PMID- 28419628
OWN - NLM
STAT- MEDLINE
DCOM- 20180413
LR  - 20180628
IS  - 1098-1004 (Electronic)
IS  - 1059-7794 (Linking)
VI  - 38
IP  - 7
DP  - 2017 Jul
TI  - HLA-HD: An accurate HLA typing algorithm for next-generation sequencing data.
PG  - 788-797
LID - 10.1002/humu.23230 [doi]
AB  - The accurate typing of human leukocyte antigen (HLA) alleles is critical for a 
      variety of medical applications, such as genomic studies of multifactorial 
      diseases, including immune system and inflammation-related disorders, and donor 
      selection in organ transplantation and regenerative medicine. Here, we developed 
      a new algorithm for determining HLA alleles using next-generation sequencing 
      (NGS) results. The method consists of constructing an extensive dictionary of HLA 
      alleles, precise mapping of the NGS reads, and calculating a score based on 
      weighted read counts to select the most suitable pair of alleles. The developed 
      algorithm compares the score of all allele pairs, taking into account variation 
      not only in the domain for antigen presentation (G-DOMAIN), but also outside this 
      domain. Using this method, HLA alleles could be determined with 6-digit 
      precision. We showed that our method was more accurate than other NGS-based 
      methods and revealed limitations of the conventional HLA typing technologies. 
      Furthermore, we determined the complete genomic sequence of an 
      HLA-A-like-pseudogene when we assembled NGS reads that had caused arguable 
      typing, and found its identity with HLA-Y*02:01. The accuracy of the HLA-A allele 
      typing was improved after the HLA-Y*02:01 sequence was included in the HLA allele 
      dictionary.
CI  - (c) 2017 The Authors. **Human Mutation published by Wiley Periodicals, Inc.
FAU - Kawaguchi, Shuji
AU  - Kawaguchi S
AUID- ORCID: 0000-0002-4045-6518
AD  - Center for Genomic Medicine, Kyoto University Graduate School of Medicine, 
      Sakyo-ku, Kyoto, Japan.
FAU - Higasa, Koichiro
AU  - Higasa K
AD  - Center for Genomic Medicine, Kyoto University Graduate School of Medicine, 
      Sakyo-ku, Kyoto, Japan.
FAU - Shimizu, Masakazu
AU  - Shimizu M
AD  - Center for Genomic Medicine, Kyoto University Graduate School of Medicine, 
      Sakyo-ku, Kyoto, Japan.
FAU - Yamada, Ryo
AU  - Yamada R
AD  - Center for Genomic Medicine, Kyoto University Graduate School of Medicine, 
      Sakyo-ku, Kyoto, Japan.
FAU - Matsuda, Fumihiko
AU  - Matsuda F
AD  - Center for Genomic Medicine, Kyoto University Graduate School of Medicine, 
      Sakyo-ku, Kyoto, Japan.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20170512
PL  - United States
TA  - Hum Mutat
JT  - Human mutation
JID - 9215429
RN  - 0 (DNA Primers)
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Algorithms
MH  - Alleles
MH  - Chromosome Mapping
MH  - Cloning, Molecular
MH  - Computational Biology/*methods
MH  - DNA Primers
MH  - Databases, Factual
MH  - Exons
MH  - Genome, Human
MH  - Genomics
MH  - HLA Antigens/biosynthesis/genetics
MH  - High-Throughput Nucleotide Sequencing/*methods
MH  - *Histocompatibility Testing
MH  - Humans
MH  - Models, Statistical
MH  - Polymerase Chain Reaction
MH  - Pseudogenes
MH  - Reproducibility of Results
MH  - Sequence Analysis, DNA/*methods
OTO - NOTNLM
OT  - HLA gene
OT  - genotyping
OT  - next-generation sequencing
OT  - software
EDAT- 2017/04/19 06:00
MHDA- 2018/04/14 06:00
CRDT- 2017/04/19 06:00
PHST- 2016/12/02 00:00 [received]
PHST- 2017/03/24 00:00 [revised]
PHST- 2017/04/09 00:00 [accepted]
PHST- 2017/04/19 06:00 [pubmed]
PHST- 2018/04/14 06:00 [medline]
PHST- 2017/04/19 06:00 [entrez]
AID - 10.1002/humu.23230 [doi]
PST - ppublish
SO  - Hum Mutat. 2017 Jul;38(7):788-797. doi: 10.1002/humu.23230. Epub 2017 May 12.