Dominant Sequences of Human Major Histocompatibility Complex Conserved Extended Haplotypes from HLA-DQA2 to DAXX

摘要: We resequenced and phased 27 kb of DNA within 580 the MHC class II region in 158 population chromosomes, most which were conserved extended haplotypes (CEHs) European descent or contained their centromeric fragments. determined single nucleotide polymorphism deletion-insertion alleles dominant sequences from HLA-DQA2 to DAXX for these CEHs. Nine 13 CEHs remained sufficiently intact possess a sequence extending at least DAXX, 230 HLA-DPB1. identified regions HLA-DQB1 instances eight “common” previously sequenced by Haplotype Project (MHP) representative those CEH sequences. Only two MHP had throughout one haplotype did not represent known anywhere region. recombination transition points other representation non-representation. Several pairs groups shared identity small blocks but significantly different (although still each separate CEH) surrounding regions. These patterns partly explain strong calculated linkage disequilibrium over only short (tens hundreds kilobases) distances context finite number observed megabase-length comprising half population's haplotypes. Our results provide clearer picture allelic structure architecture, improved regional markers, raise questions concerning hotspots.