Accurate and Efficient KIR Gene and Haplotype Inference From Genome Sequencing Reads With Novel K-mer Signatures.

ABSTRACT: The killer-cell immunoglobulin-like receptor (KIR) proteins evolve to fight viruses and mediate the body's reaction to pregnancy. These roles provide selection pressure for variation at both the structural/haplotype and base/allele levels. At the same time, the genes have evolved relatively recently by tandem duplication and therefore exhibit very high sequence similarity over thousands of bases. These variation-homology patterns make it impossible to interpret KIR haplotypes from abundant short-read genome sequencing data at population scale using existing methods. Here, we developed an efficient computational approach for in silico KIR probe interpretation (KPI) to accurately interpret individual's KIR genes and haplotype-pairs from KIR sequencing reads. We designed synthetic 25-b

SUBMITTER: Roe D 

PROVIDER: S-EPMC7727328 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature