Next-generation sequencing (NGS) enables high-throughput transcriptome profi ling 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.
CITATION STYLE
Boegel, S., Scholtalbers, J., Löwer, M., Sahin, U., & Castle, J. C. (2015). In silico HLA typing using standard RNA-seq sequence reads. Methods in Molecular Biology, 1310, 247–258. https://doi.org/10.1007/978-1-4939-2690-9_20
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