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

Yong Zhang,Weiqiang Sun,Huanming Yang,Jia Ye,Lin Fang,Huixin Xu,Zijian Zhao,Xiaoqin Yang,Jing Yan,Weipeng Hu,Jian Wang,Yongsheng Chen,Junbin Fang,Jiayin Wang,Yun Cheng

doi:10.1186/s12859-020-03624-0

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.

Highlights

The human leukocyte antigen (HLA) gene family plays a key role in the immune response and is crucial in many biomedical and clinical settings
Testing on UCLA samples and anonymous clinical samples To verify the accuracy of SOAPTyping, our test data contains 36 samples initiated for external quality assessments with the University of California Los Angeles (UCLA) International HLA DNA Exchange (Los Angeles, CA, USA)
The sequence was analyzed with SOAPTyping and uTYPE, which are used in typing application in BGI, and the typing results were compared to the consensus-based on the high resolution provided by UCLA

Summary

Results

Best practices / proposed workflow SOAPTyping works on chromatogram files with the format of ABIF, including .ab and .fsa files, which are generated from Sanger sequencing by ABI Genetic Analyzer Software (Applied Biosystems, Foster City, CA). The PCR products were directly sequenced in exons of HLA-A, −B, −C, −DRB1, and -DQB1 (Table S1) using a 3730XL DNA Analyzer (Applied Biosystems, Foster City, CA). The sequence was analyzed with SOAPTyping and uTYPE, which are used in typing application in BGI, and the typing results were compared to the consensus-based on the high resolution provided by UCLA. To further compare the performance of SOAPTyping and uTYPE in clinical, 100 anonymous clinical samples generated the same as the UCLA samples had been tested on a Thinkpad × 270 computer with Windows 10 system. Average analysis time of a sample is 8.43 s using SOAPTyping, while 46.38 s spent using uTYPE, which is about 5.5 times slower

Conclusions

Background