Fig. 6

A Linkage disequilibrium between the KIV-2B haplotype and the genotype at position 86 of KIV-3 exon 1. For each KIV domain represented, exon 1 and exon 2 are shown. The bases shown above each exon 1 corresponds to positions 14, 41, and 86 (KIV-2B canonical positions). We identified a C at position 86 in KIV-3 exon 1 (CC genotype) in non-KIV-2B individuals. KIV-2B alleles present a T at position 86 in KIV-3 (corresponds to the reference sequence) while non-KIV-2B alleles would carry the C, resulting in a CC genotype in 70% of the non-KIV-2B individuals. B Workflow of the signature-based approach for KIV-2 variant calling in WES data: starting from the input aligned BAM file (step 1), the entire LPA region is screened in FASTQ format for the KIV-2B signature sequence and (step 2) each sample is redirected to the optimal ROI strategy for (step 3) KIV-2 read extraction. (step 4) The extracted reads are realigned to one reference KIV-2 repeat for (step 5) variant calling with mutserve, resulting in a VCF output file, which can subsequently be annotated (see Github repository in the Availability of data and materials section)