HLA*LA-HLA typing from linearly projected graph alignments

被引：86

作者：

Dilthey, Alexander T. ^{[1
,2
,3
]}

Mentzer, Alexander J. ^{[3
,4
]}

Carapito, Raphael ^{[5
,6
]}

Cutland, Clare ^{[7
,8
]}

Cereb, Nezih ^{[9
]}

Madhi, Shabir A. ^{[7
,8
]}

Rhie, Arang ^{[2
]}

Koren, Sergey ^{[2
]}

Bahram, Seiamak ^{[5
,6
]}

McVean, Gil ^{[3
,4
]}

Phillippy, Adam M. ^{[2
]}

机构：

[1] Univ Hosp Dusseldorf, Inst Med Microbiol, Dusseldorf, North Rhine Wes, Germany

[2] NHGRI, Genome Informat Sect, Computat & Stat Genom Branch, Bethesda, MD 20892 USA

[3] Univ Oxford, Wellcome Ctr Human Genet, Oxford, England

[4] Univ Oxford, Big Data Inst, Li Ka Shing Ctr Hlth Informat & Discovery, Oxford, England

[5] Univ Strasbourg, Lab ImmunoRhumatol Mol, LabEx TRANSPLANTEX, Plateforme GENOMAX,Fac Med,FMTS,INSERM,UMR S 1109, Strasbourg, France

[6] Nouvel Hop Civil, Serv Immunol Biol, Strasbourg, France

[7] Univ Witwatersrand, Fac Hlth Sci, MRC, Resp & Meningeal Pathogens Res Unit, Johannesburg, South Africa

[8] Univ Witwatersrand, Fac Hlth Sci, Natl Res Fdn Vaccine Preventable Dis, Dept Sci, Johannesburg, South Africa

[9] Histogenetics, Ossining, NY 10562 USA

来源：

BIOINFORMATICS | 2019年 / 35卷 / 21期

基金：

欧洲研究理事会; 英国惠康基金; 美国国家卫生研究院;

关键词：

GENOME; MAP;

D O I：

10.1093/bioinformatics/btz235

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

A Summary: HLA*LA implements a new graph alignment model for human leukocyte antigen (HLA) type inference, based on the projection of linear alignments onto a variation graph. It enables accurate HLA type inference from whole-genome (99% accuracy) and whole-exome (93% accuracy) Illumina data; from long-read Oxford Nanopore and Pacific Biosciences data (98% accuracy for whole-genome and targeted data) and from genome assemblies. Computational requirements for a typical sample vary between 0.7 and 14 CPU hours per sample.

引用

页码：4394 / 4396

页数：3

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