Abstract
The Killer-cell Immunoglobulin-like Receptor (KIR) gene complex has considerable biomedical importance. Patterns of polymorphism in the KIR region include variability in the gene content of haplotypes and diverse structural arrangements. Droplet digital PCR (ddPCR) was used to identify different haplotype motifs and to enumerate KIR copy number variants (CNVs). ddPCR detected a variety of KIR haplotype configurations in DNA from well-characterized cell lines. Mendelian segregation of ddPCR-estimated KIR2DL5 CNVs was observed in Gambian families and CNV typing of other KIRs was shown to be accurate when compared to an established quantitative PCR method.
Highlights
A highly polymorphic gene complex on chromosome 19q13.4 encodes the Killer-cell Immunoglobulin-like Receptors (KIRs) [1]
When one of the targets is an unlinked gene of invariant copy number, the ratio between the gene of interest and the invariant gene is a direct measure of the gene of interest copy number. In this proof of principle study, we show that droplet digital polymerase chain reaction (PCR) (ddPCR) can be used to perform molecular haplotype analysis and copy number variation (CNV) enumeration in the KIR system
KIR2DL5 linkage analysis Ten specimens of DNA derived from International Histocompatibility Workshop (IHW) cell lines were selected because standard quantitative PCR had indicated that they possessed at least one copy of KIR2DL5 and either or both of KIR2DL2 and KIR3DS1
Summary
A highly polymorphic gene complex on chromosome 19q13.4 encodes the Killer-cell Immunoglobulin-like Receptors (KIRs) [1]. As natural killer (NK) cell receptors, their roles in modulating outcomes of infectious diseases [2,3], transplantation [4] and pregnancy [5] are subjects of intense research, but their genotyping and subsequent use in association studies and histocompatibility matching are made difficult by the underlying structural and sequence complexity in the KIR region. Both haplotype structural variations [6] and KIR gene copy number variations (CNVs) [7,8] contribute to the diversity of the KIR system. An individual might have up to four copies of KIR2DL5
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