PMID- 33868290
OWN - NLM
STAT- MEDLINE
DCOM- 20210928
LR  - 20210928
IS  - 1664-3224 (Electronic)
IS  - 1664-3224 (Linking)
VI  - 12
DP  - 2021
TI  - Benchmarking the Human Leukocyte Antigen Typing Performance of Three Assays and 
      Seven Next-Generation Sequencing-Based Algorithms.
PG  - 652258
LID - 10.3389/fimmu.2021.652258 [doi]
LID - 652258
AB  - With the great progress made recently in next generation sequencing (NGS) 
      technology, sequencing accuracy and throughput have increased, while the cost for 
      data has decreased. Various human leukocyte antigen (HLA) typing algorithms and 
      assays have been developed and have begun to be used in clinical practice. In 
      this study, we compared the HLA typing performance of three HLA assays and seven 
      NGS-based HLA algorithms and assessed the impact of sequencing depth and length 
      on HLA typing accuracy based on 24 benchmarked samples. The algorithms 
      HISAT-genotype and HLA-HD showed the highest accuracy at both the first field and 
      the second field resolution, followed by HLAscan. Our internal capture-based HLA 
      assay showed comparable performance with whole exome sequencing (WES). We found 
      that the minimal depth was 100X for HISAT-genotype and HLA-HD to obtain more than 
      90% accuracy at the third field level. The top three algorithms were quite robust 
      to the change of read length. Thus, we recommend using HISAT-genotype and HLA-HD 
      for NGS-based HLA genotyping because of their higher accuracy and robustness to 
      read length. We propose that a minimal sequence depth for obtaining more than 90% 
      HLA typing accuracy at the third field level is 100X. Besides, targeting 
      capture-based NGS HLA typing may be more suitable than WES in clinical practice 
      due to its lower sequencing cost and higher HLA sequencing depth.
CI  - Copyright (c) 2021 Liu, Yao, Gong, Song, Chen, Ye, Liu, Li, Dong, Meng, Chen and 
      Zheng.
FAU - Liu, Ping
AU  - Liu P
AD  - Department of Oncology, The Second Xiangya Hospital of Central South University, 
      Changsha, China.
FAU - Yao, Minya
AU  - Yao M
AD  - The First Affiliated Hospital of Zhejiang University, School of Medicine, 
      Hangzhou, China.
FAU - Gong, Yu
AU  - Gong Y
AD  - Department of Urology, Second Affiliated Hospital, Zhejiang University College of 
      Medicine, Hangzhou, China.
FAU - Song, Yunjie
AU  - Song Y
AD  - The Bioinformatics Department, 3DMed Inc., Shanghai, China.
FAU - Chen, Yanan
AU  - Chen Y
AD  - The Bioinformatics Department, 3DMed Inc., Shanghai, China.
FAU - Ye, Yizhou
AU  - Ye Y
AD  - The Bioinformatics Department, 3DMed Inc., Shanghai, China.
FAU - Liu, Xiao
AU  - Liu X
AD  - The Bioinformatics Department, 3DMed Inc., Shanghai, China.
FAU - Li, Fugen
AU  - Li F
AD  - The Bioinformatics Department, 3DMed Inc., Shanghai, China.
FAU - Dong, Hua
AU  - Dong H
AD  - The Bioinformatics Department, 3DMed Inc., Shanghai, China.
FAU - Meng, Rui
AU  - Meng R
AD  - Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 
      China.
FAU - Chen, Hao
AU  - Chen H
AD  - The Bioinformatics Department, 3DMed Inc., Shanghai, China.
FAU - Zheng, Aiwen
AU  - Zheng A
AD  - Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer 
      Hospital), Hangzhou, China.
AD  - Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, 
      Hangzhou, China.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20210331
PL  - Switzerland
TA  - Front Immunol
JT  - Frontiers in immunology
JID - 101560960
RN  - 0 (HLA Antigens)
SB  - IM
MH  - *Algorithms
MH  - Alleles
MH  - Computational Biology/methods
MH  - Genotype
MH  - HLA Antigens/*genetics/*immunology
MH  - High-Throughput Nucleotide Sequencing/*methods/standards
MH  - Histocompatibility Testing/*methods/standards
MH  - Humans
MH  - Reproducibility of Results
MH  - Sequence Analysis, DNA
MH  - Software
PMC - PMC8045758
OTO - NOTNLM
OT  - accuracy
OT  - algorithms
OT  - benchmark
OT  - human leukocyte antigen
OT  - next-generation sequencing
COIS- All authors affiliated with 3D Medicines Inc. are current or former employees. 
      There are no patents, products in development or marketed products to declare. 
      The authors declare that the research was conducted in the absence of any 
      commercial or financial relationships that could be construed as a potential 
      conflict of interest.
EDAT- 2021/04/20 06:00
MHDA- 2021/09/29 06:00
PMCR- 2021/01/01
CRDT- 2021/04/19 06:21
PHST- 2021/01/12 00:00 [received]
PHST- 2021/03/03 00:00 [accepted]
PHST- 2021/04/19 06:21 [entrez]
PHST- 2021/04/20 06:00 [pubmed]
PHST- 2021/09/29 06:00 [medline]
PHST- 2021/01/01 00:00 [pmc-release]
AID - 10.3389/fimmu.2021.652258 [doi]
PST - epublish
SO  - Front Immunol. 2021 Mar 31;12:652258. doi: 10.3389/fimmu.2021.652258. eCollection 
      2021.