HLAscan: genotyping of the HLA region using next-generation sequencing data.
HLAscan: genotyping of the HLA region using next-generation sequencing data.
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DOI：
10.1186/s12859-017-1671-3
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发表时间：
2017-05-12
影响因子：
3
通讯作者：
Jung J
中科院分区：
文献类型：
--
作者：
Ka S;Lee S;Hong J;Cho Y;Sung J;Kim HN;Kim HL;Jung J
最近的几项研究表明，基于下一代测序（NGS）的人类白细胞抗原（HLA）分型是一种可行的和有前途的技术，变异调用的高度多态性区域。然而，迄今为止，没有具有足够读取深度的方法完全解决了等位基因定相问题。在这项研究中，我们开发了一种新的方法（HLA扫描）HLA基因分型使用NGS数据。HLAScan将读段与来自国际ImmMunoGeneTics项目/人类白细胞抗原（IMGT/HLA）数据库的HLA序列进行比对。比对读数的分布用于计算评分函数，以通过逐渐去除假阳性等位基因来确定正确定相的等位基因。使用来自1000个基因组计划和国际HapMap计划的公共数据集进行的比较HLA分型测试表明，HLAScan可以比以前报道的基于NGS的方法（如HLA报告和PHLAT）更准确地进行HLA分型。此外，使用NextGen生成的数据通过HLA扫描进行的HLA-A、-B和-DRB 1分型结果与使用基于桑格测序的方法获得的结果相同。我们还将HLAscan应用于在Illumina HiSeq X-TEN平台上生成的具有各种覆盖深度的家族数据集。HLA扫描识别HLA-A、−B、−C、− DQB 1和-DRB 1等位基因类型，在≥ 90×深度的序列中具有100%的准确性，总体准确性为96.9%。HLA扫描，一个基于测序的程序，考虑到读段分布，以确定真正的等位基因类型，优于以前开发的HLA分型工具。因此，HLA扫描可以可靠地应用于确定整个基因组、外显子组和靶序列的HLA类型。本文的在线版本（doi：10.1186/s12859-017-1671-3）包含补充材料，可供授权用户使用。
Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, however, no method with sufficient read depth has completely solved the allele phasing issue. In this study, we developed a new method (HLAscan) for HLA genotyping using NGS data. HLAscan performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database. The distribution of aligned reads was used to calculate a score function to determine correctly phased alleles by progressively removing false-positive alleles. Comparative HLA typing tests using public datasets from the 1000 Genomes Project and the International HapMap Project demonstrated that HLAscan could perform HLA typing more accurately than previously reported NGS-based methods such as HLAreporter and PHLAT. In addition, the results of HLA-A, −B, and -DRB1 typing by HLAscan using data generated by NextGen were identical to those obtained using a Sanger sequencing–based method. We also applied HLAscan to a family dataset with various coverage depths generated on the Illumina HiSeq X-TEN platform. HLAscan identified allele types of HLA-A, −B, −C, −DQB1, and -DRB1 with 100% accuracy for sequences at ≥ 90× depth, and the overall accuracy was 96.9%. HLAscan, an alignment-based program that takes read distribution into account to determine true allele types, outperformed previously developed HLA typing tools. Therefore, HLAscan can be reliably applied for determination of HLA type across the whole-genome, exome, and target sequences. The online version of this article (doi:10.1186/s12859-017-1671-3) contains supplementary material, which is available to authorized users.