HLA typing from 1000 genomes whole genome and whole exome illumina data

PLoS One. 2013 Nov 6;8(11):e78410. doi: 10.1371/journal.pone.0078410. eCollection 2013.


Specific HLA genotypes are known to be linked to either resistance or susceptibility to certain diseases or sensitivity to certain drugs. In addition, high accuracy HLA typing is crucial for organ and bone marrow transplantation. The most widespread high resolution HLA typing method used to date is Sanger sequencing based typing (SBT), and next generation sequencing (NGS) based HLA typing is just starting to be adopted as a higher throughput, lower cost alternative. By HLA typing the HapMap subset of the public 1000 Genomes paired Illumina data, we demonstrate that HLA-A, B and C typing is possible from exome sequencing samples with higher than 90% accuracy. The older 1000 Genomes whole genome sequencing read sets are less reliable and generally unsuitable for the purpose of HLA typing. We also propose using coverage % (the extent of exons covered) as a quality check (QC) measure to increase reliability.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Base Sequence
  • Exome*
  • Genotype*
  • HLA Antigens / classification
  • HLA Antigens / genetics*
  • HLA Antigens / immunology
  • High-Throughput Nucleotide Sequencing
  • Histocompatibility Testing / methods*
  • Histocompatibility Testing / statistics & numerical data
  • Humans
  • Molecular Sequence Data
  • Reproducibility of Results
  • Sequence Analysis, DNA


  • HLA Antigens

Grant support

Supported by the Swiss Contribution scheme http://www.contribution-enlargement.admin.ch/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.