T1K: efficient and accurate KIR and HLA genotyping with next-generation sequencing data

Killer immunoglobulin-like receptor (KIR) genes and human leukocyte antigen (HLA) genes are highly polymorphic in a population and play important roles in innate and adaptive immunity. We have developed a novel computational method T1K that can efficiently and accurately infer the KIR or HLA alleles from next-generation sequencing data. T1K is flexible and is compatible with various sequencing platforms including RNA-seq and genomic sequencing data. We applied T1K on CD8+ T cell single-cell RNA-seq data, and identified that KIR2DL4 allele expression levels were enriched in tumor-specific CD8+ T cells.