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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
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?
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
2015 Impact Factor: 5.7
2015 SCImago Journal Rankings: 2.915
PubMed Central ID
ISI Accession Number ID

 

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.rightsCreative Commons: Attribution 3.0 Hong Kong 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-

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