title: Genetic variation and hitchhiking between structurally polymorphic Alu insertions and HLA-A, -B, and -C alleles and other retroelements within the MHC class I region.
abstract: We investigated structurally polymorphic Alu insertions (POALINs) at five loci in the major histocompatibility complex (MHC) class I genomic region to determine their allele and haplotype frequencies and associations with the human leukocyte antigen (HLA)-A, -B, and -C genes in three populations, the Australian Caucasians, Japanese, and African Americans. The POALINs varied in allelic frequency between 0% and 42.3% with significant differences between populations at three of the five loci. The linkage disequilibrium (LD) between Alu insertions and the HLA-A, -B, or -C alleles and previously published polymorphic retroelements (four SVA and human endogenous retrovirus type 9 (HERVK9) loci) within the class I region of the MHC were calculated in pairwise analyses of haplotypes to show strong allelic associations and possible crossing-over events between some loci. Each POALIN was in significant LD with a variety of HLA-A, -B, or -C two-digit alleles probably as a result of hitchhiking. The POALINs helped to further stratify the HLA-A:B:C haplotypes into different POALIN:HLA-A:B:C haplotype frequencies. Of the multilocus haplotype analyses, the seven- and eight-locus haplotypes showed the largest number of differences between the populations, and fewer matched haplotypes between populations that ranged, for example, from 49% for HLA-B:HLA-A haplotypes to 7% for AluMICB:HLA-B:HLA-C:AluTF:AluHJ:HLA-A:AluHG:AluTF haplotypes in the Japanese. This comparative study of multilocus POALINs in the HLA class I region of three ethnic populations shows that POALINs alone or together with the HLA class I alleles and other retroelements are informative ancestral markers for assessing the interrelationship of HLA class I haplotype lineages, LD, and genetic diversity within the same and/or different populations.
authors: Centre for Forensic Science, The University of Western Australia, Nedlands, WA 6008, Australia. kulski@me.com
authors: J K
authors: JK
authors: Kulski
authors: A
authors: A
authors: Shigenari
authors: H
authors: H
authors: Inoko
mesh_terms: D000483:Alleles; D020087:Alu Elements; D044466:Asian People / Q000235:genetics; D005006:Ethnicity / Q000235:genetics; D005805:Genes, MHC Class I; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D015234:HLA-A Antigens / Q000737:chemistry / Q000235:genetics*; D015235:HLA-B Antigens / Q000737:chemistry / Q000235:genetics*; D015236:HLA-C Antigens / Q000737:chemistry / Q000235:genetics*; D006239:Haplotypes; D015395:Histocompatibility Antigens Class I / Q000737:chemistry / Q000235:genetics*; D000949:Histocompatibility Antigens Class II / Q000235:genetics; D006801:Humans; D015810:Linkage Disequilibrium; D011110:Polymorphism, Genetic; D044465:White People / Q000235:genetics
chemical_list: D015234:HLA-A Antigens; D015235:HLA-B Antigens; D015236:HLA-C Antigens; D015395:Histocompatibility Antigens Class I; D000949:Histocompatibility Antigens Class II