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

TitleHLAreporter: a tool for HLA typing from next generation sequencing data
Authors
Huang, YYang, JYing, DZhang, YShotelersuk, VHirankarn, NSham, PCLau, YLYang, W
Issue Date2015
PublisherBioMed Central Ltd. The Journal's web site is located at http://genomemedicine.com/
Citation
Genome Medicine, 2015, v. 7, article no. 25 How to Cite?
DOI: http://dx.doi.org/10.1186/s13073-015-0145-3
AbstractHuman 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/.
Persistent Identifierhttp://hdl.handle.net/10722/211878
ISSN
1756-994X
2023 Impact Factor: 10.4
2023 SCImago Journal Rankings: 4.975
PubMed Central ID
PMC4407542
ISI Accession Number ID
WOS:000353264000001

 

DC FieldValueLanguage
dc.contributor.authorHuang, Y-
dc.contributor.authorYang, J-
dc.contributor.authorYing, D-
dc.contributor.authorZhang, Y-
dc.contributor.authorShotelersuk, V-
dc.contributor.authorHirankarn, N-
dc.contributor.authorSham, PC-
dc.contributor.authorLau, YL-
dc.contributor.authorYang, W-
dc.date.accessioned2015-07-21T02:14:38Z-
dc.date.available2015-07-21T02:14:38Z-
dc.date.issued2015-
dc.identifier.citationGenome Medicine, 2015, v. 7, article no. 25-
dc.identifier.issn1756-994X-
dc.identifier.urihttp://hdl.handle.net/10722/211878-
dc.description.abstractHuman 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/.-
dc.languageeng-
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://genomemedicine.com/-
dc.relation.ispartofGenome Medicine-
dc.rightsGenome Medicine. Copyright © BioMed Central Ltd.-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.titleHLAreporter: a tool for HLA typing from next generation sequencing data-
dc.typeArticle-
dc.identifier.emailYang, J: jingy09@hku.hk-
dc.identifier.emailYing, D: jonson@hku.hk-
dc.identifier.emailZhang, Y: yannizy@hku.hk-
dc.identifier.emailSham, PC: pcsham@hku.hk-
dc.identifier.emailLau, YL: lauylung@hku.hk-
dc.identifier.emailYang, W: yangwl@hkucc.hku.hk-
dc.identifier.authoritySham, PC=rp00459-
dc.identifier.authorityLau, YL=rp00361-
dc.identifier.authorityYang, W=rp00524-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/s13073-015-0145-3-
dc.identifier.pmid25908942-
dc.identifier.pmcidPMC4407542-
dc.identifier.scopuseid_2-s2.0-84928227021-
dc.identifier.hkuros244469-
dc.identifier.volume7-
dc.identifier.issue1-
dc.identifier.isiWOS:000353264000001-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl1756-994X-

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