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Methods Mol Biol. 2015;1310:247-58. doi: 10.1007/978-1-4939-2690-9_20.

In Silico HLA Typing Using Standard RNA-Seq Sequence Reads.

Author information

1
TRON gGmbH - Translational Oncology at Johannes Gutenberg-University Medical Center gGmbH Mainz, Langenbeckstr. 1, Building 708, Mainz, 55131, Germany, boegels@uni-mainz.de.

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.

PMID:
26024640
DOI:
10.1007/978-1-4939-2690-9_20
[Indexed for MEDLINE]

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