A new set of reagents and related software used for NGS based classical and non-classical HLA typing showing evidence for a greater HLA haplotype diversity

Hum Immunol. 2020 May;81(5):202-205. doi: 10.1016/j.humimm.2020.02.003. Epub 2020 Feb 28.

Abstract

To evaluate the HLA typing performance of a new Long-Range PCR NGS set of reagents and its dedicated software, a panel of 41 reference homozygous cell lines from the International Histocompatibility Working Group (IHWG) and a panel of 376 volunteer bone marrow donors were analyzed for classical and non-classical HLA class I and class II genes. All results, except HLA-DPB1, were obtained without any ambiguities at the 3rd field level. Based on the high resolution performance of the reagents, a number of new alleles have been described not only for classical but also for non-classical HLA class I genes, leading to a more accurate haplotype definition. Linkage disequilibrium between HLA-A and HLA-G genes has been defined at 4th field level of resolution. Moreover, for the first time, HLA-DQA2 and DQB2 polymorphisms and their linkage disequilibrium with DQB1 were described.

Keywords: HLA genotyping; Haplotype diversity; NGS; Non-classical HLA genes.

MeSH terms

  • Alleles
  • Bone Marrow / immunology
  • Gene Frequency
  • Genes, MHC Class I
  • Genes, MHC Class II
  • HLA Antigens / genetics*
  • Haplotypes*
  • High-Throughput Nucleotide Sequencing / methods*
  • Histocompatibility Antigens Class I / genetics*
  • Histocompatibility Antigens Class II / genetics*
  • Histocompatibility Testing / methods*
  • Humans
  • Indicators and Reagents
  • Linkage Disequilibrium
  • Polymerase Chain Reaction / methods
  • Polymorphism, Genetic*
  • Software*
  • Tissue Donors

Substances

  • HLA Antigens
  • Histocompatibility Antigens Class I
  • Histocompatibility Antigens Class II
  • Indicators and Reagents