PMID- 28499414
OWN - NLM
STAT- MEDLINE
DCOM- 20171017
LR  - 20181202
IS  - 1471-2105 (Electronic)
IS  - 1471-2105 (Linking)
VI  - 18
IP  - 1
DP  - 2017 May 12
TI  - HLAscan: genotyping of the HLA region using next-generation sequencing data.
PG  - 258
LID - 10.1186/s12859-017-1671-3 [doi]
LID - 258
AB  - 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.
FAU - Ka, Sojeong
AU  - Ka S
AD  - R&D center, Syntekabio, Inc., 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, 
      South Korea.
FAU - Lee, Sunho
AU  - Lee S
AD  - Main office, Syntekabio, Inc., 187 Techno 2-ro, Yuseong-gu, Daejeon, 34025, South 
      Korea.
FAU - Hong, Jonghee
AU  - Hong J
AD  - R&D center, Syntekabio, Inc., 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, 
      South Korea.
FAU - Cho, Yangrae
AU  - Cho Y
AD  - Main office, Syntekabio, Inc., 187 Techno 2-ro, Yuseong-gu, Daejeon, 34025, South 
      Korea.
FAU - Sung, Joohon
AU  - Sung J
AD  - Complex Disease and Genome Epidemiology Branch, Department of Epidemiology, 
      School of Public Health, Seoul National University, Seoul, 08826, South Korea.
FAU - Kim, Han-Na
AU  - Kim HN
AD  - Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, 
      07985, South Korea.
FAU - Kim, Hyung-Lae
AU  - Kim HL
AD  - Department of Biochemistry, School of Medicine, Ewha Womans University, Seoul, 
      07985, South Korea. hyung@ewha.ac.kr.
FAU - Jung, Jongsun
AU  - Jung J
AD  - Main office, Syntekabio, Inc., 187 Techno 2-ro, Yuseong-gu, Daejeon, 34025, South 
      Korea. jung@syntekabio.com.
LA  - eng
PT  - Journal Article
DEP - 20170512
PL  - England
TA  - BMC Bioinformatics
JT  - BMC bioinformatics
JID - 100965194
RN  - 0 (HLA Antigens)
RN  - 0 (HLA-A Antigens)
RN  - 0 (HLA-B Antigens)
RN  - 0 (HLA-DRB1 Chains)
SB  - IM
MH  - Alleles
MH  - Area Under Curve
MH  - Exons
MH  - Genotype
MH  - HLA Antigens/chemistry/*genetics/metabolism
MH  - HLA-A Antigens/chemistry/genetics/metabolism
MH  - HLA-B Antigens/chemistry/metabolism
MH  - HLA-DRB1 Chains/chemistry/genetics/metabolism
MH  - HapMap Project
MH  - High-Throughput Nucleotide Sequencing
MH  - Histocompatibility Testing/*methods
MH  - Humans
MH  - ROC Curve
MH  - Sequence Analysis, DNA
PMC - PMC5427585
OTO - NOTNLM
OT  - HLA typing
OT  - HLAscan
OT  - Next-generation sequencing
OT  - Phasing issue
EDAT- 2017/05/14 06:00
MHDA- 2017/10/19 06:00
PMCR- 2017/05/12
CRDT- 2017/05/14 06:00
PHST- 2016/11/17 00:00 [received]
PHST- 2017/05/03 00:00 [accepted]
PHST- 2017/05/14 06:00 [entrez]
PHST- 2017/05/14 06:00 [pubmed]
PHST- 2017/10/19 06:00 [medline]
PHST- 2017/05/12 00:00 [pmc-release]
AID - 10.1186/s12859-017-1671-3 [pii]
AID - 1671 [pii]
AID - 10.1186/s12859-017-1671-3 [doi]
PST - epublish
SO  - BMC Bioinformatics. 2017 May 12;18(1):258. doi: 10.1186/s12859-017-1671-3.