Abstract
Next-generation sequencing (NGS) enables high-throughput transcriptome profiling using the RNA-Seq assay, resulting in billions of short sequence reads. Worldwide adoption has been rapid: many laboratories worldwide generate transcriptome sequence reads daily. Here, we describe methods for obtaining a sample’s human leukocyte antigen (HLA) class I and II types and HLA expression using standard NGS RNA-Seq sequence reads. We demonstrate the application using our algorithm, seq2HLA, and a publicly available RNA-Seq dataset from the Burkitt lymphoma cell line Raji.
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Boegel, S., Scholtalbers, J., Löwer, M., Sahin, U., Castle, J.C. (2015). In Silico HLA Typing Using Standard RNA-Seq Sequence Reads. In: Bugert, P. (eds) Molecular Typing of Blood Cell Antigens. Methods in Molecular Biology, vol 1310. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2690-9_20
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DOI: https://doi.org/10.1007/978-1-4939-2690-9_20
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2689-3
Online ISBN: 978-1-4939-2690-9
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