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HLAscan: genotyping of the HLA region using next-generation sequencing data

DC Field Value Language
dc.contributor.authorKa, Sojeong-
dc.contributor.authorLee, Sunho-
dc.contributor.authorHong, Jonghee-
dc.contributor.authorCho, Yangrae-
dc.contributor.authorSung, Joohon-
dc.contributor.authorKim, Han-Na-
dc.contributor.authorKim, Hyung-Lae-
dc.contributor.authorJung, Jongsun-
dc.date.accessioned2017-05-15T00:04:46Z-
dc.date.available2017-05-15T09:24:27Z-
dc.date.issued2017-05-12-
dc.identifier.citationBMC Bioinformatics, 18(1):258ko_KR
dc.identifier.uri10.1186/s12859-017-1671-3-
dc.identifier.urihttps://hdl.handle.net/10371/117602-
dc.description.abstractBackground
Several recent studies showed that next-generation sequencing (NGS)-based human leukocyte antigen (HLA) typing is a feasible and promising technique for variant calling of highly polymorphic regions. To date, however, no method with sufficient read depth has completely solved the allele phasing issue. In this study, we developed a new method (HLAscan) for HLA genotyping using NGS data.

Results
HLAscan performs alignment of reads to HLA sequences from the international ImMunoGeneTics project/human leukocyte antigen (IMGT/HLA) database. The distribution of aligned reads was used to calculate a score function to determine correctly phased alleles by progressively removing false-positive alleles. Comparative HLA typing tests using public datasets from the 1000 Genomes Project and the International HapMap Project demonstrated that HLAscan could perform HLA typing more accurately than previously reported NGS-based methods such as HLAreporter and PHLAT. In addition, the results of HLA-A, −B, and -DRB1 typing by HLAscan using data generated by NextGen were identical to those obtained using a Sanger sequencing–based method. We also applied HLAscan to a family dataset with various coverage depths generated on the Illumina HiSeq X-TEN platform. HLAscan identified allele types of HLA-A, −B, −C, −DQB1, and -DRB1 with 100% accuracy for sequences at ≥ 90× depth, and the overall accuracy was 96.9%.

Conclusions
HLAscan, an alignment-based program that takes read distribution into account to determine true allele types, outperformed previously developed HLA typing tools. Therefore, HLAscan can be reliably applied for determination of HLA type across the whole-genome, exome, and target sequences.
ko_KR
dc.language.isoenko_KR
dc.publisherBioMed Centralko_KR
dc.subjectHLA typingko_KR
dc.subjectNext-generation sequencingko_KR
dc.subjectPhasing issueko_KR
dc.subjectHLAscanko_KR
dc.titleHLAscan: genotyping of the HLA region using next-generation sequencing datako_KR
dc.typeArticleko_KR
dc.contributor.AlternativeAuthor가소정-
dc.contributor.AlternativeAuthor이선호-
dc.contributor.AlternativeAuthor홍종희-
dc.contributor.AlternativeAuthor조양래-
dc.contributor.AlternativeAuthor성주헌-
dc.contributor.AlternativeAuthor김한나-
dc.contributor.AlternativeAuthor김형래-
dc.contributor.AlternativeAuthor정종선-
dc.language.rfc3066en-
dc.rights.holderThe Author(s).-
dc.date.updated2017-05-14T03:27:43Z-
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