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

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, follo...

Descripción completa

Detalles Bibliográficos
Autores principales: Huang, Yazhi, Yang, Jing, Ying, Dingge, Zhang, Yan, Shotelersuk, Vorasuk, Hirankarn, Nattiya, Sham, Pak Chung, Lau, Yu Lung, Yang, Wanling
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4407542/
https://www.ncbi.nlm.nih.gov/pubmed/25908942
http://dx.doi.org/10.1186/s13073-015-0145-3
_version_ 1782367926222848000
author Huang, Yazhi
Yang, Jing
Ying, Dingge
Zhang, Yan
Shotelersuk, Vorasuk
Hirankarn, Nattiya
Sham, Pak Chung
Lau, Yu Lung
Yang, Wanling
author_facet Huang, Yazhi
Yang, Jing
Ying, Dingge
Zhang, Yan
Shotelersuk, Vorasuk
Hirankarn, Nattiya
Sham, Pak Chung
Lau, Yu Lung
Yang, Wanling
author_sort Huang, Yazhi
collection PubMed
description 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. HLAreporter can be downloaded from http://paed.hku.hk/genome/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13073-015-0145-3) contains supplementary material, which is available to authorized users.
format Online
Article
Text
id pubmed-4407542
institution National Center for Biotechnology Information
language English
publishDate 2015
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-44075422015-04-24 HLAreporter: a tool for HLA typing from next generation sequencing data Huang, Yazhi Yang, Jing Ying, Dingge Zhang, Yan Shotelersuk, Vorasuk Hirankarn, Nattiya Sham, Pak Chung Lau, Yu Lung Yang, Wanling Genome Med Method 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. HLAreporter can be downloaded from http://paed.hku.hk/genome/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13073-015-0145-3) contains supplementary material, which is available to authorized users. BioMed Central 2015-03-16 /pmc/articles/PMC4407542/ /pubmed/25908942 http://dx.doi.org/10.1186/s13073-015-0145-3 Text en © Huang et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Huang, Yazhi
Yang, Jing
Ying, Dingge
Zhang, Yan
Shotelersuk, Vorasuk
Hirankarn, Nattiya
Sham, Pak Chung
Lau, Yu Lung
Yang, Wanling
HLAreporter: a tool for HLA typing from next generation sequencing data
title HLAreporter: a tool for HLA typing from next generation sequencing data
title_full HLAreporter: a tool for HLA typing from next generation sequencing data
title_fullStr HLAreporter: a tool for HLA typing from next generation sequencing data
title_full_unstemmed HLAreporter: a tool for HLA typing from next generation sequencing data
title_short HLAreporter: a tool for HLA typing from next generation sequencing data
title_sort hlareporter: a tool for hla typing from next generation sequencing data
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4407542/
https://www.ncbi.nlm.nih.gov/pubmed/25908942
http://dx.doi.org/10.1186/s13073-015-0145-3
work_keys_str_mv AT huangyazhi hlareporteratoolforhlatypingfromnextgenerationsequencingdata
AT yangjing hlareporteratoolforhlatypingfromnextgenerationsequencingdata
AT yingdingge hlareporteratoolforhlatypingfromnextgenerationsequencingdata
AT zhangyan hlareporteratoolforhlatypingfromnextgenerationsequencingdata
AT shotelersukvorasuk hlareporteratoolforhlatypingfromnextgenerationsequencingdata
AT hirankarnnattiya hlareporteratoolforhlatypingfromnextgenerationsequencingdata
AT shampakchung hlareporteratoolforhlatypingfromnextgenerationsequencingdata
AT lauyulung hlareporteratoolforhlatypingfromnextgenerationsequencingdata
AT yangwanling hlareporteratoolforhlatypingfromnextgenerationsequencingdata

Ejemplares similares