PMID- 32640979
OWN - NLM
STAT- MEDLINE
DCOM- 20200817
LR  - 20201110
IS  - 1471-2105 (Electronic)
IS  - 1471-2105 (Linking)
VI  - 21
IP  - 1
DP  - 2020 Jul 8
TI  - SOAPTyping: an open-source and cross-platform tool for sequence-based typing for 
      HLA class I and II alleles.
PG  - 295
LID - 10.1186/s12859-020-03624-0 [doi]
LID - 295
AB  - BACKGROUND: The human leukocyte antigen (HLA) gene family plays a key role in the 
      immune response and thus is crucial in many biomedical and clinical settings. 
      Utilizing Sanger sequencing, the golden standard technology for HLA typing 
      enables accurate identification of HLA alleles in high-resolution. However, only 
      the commercial software, such as uTYPE, SBT-Assign, and SBTEngine, and very few 
      open-source tools could be applied to perform HLA typing based on Sanger 
      sequencing. RESULTS: We developed a user-friendly, cross-platform and open-source 
      desktop application, known as SOAPTyping, for Sanger-based typing in HLA class I 
      and II alleles. SOAPTyping can produce accurate results with a comprehensible 
      protocol and featured functions. Moreover, SOAPTyping supports a more advanced 
      group-specific sequencing primers (GSSP) module to solve the ambiguous typing 
      results. We used SOAPTyping to analyze 36 samples with known HLA typing from the 
      University of California Los Angeles (UCLA) International HLA DNA Exchange 
      platform and 100 anonymous clinical samples, and the HLA typing results from 
      SOAPTyping are identical to the golden results and 5.5 times faster than 
      commercial software uTYPE, which shows the usability of SOAPTyping. CONCLUSIONS: 
      We introduce the SOAPTyping as the first open-source and cross-platform HLA 
      typing software with the capability of producing high-resolution HLA typing 
      predictions from Sanger sequence data.
FAU - Zhang, Yong
AU  - Zhang Y
AD  - BGI-Shenzhen, Shenzhen, 518083, China.
AD  - Department of Biology, University of Copenhagen, Copenhagen, Denmark.
FAU - Chen, Yongsheng
AU  - Chen Y
AD  - Geneplus-Beijing, Beijing, 102206, China.
FAU - Xu, Huixin
AU  - Xu H
AD  - BGI-Shenzhen, Shenzhen, 518083, China.
FAU - Fang, Junbin
AU  - Fang J
AD  - BGI Genomics, Shenzhen, 518083, China.
FAU - Zhao, Zijian
AU  - Zhao Z
AD  - BGI-Shenzhen, Shenzhen, 518083, China.
FAU - Hu, Weipeng
AU  - Hu W
AD  - BGI-Shenzhen, Shenzhen, 518083, China.
AD  - China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
FAU - Yang, Xiaoqin
AU  - Yang X
AD  - BGI Genomics, Shenzhen, 518083, China.
FAU - Ye, Jia
AU  - Ye J
AD  - BGI-Shenzhen, Shenzhen, 518083, China.
FAU - Cheng, Yun
AU  - Cheng Y
AD  - Zhejiang Hospital, No 12 Lingyin Road, Hangzhou, 310013, Xihu District, China.
FAU - Wang, Jiayin
AU  - Wang J
AD  - Department of Computer Science and Technology, Xi'an Jiaotong University, 28 West 
      Xianning Road, Xi'an, 710048, Shaanxi, China.
FAU - Sun, Weiqiang
AU  - Sun W
AD  - Shanghai Institute for Advanced Communication and Data Science, Shanghai Jiao 
      Tong University, Shanghai, 200240, China.
FAU - Wang, Jian
AU  - Wang J
AD  - BGI-Shenzhen, Shenzhen, 518083, China.
AD  - James D. Watson Institute of Genome Science, Hangzhou, 310008, China.
FAU - Yang, Huanming
AU  - Yang H
AD  - BGI-Shenzhen, Shenzhen, 518083, China.
AD  - James D. Watson Institute of Genome Science, Hangzhou, 310008, China.
FAU - Yan, Jing
AU  - Yan J
AD  - Zhejiang Hospital, No 12 Lingyin Road, Hangzhou, 310013, Xihu District, China. 
      zjicu@vip.163.com.
FAU - Fang, Lin
AU  - Fang L
AUID- ORCID: 0000-0002-5954-3435
AD  - BGI-Shenzhen, Shenzhen, 518083, China. fangl@genomics.cn.
AD  - Department of Biology, University of Copenhagen, Copenhagen, Denmark. 
      fangl@genomics.cn.
LA  - eng
GR  - 61433009/National Natural Science Foundation of China/
GR  - 2015A030308017/Guangdong Natural Science Foundation/
PT  - Journal Article
DEP - 20200708
PL  - England
TA  - BMC Bioinformatics
JT  - BMC bioinformatics
JID - 100965194
RN  - 0 (DNA Primers)
RN  - 0 (HLA Antigens)
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Histocompatibility Antigens Class II)
SB  - IM
MH  - Alleles
MH  - DNA Primers
MH  - HLA Antigens/*genetics
MH  - Histocompatibility Antigens Class I
MH  - Histocompatibility Antigens Class II
MH  - Histocompatibility Testing/*methods
MH  - Humans
MH  - *Sequence Analysis, DNA
MH  - *Software
PMC - PMC7646500
OTO - NOTNLM
OT  - Group specific sequencing primers
OT  - HLA typing
OT  - Sanger sequencing
OT  - Sequence-based typing
COIS- The authors declare that they have no competing interests.
EDAT- 2020/07/10 06:00
MHDA- 2020/08/18 06:00
PMCR- 2020/07/08
CRDT- 2020/07/10 06:00
PHST- 2019/12/30 00:00 [received]
PHST- 2020/06/22 00:00 [accepted]
PHST- 2020/07/10 06:00 [entrez]
PHST- 2020/07/10 06:00 [pubmed]
PHST- 2020/08/18 06:00 [medline]
PHST- 2020/07/08 00:00 [pmc-release]
AID - 10.1186/s12859-020-03624-0 [pii]
AID - 3624 [pii]
AID - 10.1186/s12859-020-03624-0 [doi]
PST - epublish
SO  - BMC Bioinformatics. 2020 Jul 8;21(1):295. doi: 10.1186/s12859-020-03624-0.