HLA Typing from Short-Read Sequencing Data with OptiType

Methods Mol Biol. 2018:1802:215-223. doi: 10.1007/978-1-4939-8546-3_15.

Abstract

The established standards for HLA genotyping rely on targeted DNA sequencing techniques. However, the increasing abundance of short-read sequencing data has prompted a demand for computational tools capable of HLA typing from general purpose sequencing data as well. OptiType is a software that performs HLA typing from short-read DNA and RNA sequencing data, and this chapter guides the user through its installation and usage.

Keywords: Bioinformatics; HLA class I typing; In silico; Mapping; OptiType; RNA-Seq; Whole-exome Seq.

MeSH terms

  • Alleles
  • Exome Sequencing
  • HLA Antigens / genetics
  • High-Throughput Nucleotide Sequencing / methods*
  • Histocompatibility Testing / methods*
  • Humans
  • Sequence Alignment
  • Software*

Substances

  • HLA Antigens