Abstract
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.
Competing Interest Statement
X.S.L conducted the work while being on the faculty at DFCI, and is currently a board member and CEO of GV20 Therapeutics. H.L. is a consultant of Integrated DNA Technologies and on the Scientific Advisory Boards of Sentieon and Innozeen.
Footnotes
Email addresses: Li Song: lsong{at}ds.dfci.harvard.edu, Gali Bai: galib{at}ds.dfci.harvard.edu, X. Shirley Liu: xsliu.res{at}gmail.com, Bo Li: bo.li{at}utsouthwestern.edu, Heng Li: hli{at}ds.dfci.harvard.edu
Abbreviations
- MHC
- major histocompatibility complex
- HLA
- human leukocyte antigen
- KIR
- killer immunoglobulin-like receptor
- NK cell
- natural killer cell
- IPD
- Immuno Polymorphism Database
- WES
- whole-exome sequencing
- WGS
- whole-genome sequencing
- SNP
- single nucleotide polymorphism
- HPRC
- human pangenome reference consortium
- 1kGP
- 1000 Genome Project
- LRC
- leukocyte receptor complex
