ArticleBMC bioinformatics2020
SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 11 citations in OpenAlex.
- Clinical applications and methodology updates in HLA typing.BMC immunology · 2026Review
- Healthy donor T cell receptors expand functional neoantigen recognition beyond patient vaccination.Science advances · 2026Article
- Identification of immunogenic neoantigens from intron retention in colorectal cancer.Scientific reports · 2026Article
- Computational methods and data resources for predicting tumor neoantigens.Briefings in bioinformatics · 2025Review
- Prevalence of HLA-B*58:01 allele among Malay, Chinese and Indian ethnic patients with gout attending primary care clinics in Malaysia.Journal of community genetics · 2025Article
- HLA Gene Polymorphisms in Romanian Patients with Chronic Lymphocytic Leukemia.Genetics research · 2024Article
- Artificial intelligence and neoantigens: paving the path for precision cancer immunotherapy.Frontiers in immunology · 2024Review
- Design and generation of mRNAs encoding conserved regions of SARS-CoV-2 ORF1ab for T cell-mediated immune activation.Future virology · 2023Article
Corrections and comments
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Authors and funding
15 authors at 3 institutions in 2 countries.
Funding
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.
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