title: Allele-level haplotype frequencies and pairwise linkage disequilibrium for 14 KIR loci in 506 European-American individuals.
abstract: The immune responses of natural killer cells are regulated, in part, by killer cell immunoglobulin-like receptors (KIR). The 16 closely-related genes in the KIR gene system have been diversified by gene duplication and unequal crossing over, thereby generating haplotypes with variation in gene copy number. Allelic variation also contributes to diversity within the complex. In this study, we estimated allele-level haplotype frequencies and pairwise linkage disequilibrium statistics for 14 KIR loci. The typing utilized multiple methodologies by four laboratories to provide at least 2x coverage for each allele. The computational methods generated maximum-likelihood estimates of allele-level haplotypes. Our results indicate the most extensive allele diversity was observed for the KIR framework genes and for the genes localized to the telomeric region of the KIR A haplotype. Particular alleles of the stimulatory loci appear to be nearly fixed on specific, common haplotypes while many of the less frequent alleles of the inhibitory loci appeared on multiple haplotypes, some with common haplotype structures. Haplotype structures cA01 and/or tA01 predominate in this cohort, as has been observed in most populations worldwide. Linkage disequilibrium is high within the centromeric and telomeric haplotype regions but not between them and is particularly strong between centromeric gene pairs KIR2DL5∼KIR2DS3S5 and KIR2DS3S5∼KIR2DL1, and telomeric KIR3DL1∼KIR2DS4. Although 93% of the individuals have unique pairs of full-length allelic haplotypes, large genomic blocks sharing specific sets of alleles are seen in the most frequent haplotypes. These high-resolution, high-quality haplotypes extend our basic knowledge of the KIR gene system and may be used to support clinical studies beyond single gene analysis.
authors.affiliation: Center for International Blood and Marrow Transplant Research, Minneapolis, Minnesota, USA.
authors.forename: Cynthia
authors.initials: C
authors.lastname: Vierra-Green
authors.forename: David
authors.initials: D
authors.lastname: Roe
authors.forename: Lihua
authors.initials: L
authors.lastname: Hou
authors.forename: Carolyn Katovich
authors.initials: CK
authors.lastname: Hurley
authors.forename: Raja
authors.initials: R
authors.lastname: Rajalingam
authors.forename: Elaine
authors.initials: E
authors.lastname: Reed
authors.forename: Tatiana
authors.initials: T
authors.lastname: Lebedeva
authors.forename: Neng
authors.initials: N
authors.lastname: Yu
authors.forename: Mary
authors.initials: M
authors.lastname: Stewart
authors.forename: Harriet
authors.initials: H
authors.lastname: Noreen
authors.forename: Jill A
authors.initials: JA
authors.lastname: Hollenbach
authors.forename: Lisbeth A
authors.initials: LA
authors.lastname: Guethlein
authors.forename: Tao
authors.initials: T
authors.lastname: Wang
authors.forename: Stephen
authors.initials: S
authors.lastname: Spellman
authors.forename: Martin
authors.initials: M
authors.lastname: Maiers
mesh_terms: D000483:Alleles; D005787:Gene Frequency / Q000235:genetics*; D056426:Genetic Loci / Q000235:genetics*; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics*; D054340:Receptors, KIR / Q000235:genetics*; D014481:United States; D044465:White People / Q000235:genetics*
chemical_list: D054340:Receptors, KIR