Introduction

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.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%.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.

Publications

  1. HLAscan: genotyping of the HLA region using next-generation sequencing data.
    Cite this
    Ka S, Lee S, Hong J, Cho Y, Sung J, Kim HN, Kim HL, Jung J, 2017-05-01 - BMC Bioinformatics

Credits

  1. Sojeong Ka
    Developer

    R&D center, Syntekabio, Korea (Republic of)

  2. Sunho Lee
    Developer

    Main office, Syntekabio, Korea (Republic of)

  3. Jonghee Hong
    Developer

    R&D center, Syntekabio, Korea (Republic of)

  4. Yangrae Cho
    Developer

    Main office, Syntekabio, Korea (Republic of)

  5. Joohon Sung
    Developer

    Complex Disease and Genome Epidemiology Branch, Department of Epidemiology, Korea (Republic of)

  6. Han-Na Kim
    Developer

    Department of Biochemistry, School of Medicine, Korea (Republic of)

  7. Hyung-Lae Kim
    Developer

    Department of Biochemistry, School of Medicine, Korea (Republic of)

  8. Jongsun Jung
    Investigator

    Main office, Syntekabio, Korea (Republic of)

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Summary
AccessionBT000470
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionKorea (Republic of)
Submitted ByJongsun Jung