LPA Caller
The LPA Caller is capable of identifying the LPA Kringle-IV-2 (KIV-2) VNTR unit copy number from whole-genome sequencing (WGS) data. Due to high sequence similarity between the genes, a specialized caller is necessary to resolve the VNTR unit copy number.
The LPA Caller performs the following steps:
Determines total LPA KIV-2 VNTR unit copy number.
Determines the heterozygous LPA KIV-2 VNTR unit copy number if heterozygous KIV-2 markers are present.
Calls small variants in the LPA KIV-2 VNTR region based on the unit copy number along with allele counts from read information.
The LPA Caller requires WGS data aligned to a human reference genome with at least 30x coverage. Reference genome builds must be based on hg19, GRCh37, or hg38.
Total LPA KIV-2 VNTR Unit Copy Number
The first step of LPA calling is to determine the unit copy number of LPA KIV-2. Reads aligned to the LPA KIV-2 are counted. The counts in each region are corrected for GC-bias, and then normalized to a diploid baseline. The GC-bias correction and normalization factors are determined from read counts in 3000 preselected 2 kb regions across the genome. These 3000 normalization regions were randomly selected from the portion of the reference genome having stable coverage across population samples.
Heterozygous LPA KIV-2 VNTR Unit Copy Number
The second step of LPA calling is to determine the heterozygous unit copy numbert of LPA KIV-2. Heterozygous unit copy number is determined using two specific linked SNV sites that have been identified as a combined marker allele that is always present in every copy of the repeat unit concordantly. That is, if any copy of the repeat unit in an LPA haplotype contains the ALT alleles at those two SNV sites, then every copy of the repeat unit in that LPA haplotype contains the ALT alleles at those two sites. The relative read coverage for the ALT and REF cases at these sites can therefore be used to determine the proportions of overall copy numbers across the KIV repeat array that belong to each haplotype.
Small Variant Calling
2 small variants are detected from the read alignments. These variants occur in the LPA KIV-2 VNTR region where reads mapping to either of the 6 units in the reference are used for variant calling.
For each variant, reads containing either the variant allele or the nonvariant allele are counted and a binomial model is used to determine the likelihood for each possible variant allele copy number up to the maximum possible as determined from the LPA KIV-2 VNTR unit copy number.
LPA Output File
The LPA Caller generates a <output-file-prefix>.targeted.json file in the output directory. The output file is a JSON formatted file containing the fields below.
sample
The sample name.
string
dragenVersion
The version of DRAGEN.
string
lpa
The LPA targeted caller specific fields.
dictionary
The lpa fields are defined as below.
kiv2CopyNumber
Total KIV-2 unit copy number
float
refMarkerAlleleCopyNumber
Null if Homozygous REF/ALT markers call
float, null
Float if Heterozygous markers call and stores the KIV-2 unit copy number of the allele having REF markers
altMarkerAlleleCopyNumber
Null if Homozygous REF/ALT markers call
float, null
Float if Heterozygous markers call and stores the KIV-2 unit copy number of the allele having ALT markers
type
"Heterozygous markers call" if we observe both REF and ALT markers
string, "Heterozygous markers call", "Homozygous REF markers call", "Homozygous ALT markers call"
"Homozygous REF markers call" if we observe only REF markers
"Homozygous ALT markers call" if we observe only ALT markers
variants
List of known variants that were detected in the KIV-2 region.
list of variants
For the variants the fields are defined as below.
hgvs
HGVS identifier of the variant
string
qual
Phred QUAL score of the variant
double
altCopyNumber
Copy number of the ALT variant
double
altCopyNumberQuality
Phred QUAL copy number of the ALT variant
double
The LPA Caller also generates a <output-file-prefix>.targeted.vcf[.gz] file in the output directory. The output file is a VCFv4.2 formatted file possibly compressed.
JSON Output File Examples
Examples of the LPA Caller content in the output json file are shown below.
VCF Output File Examples
The following are example output files:
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