Thorstenson Yvonne R, Creary Lisa E, Huang Huang, Rozot Virginie, Nguyen Tracy T, Babrzadeh Farbod, Kancharla Sandeep, Fukushima Marilyn, Kuehn Raquel, Wang Chunlin, Li Ming, Krishnakumar Sujatha, Mindrinos Michael, Fernandez Viña Marcelo A, Scriba Thomas J, Davis Mark M
Immucor, Sirona Genomics, Mountain View, CA, USA.
Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
Hum Immunol. 2018 Dec;79(12):839-847. doi: 10.1016/j.humimm.2018.09.004. Epub 2018 Sep 18.
The development of next-generation sequencing (NGS) methods for HLA genotyping has already had an impact on the scope and precision of HLA research. In this study, allelic resolution HLA typing was obtained for 402 individuals from Cape Town, South Africa. The data were produced by high-throughput NGS sequencing as part of a study of T-cell responses to Mycobacterium tuberculosis in collaboration with the University of Cape Town and Stanford University. All samples were genotyped for 11 HLA loci, namely HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4, and -DRB5. NGS HLA typing of samples from Cape Town inhabitants revealed a unique cohort, including unusual haplotypes, and 22 novel alleles not previously reported in the IPD-IMGT/HLA Database. Eight novel alleles were in Class I loci and 14 were in Class II. There were 62 different alleles of HLA-A, 72 of HLA-B, and 47 of HLA-C. Alleles A∗23:17, A∗43:01, A∗29:11, A∗68:27:01, A∗01:23, B∗14:01:01, B∗15:10:01, B∗39:10:01, B∗45:07, B∗82:02:01 and C∗08:04:01 were notably more frequent in Cape Town compared to other populations reported in the literature. Class II loci had 21 different alleles of DPA1, 46 of DPB1, 27 of DQA1, 26 of DQB1, 41 of DRB1, 5 of DRB3, 4 of DRB4 and 6 of DRB5. The Cape Town cohort exhibited high degrees of HLA diversity and relatively high heterozygosity at most loci. Genetic distances between Cape Town and five other sub-Saharan African populations were also calculated and compared to European Americans.
下一代测序（NGS）方法用于HLA基因分型的发展已经对HLA研究的范围和精度产生了影响。在本研究中，对来自南非开普敦的402名个体进行了等位基因分辨率HLA分型。这些数据是通过高通量NGS测序产生的，作为与开普敦大学和斯坦福大学合作进行的关于T细胞对结核分枝杆菌反应研究的一部分。所有样本均对11个HLA基因座进行基因分型，即HLA-A、-B、-C、-DPA1、-DPB1、-DQA1、-DQB1、-DRB1、-DRB3、-DRB4和-DRB5。对开普敦居民样本的NGS HLA分型揭示了一个独特的队列，包括不寻常的单倍型，以及22个以前在IPD-IMGT/HLA数据库中未报告的新等位基因。8个新等位基因位于I类基因座，14个位于II类基因座。HLA-A有62个不同的等位基因，HLA-B有72个，HLA-C有47个。与文献中报道的其他人群相比，等位基因A∗23:17、A∗43:01、A∗29:11、A∗68:27:01、A∗01:23、B∗14:01:01、B∗15:10:01、B∗39:10:01、B∗45:07、B∗82:02:01和C∗08:04:01在开普敦更为常见。II类基因座中，DPA1有21个不同的等位基因，DPB1有46个，DQA1有27个，DQB1有26个，DRB1有41个，DRB3有5个，DRB4有4个，DRB5有6个。开普敦队列在大多数基因座上表现出高度的HLA多样性和相对较高的杂合性。还计算了开普敦与其他五个撒哈拉以南非洲人群之间的遗传距离，并与欧裔美国人进行了比较。
