16th IHIW: Review of HLA typing by NGS
16th IHIW: Review of HLA typing by NGS
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DOI：
10.1111/iji.12024
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发表时间：
2013-02-01
影响因子：
2.2
通讯作者：
Allcock, R. J. N.
中科院分区：
文献类型：
--
作者：
De Santis, D.;Dinauer, D.;Allcock, R. J. N.
人类白细胞抗原（HLA）基因在器官移植的成功中起着重要作用，并与自身免疫性疾病和感染性疾病有关。目前基于DNA的基因分型方法，包括基于桑格序列的分型（SSBT），已经确定了高度的多态性。这种多态性水平使得高分辨率HLA基因分型具有挑战性，由于无法分辨相位和/或定义位于扩增区域之外的多态性，导致分型结果不明确。下一代测序（NGS）可以通过克隆扩增（提供相位信息）和测序更大区域基因（包括内含子）的能力的组合来解决这个问题，而无需与当前方法相关的额外工作或成本。16 IHIW的NGS HLA测序项目旨在讨论以下不同方法：（i）模板制备，包括短程和长程PCR扩增子、外显子组捕获和全基因组;（ii）测序平台，包括GS 454 FLX、Ion Torrent PGM、Illumina MiSeq/HiSeq和Pacific Biosciences SMRT;（iii）数据分析，特别是等位基因调用软件。在研讨会上提出的试点研究表明，虽然个别测序仪有非常不同的性能特点，所有产生的序列数据适用于解决HLA基因分型的模糊性。在这次研讨会上提出的发展清楚地强调了HLA实验室中NGS的潜在好处。
Human leucocyte antigen (HLA) genes play an important role in the success of organ transplantation and are associated with autoimmune and infectious diseases. Current DNA-based genotyping methods, including Sanger sequence-based typing (SSBT), have identified a high degree of polymorphism. This level of polymorphism makes high-resolution HLA genotyping challenging, resulting in ambiguous typing results due to an inability to resolve phase and/or defining polymorphisms lying outside the region amplified. Next-generation sequencing (NGS) may resolve the issue through the combination of clonal amplification, which provides phase information, and the ability to sequence larger regions of genes, including introns, without the additional effort or cost associated with current methods. The NGS HLA sequencing project of the 16IHIW aimed to discuss the different approaches to (i) template preparation including short- and long-range PCR amplicons, exome capture and whole genome; (ii) sequencing platforms, including GS 454 FLX, Ion Torrent PGM, Illumina MiSeq/HiSeq and Pacific Biosciences SMRT; (iii) data analysis, specifically allele-calling software. The pilot studies presented at the workshop demonstrated that although individual sequencers have very different performance characteristics, all produced sequence data suitable for the resolution of HLA genotyping ambiguities. The developments presented at this workshop clearly highlight the potential benefits of NGS in the HLA laboratory.