In Silico Typing of Classical and Non-classical HLA Alleles from Standard RNA-Seq Reads.
Next-Generation Sequencing (NGS) enables the rapid generation of billions of short nucleic acid sequence fragments (i.e., "sequencing reads"). Especially, the adoption of gene expression profiling using whole transcriptome sequencing (i.e., "RNA-Seq") has been rapid. Here, we describe an in silico method, seq2HLA, that takes standard RNA-Seq reads as input and determines a sample's (classical and non-classical) HLA class I and class II types as well as HLA expression. We demonstrate the application of seq2HLA using publicly available RNA-Seq data from the Burkitt's lymphoma cell line DAUDI and the choriocarcinoma cell line JEG-3.
['Boegel|Sebastian|S|', 'Bukur|Thomas|T|', 'Castle|John C|JC|', 'Sahin|Ugur|U|']
D000483:Alleles D003198:Computer Simulation D005787:Gene Frequency D006680:HLA Antigens D015395:Histocompatibility Antigens Class I D000949:Histocompatibility Antigens Class II D006650:Histocompatibility Testing D006801:Humans D017423:Sequence Analysis, RNA
In silico RNA-Seq NGS HLA expression HLA type Immunoinformatics Non-classical HLA class I