PMID- 30942618
OWN - NLM
STAT- MEDLINE
DCOM- 20200714
LR  - 20200714
IS  - 1557-8666 (Electronic)
IS  - 1066-5277 (Print)
IS  - 1066-5277 (Linking)
VI  - 26
IP  - 9
DP  - 2019 Sep
TI  - ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation 
      Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence 
      Data.
PG  - 923-937
LID - 10.1089/cmb.2018.0224 [doi]
AB  - Human leukocyte antigen (HLA) genes provide useful information on the 
      relationship between cancer and the immune system. Despite the ease of obtaining 
      these data through next-generation sequencing methods, interpretation of these 
      relationships remains challenging owing to the complexity of HLA genes. To 
      resolve this issue, we developed a Bayesian method, ALPHLARD-NT, to identify HLA 
      germline and somatic mutations as well as HLA genotypes from whole-exome 
      sequencing (WES) and whole-genome sequencing (WGS) data. ALPHLARD-NT showed 99.2% 
      accuracy for WGS-based HLA genotyping and detected five HLA somatic mutations in 
      25 colon cancer cases. In addition, ALPHLARD-NT identified 88 HLA somatic 
      mutations, including recurrent mutations and a novel HLA-B type, from WES data of 
      343 colon adenocarcinoma cases. These results demonstrate the potential of 
      ALPHLARD-NT for conducting an accurate analysis of HLA genes even from 
      low-coverage data sets. This method can become an essential tool for 
      comprehensive analyses of HLA genes from WES and WGS data, helping to advance 
      understanding of immune regulation in cancer as well as providing guidance for 
      novel immunotherapy strategies.
FAU - Hayashi, Shuto
AU  - Hayashi S
AD  - Human Genome Center, The Institute of Medical Science, The University of Tokyo, 
      Tokyo, Japan.
FAU - Moriyama, Takuya
AU  - Moriyama T
AD  - Human Genome Center, The Institute of Medical Science, The University of Tokyo, 
      Tokyo, Japan.
FAU - Yamaguchi, Rui
AU  - Yamaguchi R
AD  - Human Genome Center, The Institute of Medical Science, The University of Tokyo, 
      Tokyo, Japan.
FAU - Mizuno, Shinichi
AU  - Mizuno S
AD  - Department of Health Sciences, Faculty of Medical Sciences, Kyushu University, 
      Fukuoka, Japan.
FAU - Komura, Mitsuhiro
AU  - Komura M
AD  - Human Genome Center, The Institute of Medical Science, The University of Tokyo, 
      Tokyo, Japan.
FAU - Miyano, Satoru
AU  - Miyano S
AD  - Human Genome Center, The Institute of Medical Science, The University of Tokyo, 
      Tokyo, Japan.
FAU - Nakagawa, Hidewaki
AU  - Nakagawa H
AD  - RIKEN Center for Integrative Medical Sciences, Tokyo, Japan.
FAU - Imoto, Seiya
AU  - Imoto S
AD  - Health Intelligence Center, The Institute of Medical Science, The University of 
      Tokyo, Tokyo, Japan.
LA  - eng
PT  - Journal Article
DEP - 20190403
PL  - United States
TA  - J Comput Biol
JT  - Journal of computational biology : a journal of computational molecular cell 
      biology
JID - 9433358
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Bayes Theorem
MH  - Computational Biology/*methods
MH  - Genotyping Techniques/*methods
MH  - HLA Antigens/*genetics
MH  - Humans
MH  - Mutation Rate
MH  - Neoplasms/*genetics
MH  - *Software
MH  - Whole Genome Sequencing/*methods
PMC - PMC6748403
OTO - NOTNLM
OT  - Bayesian model
OT  - HLA genotyping
OT  - HLA mutation calling
OT  - whole-exome sequencing
OT  - whole-genome sequencing
COIS- The authors declare there are no competing financial interests.
EDAT- 2019/04/04 06:00
MHDA- 2020/07/15 06:00
PMCR- 2019/09/05
CRDT- 2019/04/04 06:00
PHST- 2019/04/04 06:00 [pubmed]
PHST- 2020/07/15 06:00 [medline]
PHST- 2019/04/04 06:00 [entrez]
PHST- 2019/09/05 00:00 [pmc-release]
AID - 10.1089/cmb.2018.0224 [pii]
AID - 10.1089/cmb.2018.0224 [doi]
PST - ppublish
SO  - J Comput Biol. 2019 Sep;26(9):923-937. doi: 10.1089/cmb.2018.0224. Epub 2019 Apr 
      3.