Human Longevity Singapore Pte Ltd., Singapore 138543;
Human Longevity Singapore Pte Ltd., Singapore 138543.
Proc Natl Acad Sci U S A. 2017 Jul 25;114(30):8059-8064. doi: 10.1073/pnas.1707945114. Epub 2017 Jul 3.
The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. Here, we introduce an algorithm, xHLA, that iteratively refines the mapping results at the amino acid level to achieve 99-100% four-digit typing accuracy for both class I and II HLA genes, taking only [Formula: see text]3 min to process a 30× whole-genome BAM file on a desktop computer.
人类 6 号染色体上的 HLA 基因复合体是人类基因组中多态性最高的区域之一,在很大程度上促成了免疫系统的多样性。由于多态性等位基因之间的序列相似性,历史上使用短读测序数据准确地对 HLA 基因进行分型一直很困难。在这里,我们引入了一种算法 xHLA,它在氨基酸水平上迭代地优化映射结果,实现了 I 类和 II 类 HLA 基因四位数字分型的 99-100%准确率,仅需 3 分钟即可在台式计算机上处理 30×全基因组 BAM 文件。