PMID- 33655664
OWN - NLM
STAT- MEDLINE
DCOM- 20210707
LR  - 20210707
IS  - 2059-2310 (Electronic)
IS  - 2059-2302 (Linking)
VI  - 97
IP  - 6
DP  - 2021 Jun
TI  - Systematic comparative study of computational methods for HLA typing from 
      next-generation sequencing.
PG  - 481-492
LID - 10.1111/tan.14244 [doi]
AB  - The human leukocyte antigen (HLA) system plays an important role in hematopoietic 
      stem cell transplantation (HSCT) and organ transplantations, immune disorders as 
      well as oncological immunotherapy. However, HLA typing remains a challenging task 
      due to the high level of polymorphism and homology among HLA genes. Based on the 
      high-throughput next-generation sequencing data, new HLA typing algorithms and 
      software tools were developed. But there is still a deficit of systematic 
      comparative studies to assist in the selection of the optimal analytical 
      approaches under different conditions. Here, we present a detailed comparison of 
      eight software tools for HLA typing on different real datasets (whole-genome 
      sequencing, whole-exome sequencing and transcriptomic sequencing data) and 
      in-silico samples with different sequencing lengths, depths, and error rates. We 
      figure out the algorithms with the best efficiency in different scenarios, and 
      demonstrate the effect of different raw reads on analytical performances. Our 
      results provide a comprehensive picture of specifications and performances of the 
      eight existing HLA genotyping algorithms, which could assist researchers in 
      selecting the most appropriate tool for specific raw datasets.
CI  - (c) 2021 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.
FAU - Yu, Yuechun
AU  - Yu Y
AUID- ORCID: 0000-0001-7244-3554
AD  - Bio-X Institutes, Key Laboratory for the Genetics of Developmental and 
      Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation 
      Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China.
FAU - Wang, Ke
AU  - Wang K
AD  - Bio-X Institutes, Key Laboratory for the Genetics of Developmental and 
      Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation 
      Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China.
FAU - Fahira, Aamir
AU  - Fahira A
AD  - Bio-X Institutes, Key Laboratory for the Genetics of Developmental and 
      Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation 
      Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China.
FAU - Yang, Qiangzhen
AU  - Yang Q
AD  - Bio-X Institutes, Key Laboratory for the Genetics of Developmental and 
      Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation 
      Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China.
FAU - Sun, Renliang
AU  - Sun R
AD  - Bio-X Institutes, Key Laboratory for the Genetics of Developmental and 
      Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation 
      Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China.
FAU - Li, Zhiqiang
AU  - Li Z
AD  - Bio-X Institutes, Key Laboratory for the Genetics of Developmental and 
      Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation 
      Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China.
FAU - Wang, Zhuo
AU  - Wang Z
AD  - Bio-X Institutes, Key Laboratory for the Genetics of Developmental and 
      Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation 
      Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China.
FAU - Shi, Yongyong
AU  - Shi Y
AD  - Bio-X Institutes, Key Laboratory for the Genetics of Developmental and 
      Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation 
      Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20210502
PL  - England
TA  - HLA
JT  - HLA
JID - 101675570
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Alleles
MH  - *HLA Antigens/genetics
MH  - *High-Throughput Nucleotide Sequencing
MH  - Histocompatibility Testing
MH  - Humans
MH  - Sequence Analysis, DNA
OTO - NOTNLM
OT  - HLA genotyping
OT  - benchmarking
OT  - human leukocyte antigens
OT  - next-generation sequencing
EDAT- 2021/03/04 06:00
MHDA- 2021/07/08 06:00
CRDT- 2021/03/03 05:55
PHST- 2021/02/21 00:00 [revised]
PHST- 2020/11/24 00:00 [received]
PHST- 2021/02/25 00:00 [accepted]
PHST- 2021/03/04 06:00 [pubmed]
PHST- 2021/07/08 06:00 [medline]
PHST- 2021/03/03 05:55 [entrez]
AID - 10.1111/tan.14244 [doi]
PST - ppublish
SO  - HLA. 2021 Jun;97(6):481-492. doi: 10.1111/tan.14244. Epub 2021 May 2.