Xegen, Gemenos, France.
Laboratory of Personalized Genomic Medicine, Columbia University, New York, New York, United States of America.
PLoS One. 2020 Nov 12;15(11):e0242168. doi: 10.1371/journal.pone.0242168. eCollection 2020.
Many questions can be explored thanks to whole-genome data. The aim of this study was to overcome their main limits, software availability and database accuracy, and estimate the feasibility of red blood cell (RBC) antigen typing from whole-genome sequencing (WGS) data. We analyzed whole-genome data from 79 individuals for HLA-DRB1 and 9 RBC antigens. Whole-genome sequencing data was analyzed with software allowing phasing of variable positions to define alleles or haplotypes and validated for HLA typing from next-generation sequencing data. A dedicated database was set up with 1648 variable positions analyzed in KEL (KEL), ACKR1 (FY), SLC14A1 (JK), ACHE (YT), ART4 (DO), AQP1 (CO), CD44 (IN), SLC4A1 (DI) and ICAM4 (LW). Whole-genome sequencing typing was compared to that previously obtained by amplicon-based monoallelic sequencing and by SNaPshot analysis. Whole-genome sequencing data were also explored for other alleles. Our results showed 93% of concordance for blood group polymorphisms and 91% for HLA-DRB1. Incorrect typing and unresolved results confirm that WGS should be considered reliable with read depths strictly above 15x. Our results supported that RBC antigen typing from WGS is feasible but requires improvements in read depth for SNV polymorphisms typing accuracy. We also showed the potential for WGS in screening donors with rare blood antigens, such as weak JK alleles. The development of WGS analysis in immunogenetics laboratories would offer personalized care in the management of RBC disorders.
得益于全基因组数据，人们可以探索许多问题。本研究旨在克服其主要限制，包括软件可用性和数据库准确性，并评估从全基因组测序（WGS）数据中进行红细胞（RBC）抗原分型的可行性。我们分析了 79 个人的 HLA-DRB1 和 9 个 RBC 抗原的全基因组数据。使用允许对可变位置进行相位分析以定义等位基因或单倍型的软件分析全基因组测序数据，并对下一代测序数据的 HLA 分型进行验证。建立了一个专用数据库，其中分析了 1648 个 KEL（KEL）、ACKR1（FY）、SLC14A1（JK）、ACHE（YT）、ART4（DO）、AQP1（CO）、CD44（IN）、SLC4A1（DI）和 ICAM4（LW）的可变位置。将全基因组测序分型与先前通过基于扩增子的单等位基因测序和 SNaPshot 分析获得的分型进行比较。还探索了全基因组测序数据中的其他等位基因。我们的结果显示，血型多态性的一致性为 93%，HLA-DRB1 的一致性为 91%。错误的分型和未解决的结果证实，WGS 应被认为是可靠的，其读取深度严格高于 15x。我们的结果支持从 WGS 进行 RBC 抗原分型是可行的，但需要提高单核苷酸变异（SNV）多态性分型准确性的读取深度。我们还展示了 WGS 在筛选具有稀有血液抗原（如弱 JK 等位基因）的供体方面的潜力。免疫遗传学实验室中 WGS 分析的发展将为 RBC 疾病的管理提供个性化护理。
