An NGS-based HLA haplotype analysis and population comparison between two cities in Rio de Janeiro, Brazil

HLA genes can exhibit extensive variations in frequency, especially in highly admixed populations, such as that of Brazil. In this study, we demonstrated NGS-based HLA typing in our laboratory using an Illumina HiSeq 2500 sequencing platform and downstream analysis. We herein describe and compare the allele and haplotype frequencies of the populations in Barra Mansa (BM) and Rio de Janeiro (RJ), using the acquired genetic data. Sequences encompassing 7 HLA loci (HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQB1, HLA-DPA1, and HLA-DPB1) were amplified from a total of 1435 bone marrow samples donated by volunteers recruited in BM (37.56%) and RJ (62.44%) using polymerase chain reactions, and were sequenced using five distinct HiSeq 2500 runs. Alleles were analyzed to generate 2-locus haplotypes and extended haplotypes encompassing more than two loci. The most frequent haplotype was A*01:01:01~C*07:01:01~B*08:01:01~DRB1*03:01:01~DQB1*02:01:01~DPA1*01:03:01~DPB1*04:01:01 in both populations. The populations of BM and RJ exhibited a significant difference in genetic composition (P = .03) but not in genetic variance (P = .45). However, some groups of subjects, classified based on self-declared ethnicity, particularly Branca and Preta, displayed significant genetic variance (P < .05). In conclusion, these genetic data indicate no differences in HLA loci between the populations of these two cities, but were informative with respect to variations in ancestry composition.