LAUSR

Aim Here we propose a NGS strategy to evaluate the HLA-A coding and 3′UTR variability and get reliable haplotypes. Then, we present the data obtained in very admixed population (Brazil). Methods The HLA-Agene segment was amplified in a unique amplicon considering 408 Brazilian individuals. Amplicons were sequenced by NGS and data processed using hla-mapper and a local pipeline to get genotypes and haplotypes. Allele and haplotype frequencies, together with Linkage Disequilibrium (LD) plots, were also calculated. Results According to the human genome draft version hg38, and known HLA-A transcripts available, the HLA-A 3′UTR comprises a segment of 433 nucleotides. However, only 70 percent of this segment is considered at the IPD-IMGT/HLA database. A total of 21 variable sites were found in the 3′UTR and, together, they were organized in 11 different haplotypes. Seven of those variants were detected outside the segment tracked by the IMGT/HLA database. We observed a high LD throughout the HLA-A locus and associations between each of these 3′UTR haplotypes and specific coding alleles. Thus, in many cases, it is possible to detect the HLA-A allele group by targeting one or two variations at the 3′UTR. Although few haplotypes were detected, they were quite frequent. It is possible that the variability detected at this segment would influence allelic expression, mainly by posttranscriptional mechanisms through microRNA binding. Conclusions The HLA-A locus is one of the most variable genes on the human genome. Most of its variability was described within exons 2 and 3, which encode the peptide-binding groove. Thus, these segment are usually the only ones targeted by many HLA-A studies. Little is known regarding the HLA-Aregulatory segments variability, including its 3′ untranslated region (3′UTR). Thus, HLA-A 3′UTR present few but frequent haplotypes, and each of these haplotype is associated with a specific group of coding alleles, which in turn may present a similar post transcriptional profile.