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Abstract
Killer cell immunoglobulin-like receptors (KIRs) are a set of inhibitory and activating immune receptors, on natural killer (NK) and T cells, encoded by a polymorphic cluster of genes on chromosome 19. Their best-characterized ligands are the human leukocyte antigen (HLA) molecules that are encoded within the major histocompatibility complex (MHC) locus on chromosome 6. There is substantial evidence that they play a significant role in immunity, reproduction, and transplantation, making it crucial to have techniques that can accurately genotype them. However, high-sequence homology, as well as allelic and copy number variation, make it difficult to design methods that can accurately and efficiently genotype all KIR genes. Traditional methods are usually limited in the resolution of data obtained, throughput, cost-effectiveness, and the time taken for setting up and running the experiments. We describe a method called quantitative KIR semi-automated typing (qKAT), which is a high-throughput multiplex real-time polymerase chain reaction method that can determine the gene copy numbers for all genes in the KIR locus. qKAT is a simple high-throughput method that can provide high-resolution KIR copy number data, which can be further used to infer the variations in the structurally polymorphic haplotypes that encompass them. This copy number and haplotype data can be beneficial for studies on large-scale disease associations, population genetics, as well as investigations on expression and functional interactions between KIR and HLA.
Highlights
In humans, the killer immunoglobulin-like receptor(KIR) locus is mapped on the long arm of chromosome 19 within the leukocyte receptor complex (LRC)
The results in the figure show the polymerase chain reaction (PCR) amplification plots observed on the qPCR software and the copy number data generated from the qPCR data
We described a novel semi-automated high-throughput method, called quantitative KIR semi-automated typing (qKAT), which facilitates copy number typing of Killer cell immunoglobulin-like receptors (KIRs) genes
Summary
The killer immunoglobulin-like receptor(KIR) locus is mapped on the long arm of chromosome 19 within the leukocyte receptor complex (LRC). QKAT consists of ten multiplex reactions, each of which targets two KIR loci and one reference gene of a fixed copy number in the genome (STAT6) used for the relative quantification of the KIR gene copy number[23] This assay has been successfully used in studies involving large population panels and disease cohorts on infectious diseases such as HCV, autoimmune conditions like type 1 diabetes, and pregnancy disorders such as preeclampsia, as well as providing a genetic underpinning to studies aimed at understanding the NK cell function[1,4,24,25,26]
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