View : 30 Download: 8

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

Title
HLAscan: genotyping of the HLA region using next-generation sequencing data
Authors
Ka, SojeongLee, SunhoHong, JongheeCho, YangraeSung, JoohonKim, Han-NaKim, Hyung-LaeJung, Jongsun
Ewha Authors
김형래김한나
SCOPUS Author ID
김형래scopus; 김한나scopus
Issue Date
2017
Journal Title
BMC BIOINFORMATICS
ISSN
1471-2105JCR Link
Citation
vol. 18
Keywords
HLA typingNext-generation sequencingPhasing issueHLAscan
Publisher
BIOMED CENTRAL LTD
Indexed
SCIE; SCOPUS WOS scopus
Abstract
Background: 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 >= 90x 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.
DOI
10.1186/s12859-017-1671-3
Appears in Collections:
의학전문대학원 > 의학과 > Journal papers
Files in This Item:
HLAscan.pdf(1.06 MB)Download
Export
RIS (EndNote)
XLS (Excel)
XML


qrcode

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

BROWSE