Limin Jiang, Steven F. Baker, Michele Ceccarelil, Yan Guo
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引用次数: 0
Abstract
HLA typing is crucial for clinical and research applications, including transplantation, disease association studies and personalised medicine. This study provides an in-depth analysis of five key challenges in computational HLA typing methods: varying lengths, high polymorphism, complex phylogenetic structures, high sequence similarity and the requirement for frequent updates. This study evaluates 27 computation-based HLA typing tools developed over the past 12 years, using a novel sequencing dataset of A549 cell lines with matched short-read RNA-Seq and long-read Iso-Seq data. We comprehensively investigated these 27 tools in terms of accessibility, capability, reliability, reproducibility, scalability and performance. In addition, we discuss the advantages and disadvantages of current tools and identify critical areas for future research and development to advance HLA typing technologies.
期刊介绍：
HLA, the journal, publishes articles on various aspects of immunogenetics. These include the immunogenetics of cell surface antigens, the ontogeny and phylogeny of the immune system, the immunogenetics of cell interactions, the functional aspects of cell surface molecules and their natural ligands, and the role of tissue antigens in immune reactions. Additionally, the journal covers experimental and clinical transplantation, the relationships between normal tissue antigens and tumor-associated antigens, the genetic control of immune response and disease susceptibility, and the biochemistry and molecular biology of alloantigens and leukocyte differentiation. Manuscripts on molecules expressed on lymphoid cells, myeloid cells, platelets, and non-lineage-restricted antigens are welcomed. Lastly, the journal focuses on the immunogenetics of histocompatibility antigens in both humans and experimental animals, including their tissue distribution, regulation, and expression in normal and malignant cells, as well as the use of antigens as markers for disease.
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