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

BMC Bioinformatics
Sojeong KaJongsun Jung

Abstract

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. H...Continue Reading

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Citations

Aug 5, 2017·Sensors·Guoxia LiuJean-François Picimbon
Sep 10, 2019·HLA : Immune Response Genetics·Angelina SverchkovaTrevor Clancy
Jul 7, 2019·Nature Reviews. Cancer·Christof C SmithJonathan S Serody
Aug 30, 2019·Genome Medicine·Megan M RichtersMalachi Griffith
Jun 21, 2019·Nature Protocols·James BlackburnTim R Mercer
Dec 18, 2019·European Journal of Human Genetics : EJHG·Jessika NordinJennifer R S Meadows
Sep 26, 2020·Frontiers in Oncology·Kiran K MangalaparthiHarsha Gowda
Nov 10, 2018·Frontiers in Genetics·Amit Kishore, Martin Petrek
Aug 24, 2019·Cells·Roger L Dawkins, Sally S Lloyd
Nov 4, 2020·The Journal of Rheumatology·Wenqing Qiu, Yun Liu
Mar 25, 2021·Briefings in Bioinformatics·Irina ChelyshevaDaniel O'Connor
Apr 28, 2020·Combinatorial Chemistry & High Throughput Screening·Houda N WashahMahmoud E S Soliman
Aug 3, 2021·Frontiers in Genetics·Jessika NordinJennifer R S Meadows

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Methods Mentioned

BETA
amplicon sequencing
PCR
Exome Sequencing
genotyping

Software Mentioned

Target HLA
PrintReads
RealignerTargetCreator
ROC Analysis
GATK
bwa
uTYPE HLA SBT
mem
Sequencher
Omixon

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