Typing and copy number determination for HLA-DRB3, -DRB4 and -DRB5 from next-generation sequencing data

HLA. 2017 Mar;89(3):150-157. doi: 10.1111/tan.12966. Epub 2017 Feb 1.

Abstract

Background: HLA-DRB3, DRB4 and DRB5 (DRB3/4/5) are paralogues of HLA-DRB1. They have important roles in transplantation and have been reported to be related to many diseases. HLA typing methods for DRB3/4/5 based on NGS data have many limitations now, such as need of polymerase chain reaction (PCR) or low accuracy.

Materials and methods: We present a HLA typing method for DRB3/4/5 based on read mapping and haplotype assembly from NGS data. Also, copy number of DRB3/4/5 is determined by a k-means clustering method according to ratio of sequencing depth between DRB3/4/5 and DRB1.

Results: We achieved 100%, 100%, 100% accuracy on simulated data and 95.88%, 98.89%, 99.34% accuracy on MHC capture Illumina sequencing data at 4-digit resolution with 30-fold coverage for DRB3/4/5 separately. We also explored the DRB3/4/5 profiles in five continental populations through low coverage WGS data generated by the 1000 Genome Project. We found that frequency of DRB4 in African were significantly lower than that in all other populations.

Conclusion: Our method for DRB3/4/5 typing has high accuracy. It is a good supplement to regular HLA typing and could help in disease studies, medical applications and human population diversity studies.

Keywords: DRB3; DRB4; DRB5; HLA typing; NGS; copy number.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Chromosome Mapping / methods*
  • Continental Population Groups
  • Gene Dosage
  • Gene Expression
  • Gene Frequency
  • HLA-DRB3 Chains / genetics*
  • HLA-DRB3 Chains / immunology
  • HLA-DRB4 Chains / genetics*
  • HLA-DRB4 Chains / immunology
  • HLA-DRB5 Chains / genetics*
  • HLA-DRB5 Chains / immunology
  • Haplotypes
  • High-Throughput Nucleotide Sequencing
  • Histocompatibility Testing / methods*
  • Histocompatibility Testing / statistics & numerical data
  • Human Genome Project
  • Humans
  • Sequence Analysis, DNA / statistics & numerical data*

Substances

  • HLA-DRB3 Chains
  • HLA-DRB4 Chains
  • HLA-DRB5 Chains