P075Extended HLA haplotypes in a greek population by NGS technology

Abstract

Aim HLA alleles are observed in specific haplotypes due to Linkage Disequilibrium (LD) between certain alleles. Recent improvements in Next-Generation Sequencing (NGS) technologies accommodate the tight linkage disequilibrium between genes as well as the high degree of polymorphism of the MHC. In order to assign HLA haplotypes at allele level (4-fields) in a Greek population, in the context of 17th IHWS, 25 families including parents and siblings (95 subjects), all of Greek origin, were typed at 11 loci (HLA-A*, -B*, -C*, -DRB1*, DRB3/4/5*, -DQA1*, -DQB1*, -DPA1* and -DPB1*) by NGS technology. Methods Instrument and Chemistry: Illumina MiSeq, v2 chemistry, 300 cycles (2X150) and standard flow cell size. Illumina TruSight HLA v2.0 and Omixon Holotype HLA kits were used. HLA haplotype count and frequency (%) were estimated according to the number of parental haplotypes identified in the whole cohort. Additionally, haplotype count in families (N = 25) and subjects (N = 95) were calculated. Results HLA-A*01:01:01:01-C*07:01:01:01-B*08:01:01:01-DRB3*01:01:02:01-HLA-DRB1*03:01:01:01/02-DQA1*05:01:01:02-DQB1*02:01:01-DPA1*01:03:01:02-DPB1*04:01:01:01/02 haplotype was found in 3 members of 2 families (haplotype frequency 2%). All other haplotypes were observed once, giving haplotype frequency = 1%. Conclusions It is confirmed that the HLA-A*01-Cw*07-B*08-DRB1*03:01-DQB1*02 haplotype, defined by low-resolution molecular techniques, is the most common in Greeks, as in all Caucasians. These results are useful as reference data (controls) in disease association studies as well as in population genetics.