Potential Therapeutic Targets
BioMed Research International / link
Mutations in PDLIM5 are rare in dilated cardiomyopathy but are emerging as potential disease modifiers
Molecular Genetics & Genomic Medicine / link
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
alignment
2018
On the verge of diagnosis: Detection, reporting, and investigation of de novo variants in novel genes identified by clinical sequencing
Human Mutation / link
v2
Improving classification of melanocytic nevi: Association of BRAF V600E expression with distinct histomorphologic features
Journal of the American Academy of Dermatology / link
DRAGEN server
Comprehensive genetic testing for female and male infertility using next-generation sequencing
Journal of Assisted Reproduction and Genetics / link
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
Rapid whole-genome sequencing identifies a novel AIRE variant associated with autoimmune polyendocrine syndrome type 1
Cold Spring Harbor Molecular Case Studies / link
Whole‐exome sequencing in 20,197 persons for rare variants in Alzheimer's disease
Annals of Clinical and Translational Neurology / link
Urea Cycle Dysregulation Generates Clinically Relevant Genomic and Biochemical Signatures
Cell / link
Integrated genome sizing (IGS) approach for the parallelization of whole genome analysis
BMC Bioinformatics / link
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
Novel Factor XIII variant identified through whole-genome sequencing in a child with intracranial hemorrhage
Cold Spring Harbor Molecular Case Studies / link
2017
Genome-Wide Exome Analysis of Cmv5-Disparate Mouse Strains that Differ in Host Resistance to Murine Cytomegalovirus Infection
G3 Genes|Genomes|Genetics / link
Ultra-Fast Next Generation Human Genome Sequencing Data Processing Using DRAGENTM Bio-IT Processor for Precision Medicine
Open Journal of Genetics / link
A high-throughput molecular data resource for cutaneous neurofibromas
Scientific Data / link
alignment
Rapid whole-genome sequencing identifies a novel GABRA1 variant associated with West syndrome
Cold Spring Harbor Molecular Case Studies / link
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
Orion: Detecting regions of the human non-coding genome that are intolerant to variation using population genetics
PLOS ONE / link
alignment
Whole genome sequencing of an African American family highlights toll like receptor 6 variants in Kawasaki disease susceptibility
PLoS ONE / link
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
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
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