HLAreporter: a tool for HLA typing from next generation sequencing data

被引：58

作者：

Huang, Yazhi ^{[1
]}

Yang, Jing ^{[1
]}

Ying, Dingge ^{[1
]}

Zhang, Yan ^{[1
]}

Shotelersuk, Vorasuk ^{[3
]}

Hirankarn, Nattiya ^{[4
]}

Sham, Pak Chung ^{[2
]}

Lau, Yu Lung ^{[1
]}

Yang, Wanling ^{[1
]}

机构：

[1] Univ Hong Kong, Li Ka Shing Fac Med, Dept Paediat & Adolescent Med, Hong Kong, Hong Kong, Peoples R China

[2] Univ Hong Kong, Li Ka Shing Fac Med, Dept Psychiat, Hong Kong, Hong Kong, Peoples R China

[3] Chulalongkorn Univ, Fac Med, King Chulalongkorn Mem Hosp, Dept Pediat, Bangkok 10330, Thailand

[4] Chulalongkorn Univ, Fac Med, Dept Microbiol, Immunol Unit, Bangkok 10330, Thailand

来源：

GENOME MEDICINE | 2015年 / 7卷

关键词：

HIGH-RESOLUTION HLA; ASSOCIATION; LOCI; RNA;

D O I：

10.1186/s13073-015-0145-3

中图分类号：

Q3 [遗传学];

学科分类号：

071007 [遗传学];

摘要：

Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for widespread applications. Here we introduce a novel tool (HLAreporter) for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles, followed by de novo assembly of the gene-specific short reads. Accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly developed tools such as HLAminer and PHLAT.

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页数：12

相关论文

共 16 条

[1]

Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads [J].

Bai, Yu ;

Ni, Min ;

Cooper, Blerta ;

Wei, Yi ;

Fury, Wen .

BMC GENOMICS, 2014, 15

[2]

High-resolution, high-throughput HLA genotyping by next-generation sequencing [J].

Bentley, G. ;

Higuchi, R. ;

Hoglund, B. ;

Goodridge, D. ;

Sayer, D. ;

Trachtenberg, E. A. ;

Erlich, H. A. .

TISSUE ANTIGENS, 2009, 74 (05) :393-403

[3]

HLA typing from RNA-Seq sequence reads [J].

Boegel, Sebastian ;

Loewer, Martin ;

Schaefer, Michael ;

Bukur, Thomas ;

de Graaf, Jos ;

Boisguerin, Valesca ;

Tuereci, Oezlem ;

Diken, Mustafa ;

Castle, John C. ;

Sahin, Ugur .

GENOME MEDICINE, 2012, 4

[4]

A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC [J].

de Bakker, Paul I. W. ;

McVean, Gil ;

Sabeti, Pardis C. ;

Miretti, Marcos M. ;

Green, Todd ;

Marchini, Jonathan ;

Ke, Xiayi ;

Monsuur, Alienke J. ;

Whittaker, Pamela ;

Delgado, Marcos ;

Morrison, Jonathan ;

Richardson, Angela ;

Walsh, Emily C. ;

Gao, Xiaojiang ;

Galver, Luana ;

Hart, John ;

Hafler, David A. ;

Pericak-Vance, Margaret ;

Todd, John A. ;

Daly, Mark J. ;

Trowsdale, John ;

Wijmenga, Cisca ;

Vyse, Tim J. ;

Beck, Stephan ;

Murray, Sarah Shaw ;

Carrington, Mary ;

Gregory, Simon ;

Deloukas, Panos ;

Rioux, John D. .

NATURE GENETICS, 2006, 38 (10) :1166-1172

[5]

Interrogating the major histocompatibility complex with high-throughput genomics [J].

de Bakker, Paul I. W. ;

Raychaudhuri, Soumya .

HUMAN MOLECULAR GENETICS, 2012, 21 :R29-R36

[6]

Next-generation sequencing for HLA typing of class I loci [J].

Erlich, Rachel L. ;

Jia, Xiaoming ;

Anderson, Scott ;

Banks, Eric ;

Gao, Xiaojiang ;

Carrington, Mary ;

Gupta, Namrata ;

DePristo, Mark A. ;

Henn, Matthew R. ;

Lennon, Niall J. ;

de Bakker, Paul I. W. .

BMC GENOMICS, 2011, 12

[7]

Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations [J].

Gonzalez-Galarza, Faviel F. ;

Christmas, Stephen ;

Middleton, Derek ;

Jones, Andrew R. .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D913-D919

[8]

IMGT/HLA, 1998, IMGT HLA INT IMM PRO

[9]

Fast and accurate long-read alignment with Burrows-Wheeler transform [J].

Li, Heng ;

Durbin, Richard .

BIOINFORMATICS, 2010, 26 (05) :589-595

[10]

Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing [J].

Lind, C. ;

Ferriola, D. ;

Mackiewicz, K. ;

Heron, S. ;

Rogers, M. ;

Slavich, L. ;

Walker, R. ;

Hsiao, T. ;

McLaughlin, L. ;

D'Arcy, M. ;

Gai, X. ;

Goodridge, D. ;

Sayer, D. ;

Monos, D. .

HUMAN IMMUNOLOGY, 2010, 71 (10) :1033-1042