Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA.
Omixon Biocomputing, Budapest, Hungary.
Clin Chem. 2016 Dec;62(12):1630-1638. doi: 10.1373/clinchem.2016.260661. Epub 2016 Sep 27.
Routine, high-resolution human leukocyte antigen (HLA) genotyping by next generation sequencing within clinical immunogenetics laboratories can now provide the full-length gene sequence characterization of fully phased HLA alleles. This powerful technique provides insights into HLA variation beyond the traditionally characterized antigen recognition domain, providing sequence annotation across the entire gene including untranslated and intronic regions and may be used to characterize novel alleles from massively parallel sequencing runs.
We evaluated the utility of the Omixon Holotype HLA assay to generate credible, fully phased full-length gene consensus sequences for 50 individuals at major histocompatibility complex, class I, A (HLA-A), HLA-B, and HLA-C loci (300 genotyped alleles in total) to identify and characterize novel class I HLA alleles using our downstream analytical pipeline.
Our analysis revealed that 7.7% (23/300) of genotyped class I HLA alleles contain novel polymorphisms. Interestingly, all of the novel alleles identified by our analysis were found to harbor sequence variations within intronic regions of the respective locus. In total our analysis identified 17 unique novel class I HLA alleles from 23 of the 300 genotyped alleles and generated full-length gene sequence annotations for 9 previously incompletely annotated HLA class I allele sequences derived from 14 of the 300 genotyped alleles.
The demonstrated utility of the Omixon Holotype HLA assay in combination with our downstream analytical framework to generate fully phased, full-length gene consensus sequences for the identification and characterization of novel HLA alleles, facilitates the study of HLA polymorphism beyond the antigen recognition domain in human health and disease.
临床免疫遗传学实验室中通过下一代测序进行常规、高分辨率的人类白细胞抗原（HLA）基因分型现在可以提供完全定型 HLA 等位基因的全长基因序列特征。这项强大的技术提供了对 HLA 变异的深入了解，超出了传统的抗原识别结构域特征化，提供了整个基因的序列注释，包括非翻译和内含子区域，并可用于从大规模平行测序运行中描述新的等位基因。
我们评估了 Omixon Holotype HLA 测定在生成 50 个人的主要组织相容性复合体、I 类、A（HLA-A）、HLA-B 和 HLA-C 基因座（总共 300 个基因分型等位基因）的可信、完全定型的全长基因共识序列方面的实用性，以使用我们的下游分析管道来鉴定和描述新的 I 类 HLA 等位基因。
我们的分析显示，7.7%（23/300）的 I 类 HLA 基因分型等位基因含有新的多态性。有趣的是，我们分析确定的所有新等位基因都在各自基因座的内含子区域内发现了序列变异。我们的分析总共从 300 个基因分型等位基因中的 23 个鉴定了 17 个独特的新的 I 类 HLA 等位基因，并为 9 个先前不完全注释的 HLA I 类等位基因序列生成了全长基因序列注释，这些序列来自 300 个基因分型等位基因中的 14 个。
证明了 Omixon Holotype HLA 测定与我们的下游分析框架结合使用，可生成完全定型的全长基因共识序列，用于鉴定和描述新的 HLA 等位基因，促进了人类健康和疾病中 HLA 多态性的研究，超出了抗原识别结构域。
