OR41: HLA-E POLYMORPHISM IN VIEW OF THE 1000 GENOMES PROJECT: A FULL LENGTH HLA-E SEQUENCING APPROACH REVEALS NEW AND NULL ALLELES

Abstract

The limited polymorphism of HLA-E is in sharp contrast with the classical HLA loci on chromosome 6. Two phenotypes, HLA-E∗01:01 and ∗01:03, have previously been characterized as functional relevant alleles in the innate (NK-cells) and the adaptive immune response (T-cells). Within the 1000 Genomes (1 KG) project the sequence variation of the complete human genome of 1092 individuals in 14 different populations has been determined with high-throughput platforms and is available in a public database combined with the information of other sources (e.g. dbSNP and ESP). We analyzed the sequence variation of HLA-E in this database and identified 117 new SNP’s or indel positions compared to the HLA-E alleles described in the IMGT/HLA database (V3.15.0). In the coding region of HLA-E, 7 synonymous and 30 non-synonymous substitutions are found, whereas 48 new polymorphic positions are located in the introns and 32 in the untranslated regions. Apparently, the HLA-E gene seems more variable than currently indicated in the IMGT/HLA database. We developed a full length sequencing approach to investigate the suggested extended HLA-E polymorphism in 40 selected individuals, previously typed for HLA-E by SSP or SSO (One Lambda, Luminex). Retyping with our full length SBT approach revealed 8 different typing results; 5 alleles were identical to the recently discovered HLA-E∗01:06 (exon 4 pos 862, C to T), two alleles showed new intron variation and one was identified as a null allele. The null allele resulted from a substitution in exon 2 pos 315 (C to G) leading to a stop codon (TAG). Two of the 3 new substitutions were not identified as SNP in the 1 KG project. In conclusion, full length sequence analysis defines the polymorphic content of HLA-E and 1 KG is useful in the evaluation of gene polymorphism.