Multilocus HLA haplotypes <i>(A-B-C-DRB1-DRB3/DRB4/DRB5-DQA1-DQB1-DPA1-DPB1)</i> in families of patients scheduled for allogeneic hematopoietic stem cell transplantation

Abstract

HLA haplotype is a block of HLA genes located on the same chromosome. Highly polymorphic HLA genes display strong linkage disequilibrium, which results in conserved multilocus HLA haplotypes. Assessment of HLA haplotypic diversity of a specific population is important, particularly for allogeneic hematopoietic stem cell transplantation. Family pedigrees remain the gold standard for studying HLA haplotype segregation. HLA haplotypes, obtained by observations of the segregation of HLA alleles within the family, really exist in the human population. The aim of this work has been to establish the frequencies of HLA haplotypes A-B-C-DRB1-DRB3/DRB4/DRB5-DQA1-DQB1-DPA1-DPB1 in families of patients with assignment to HLA-typing for allogeneic hematopoietic stem cell transplantation. The study included 109 families of patients, in which patients and their potential relative donors of allogeneic hematopoietic stem cell were subjected to HLA-typing. Patients and members of their families were typed by the NGS method in the Laboratory of Tissue Typing at the National Medical Research Center for Hematology for 11 HLA genes – A, B, C, DRB1, DRB3, DRB4, DRB5, DQA1, DQB1, DPA1 and DPB1. The genotyping was performed by the NGS method using the AllType NGS 11 Loci Amplification Kits (One Lambda, USA) on the MiSeq sequencing platform (Illumina, USA). The sequences were analyzed using the TypeStream Visual Software (TSV) (One Lambda, USA) and the IPD-IMGT/HLA database 3.44. 360 copies of HLA-haplotypes were found in the studied families. The frequencies of HLA haplotypes were determined by direct counting. The most common 7-locus haplotype was A*01:01-B*08:01-C*07:01-DRB1*03:01-(DRB3*01:01-DQA1*05:01)-DQB1*02:01/163N, the most common 9-locus haplotype was A*03:01-B*07:02-C*07:02-DRB1*15:01-DRB5*01:01-DQA1*01:02-DQB1*06:02-DPA1*01:03-DPB1*04:01P. These HLA haplotypes (in brief, A-B-C-DRB1-DQB1) are the first and second most common HLA haplotypes in most Russian registries of bone marrow donors. Despite several differences, the distribution of HLA haplotypes in families of the patients and in donor registries is similar, and the probability of finding a compatible donor for patients with common HLA-haplotypes in Russian registries is quite high. Most of 7-locus haplotypes are associated with different alleles of the HLA-DP locus in the 9-locus haplotypes, due to presence of a recombination hot spot. The study revealed strong linkage disequilibrium between the HLA alleles DRB1*03:01 and DPB1*01:01P (D’ = 0.579), DRB1*07:01, and DPB1*17:01 (D’ = 0.808), DRB1*09:01 and DPB1*04:02P (D’ = 0.502). The information obtained about real 7- and 9-locus HLA-haplotypes in families may be used in clinical practice as a reference for analyzing the results of HLA-typing and predicting the expected HLA-haplotypes. It has been shown that, despite recombination hot spot between the HLA-DP locus and the rest of the HLA complex, there is strong linkage disequilibrium between some alleles of the DRB1 and DPB1 genes.