In Silico Typing of Classical and Non-classical HLA Alleles from Standard RNA-Seq Reads

Methods Mol Biol. 2018;1802:177-191. doi: 10.1007/978-1-4939-8546-3_12.


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.

Keywords: HLA expression; HLA type; Immunoinformatics; In silico; NGS; Non-classical HLA class I; RNA-Seq.

MeSH terms

  • Alleles*
  • Computer Simulation*
  • Gene Frequency / genetics
  • HLA Antigens / genetics*
  • Histocompatibility Antigens Class I / genetics
  • Histocompatibility Antigens Class II / genetics
  • Histocompatibility Testing / methods*
  • Humans
  • Sequence Analysis, RNA / methods*


  • HLA Antigens
  • Histocompatibility Antigens Class I
  • Histocompatibility Antigens Class II