KIR genes

T1K

KIR (killer-cell immunoglobulin-like receptors) sit on natural killer cells and probe the HLA class I molecules of other cells. The KIR gene complex on chromosome 19 is highly variable: people differ in the number and type of their KIR genes. Genome genotypes KIR from sequence data.

KIR RECEPTOR · NK CELL HLA LIGAND · TARGET CELL KIR2DL1 inhibitory HLA-C group 2 C2 · lysine 80 KIR2DL2 / 2DL3 inhibitory HLA-C group 1 C1 · asparagine 80 KIR3DL1 inhibitory HLA-B Bw4 motif KIR3DL2 inhibitory HLA-A A*03 / A*11 If self HLA-I is missing (missing self), inhibition is lost and the NK cell is activated.

A variable gene complex

The KIR locus spans up to 14 genes that are not all present in every person. Two haplotype groups are distinguished: A haplotypes are mostly inhibitory, B haplotypes carry more activating KIR. This diversity arises from gene duplication and deletion and makes KIR as demanding as HLA.

How Genome genotypes

Genome uses T1K, which determines KIR and HLA alleles directly from short reads by matching against the IPD-KIR reference. T1K returns per-locus allele calls with quality scores. It replaces the earlier tool Geny and covers KIR genotyping and HLA typing in one step.

What Genome measures. Which KIR genes are present and in which alleles, each with a per-call quality score. The complex is shown as independent technical evidence alongside HLA typing.

Related topics

HLA typingKIR-HLA ligand context

Sources

  1. 1Song et al., 2023 T1K: efficient and accurate KIR and HLA genotyping with next-generation sequencing data. Genome Research 33:1093–1103. doi.org/10.1101/gr.277585.122
  2. 2Parham & Moffett, 2013 Variable NK cell receptors and their MHC class I ligands in immunity, reproduction and human evolution. Nature Reviews Immunology 13:133–144. doi.org/10.1038/nri3370
  3. 3Robinson et al., 2015 The IPD and IPD-IMGT/HLA Database: allele variant databases (IPD-KIR). Nucleic Acids Research 43:D423–D431. doi.org/10.1093/nar/gku1161