SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles

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Standard

SOAPTyping : an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles. / Zhang, Yong; Chen, Yongsheng; Xu, Huixin; Fang, Junbin; Zhao, Zijian; Hu, Weipeng; Yang, Xiaoqin; Ye, Jia; Cheng, Yun; Wang, Jiayin; Sun, Weiqiang; Wang, Jian; Yang, Huanming; Yan, Jing; Fang, Lin.

I: BMC Bioinformatics, Bind 21, 295, 2020.

Publikation: Bidrag til tidsskriftTidsskriftartikelfagfællebedømt

Harvard

Zhang, Y, Chen, Y, Xu, H, Fang, J, Zhao, Z, Hu, W, Yang, X, Ye, J, Cheng, Y, Wang, J, Sun, W, Wang, J, Yang, H, Yan, J & Fang, L 2020, 'SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles', BMC Bioinformatics, bind 21, 295. https://doi.org/10.1186/s12859-020-03624-0

APA

Zhang, Y., Chen, Y., Xu, H., Fang, J., Zhao, Z., Hu, W., Yang, X., Ye, J., Cheng, Y., Wang, J., Sun, W., Wang, J., Yang, H., Yan, J., & Fang, L. (2020). SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles. BMC Bioinformatics, 21, [295]. https://doi.org/10.1186/s12859-020-03624-0

Vancouver

Zhang Y, Chen Y, Xu H, Fang J, Zhao Z, Hu W o.a. SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles. BMC Bioinformatics. 2020;21. 295. https://doi.org/10.1186/s12859-020-03624-0

Author

Zhang, Yong ; Chen, Yongsheng ; Xu, Huixin ; Fang, Junbin ; Zhao, Zijian ; Hu, Weipeng ; Yang, Xiaoqin ; Ye, Jia ; Cheng, Yun ; Wang, Jiayin ; Sun, Weiqiang ; Wang, Jian ; Yang, Huanming ; Yan, Jing ; Fang, Lin. / SOAPTyping : an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles. I: BMC Bioinformatics. 2020 ; Bind 21.

Bibtex

@article{e4654b7c7c394bc3b3903583df46beef,
title = "SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles",
abstract = "BackgroundThe 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.ResultsWe 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.ConclusionsWe 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.",
keywords = "HLA typing, Sequence-based typing, Sanger sequencing, Group specific sequencing primers",
author = "Yong Zhang and Yongsheng Chen and Huixin Xu and Junbin Fang and Zijian Zhao and Weipeng Hu and Xiaoqin Yang and Jia Ye and Yun Cheng and Jiayin Wang and Weiqiang Sun and Jian Wang and Huanming Yang and Jing Yan and Lin Fang",
year = "2020",
doi = "10.1186/s12859-020-03624-0",
language = "English",
volume = "21",
journal = "B M C Bioinformatics",
issn = "1471-2105",
publisher = "BioMed Central Ltd.",

}

RIS

TY - JOUR

T1 - SOAPTyping

T2 - an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles

AU - Zhang, Yong

AU - Chen, Yongsheng

AU - Xu, Huixin

AU - Fang, Junbin

AU - Zhao, Zijian

AU - Hu, Weipeng

AU - Yang, Xiaoqin

AU - Ye, Jia

AU - Cheng, Yun

AU - Wang, Jiayin

AU - Sun, Weiqiang

AU - Wang, Jian

AU - Yang, Huanming

AU - Yan, Jing

AU - Fang, Lin

PY - 2020

Y1 - 2020

N2 - BackgroundThe 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.ResultsWe 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.ConclusionsWe 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.

AB - BackgroundThe 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.ResultsWe 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.ConclusionsWe 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.

KW - HLA typing

KW - Sequence-based typing

KW - Sanger sequencing

KW - Group specific sequencing primers

U2 - 10.1186/s12859-020-03624-0

DO - 10.1186/s12859-020-03624-0

M3 - Journal article

C2 - 32640979

VL - 21

JO - B M C Bioinformatics

JF - B M C Bioinformatics

SN - 1471-2105

M1 - 295

ER -

ID: 246783587