ATHLATES: accurate typing of human leukocyte antigen through exome sequencing

被引：87

作者：

Liu, Chang ^{[1
]}

Yang, Xiao ^{[2
]}

Duffy, Brian ^{[3
]}

Mohanakumar, Thalachallour ^{[1
,4
]}

Mitra, Robi D. ^{[4
,5
]}

Zody, Michael C. ^{[2
]}

Pfeifer, John D. ^{[1
]}

机构：

[1] Washington Univ, Sch Med, Dept Pathol & Immunol, St Louis, MO 63110 USA

[2] Broad Inst MIT & Harvard, Genome Sequencing & Anal Program, Cambridge, MA 02142 USA

[3] Barnes Jewish Hosp, HLA Lab, St Louis, MO 63110 USA

[4] Washington Univ, Sch Med, Dept Surg, St Louis, MO 63110 USA

[5] Washington Univ, Sch Med, Ctr Genome Sci & Syst Biol, St Louis, MO 63110 USA

来源：

NUCLEIC ACIDS RESEARCH | 2013年 / 41卷 / 14期

基金：

美国国家卫生研究院;

关键词：

HIGH-RESOLUTION; HIGH-THROUGHPUT; HLA;

D O I：

10.1093/nar/gkt481

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Human leukocyte antigen (HLA) typing at the allelic level can in theory be achieved using whole exome sequencing (exome-seq) data with no added cost but has been hindered by its computational challenge. We developed ATHLATES, a program that applies assembly, allele identification and allelic pair inference to short read sequences, and applied it to data from Illumina platforms. In 15 data sets with adequate coverage for HLA-A, -B, -C, -DRB1 and -DQB1 genes, ATHLATES correctly reported 74 out of 75 allelic pairs with an overall concordance rate of 99% compared with conventional typing. This novel approach should be broadly applicable to research and clinical laboratories.

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