Vianna Romulo, Secco Danielle, Hanhoerderster Leonardo, Motta Juliana, Cardoso Juliana, Porto Luís Cristóvão
Histocompatibility and Cryopreservation Laboratory, Rio de Janeiro State University, Rio de Janeiro, Brazil.
HLA. 2020 Sep;96(3):268-276. doi: 10.1111/tan.13940. Epub 2020 Jun 13.
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 A01:01:01~C07:01:01B*08:01:01DRB103:01:01~DQB102:01:01DPA1*01:03:01DPB1*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.
HLA基因在频率上可表现出广泛的差异，尤其是在高度混合的人群中，如巴西人群。在本研究中，我们在实验室中使用Illumina HiSeq 2500测序平台及下游分析展示了基于二代测序（NGS）的HLA分型。我们利用所获取的基因数据，在此描述并比较了巴拉曼萨（BM）和里约热内卢（RJ）人群的等位基因和单倍型频率。使用聚合酶链反应从BM（37.56%）和RJ（62.44%）招募的志愿者捐赠的总共1435份骨髓样本中扩增包含7个HLA位点（HLA - A、HLA - B、HLA - C、HLA - DRB1、HLA - DQB1、HLA - DPA1和HLA - DPB1）的序列，并使用5次不同的HiSeq 2500运行进行测序。分析等位基因以生成双位点单倍型和包含两个以上位点的扩展单倍型。在两个人群中最常见的单倍型是A01:01:01~C07:01:01B*08:01:01DRB103:01:01~DQB102:01:01DPA1*01:03:01DPB1*04:01:01。BM和RJ人群在基因组成上存在显著差异（P = 0.03），但在基因方差上无显著差异（P = 0.45）。然而，一些根据自我申报的种族分类的受试者群体，特别是白种人和黑种人，表现出显著的基因方差（P < 0.05）。总之，这些基因数据表明这两个城市的人群在HLA位点上没有差异，但在祖先组成的变异方面提供了信息。
