TY - JOUR
T1 - Extensive variation in gene copy number at the killer immunoglobulin-like receptor locus in humans
AU - Vendelbosch, Sanne
AU - de Boer, Martin
AU - Gouw, Remko A T W
AU - Ho, Cynthia K Y
AU - Geissler, Judy
AU - Swelsen, Wendy T N
AU - Moorhouse, Michael J
AU - Lardy, Neubury M
AU - Roos, Dirk
AU - van den Berg, Timo K
AU - Kuijpers, Taco W
PY - 2013
Y1 - 2013
N2 - Killer immunoglobulin-like receptors (KIRs) are involved in the regulation of natural killer cell cytotoxicity. Within the human genome seventeen KIR genes are present, which all contain a large number of allelic variants. The high level of homology among KIR genes has hampered KIR genotyping in larger cohorts, and determination of gene copy number variation (CNV) has been difficult. We have designed a multiplex ligation-dependent probe amplification (MLPA) technique for genotyping and CNV determination in one single assay and validated the results by next-generation sequencing and with a KIR gene-specific short tandem repeat assay. In this way, we demonstrate in a cohort of 120 individuals a high level of CNV for all KIR genes except for the framework genes KIR3DL3 and KIR3DL2. Application of our MLPA assay in segregation analyses of families from the Centre d'Etude du Polymorphisme Humaine, previously KIR-genotyped by classical techniques, confirmed an earlier reported duplication and resulted in the identification of a novel duplication event in one of these families. In summary, our KIR MLPA assay allows rapid and accurate KIR genotyping and CNV detection, thus rendering improved transplantation programs and oncology treatment feasible, and enables more detailed studies on the role of KIRs in human (auto)immunity and infectious disease.
AB - Killer immunoglobulin-like receptors (KIRs) are involved in the regulation of natural killer cell cytotoxicity. Within the human genome seventeen KIR genes are present, which all contain a large number of allelic variants. The high level of homology among KIR genes has hampered KIR genotyping in larger cohorts, and determination of gene copy number variation (CNV) has been difficult. We have designed a multiplex ligation-dependent probe amplification (MLPA) technique for genotyping and CNV determination in one single assay and validated the results by next-generation sequencing and with a KIR gene-specific short tandem repeat assay. In this way, we demonstrate in a cohort of 120 individuals a high level of CNV for all KIR genes except for the framework genes KIR3DL3 and KIR3DL2. Application of our MLPA assay in segregation analyses of families from the Centre d'Etude du Polymorphisme Humaine, previously KIR-genotyped by classical techniques, confirmed an earlier reported duplication and resulted in the identification of a novel duplication event in one of these families. In summary, our KIR MLPA assay allows rapid and accurate KIR genotyping and CNV detection, thus rendering improved transplantation programs and oncology treatment feasible, and enables more detailed studies on the role of KIRs in human (auto)immunity and infectious disease.
KW - DNA Copy Number Variations/genetics
KW - Gene Dosage/genetics
KW - Genetic Loci/genetics
KW - Genome, Human/genetics
KW - Genotype
KW - Humans
KW - Multiplex Polymerase Chain Reaction/methods
KW - Receptors, KIR/genetics
KW - Receptors, KIR3DL2/genetics
U2 - https://doi.org/10.1371/journal.pone.0067619
DO - https://doi.org/10.1371/journal.pone.0067619
M3 - Article
C2 - 23840750
SN - 1932-6203
VL - 8
SP - e67619
JO - PLOS ONE
JF - PLOS ONE
IS - 6
ER -