Determination of HLA-A, -C, -B, -DRB1 allele and haplotype frequency in Japanese population based on family study.

N Ikeda,D Middleton,T Futagami,Y Kusunoki,H Tanaka,M Nishikawa,S Suegami,T Tsujino,Y Miyazaki,N Fujii,H Kojima,K Hayashi,H Saji

doi:10.1111/tan.12536

Abstract

The present study investigates the human leucocyte antigen (HLA) allele and haplotype frequencies in Japanese population. We carried out the frequency analysis in 5824 families living across Japanese archipelago. The studied population has mainly been typed for the purpose of transplant, especially the hematopoietic stem cell transplantation (HSCT). We determined HLA class I (A, B, and C) and HLA class II (DRB1) using Luminex technology. The haplotypes were directly counted by segregation. A total of 44 HLA‐A, 29 HLA‐C, 75 HLA‐B, and 42 HLA‐DRB1 alleles were identified. In the HLA haplotypes of A‐C‐B‐DRB1 and C‐B, the pattern of linkage disequilibrium peculiar to Japanese population has been confirmed. Moreover, the haplotype frequencies based on family study was compared with the frequencies estimated by maximum likelihood estimation (MLE), and the equivalent results were obtained. The allele and haplotype frequencies obtained in this study could be useful for anthropology, transplantation therapy, and disease association studies.

Highlights

The human leukocyte antigen (HLA) gene family is characterized by extreme degree of genetic polymorphism and linkage disequilibrium (LD)
Our study attempts to determine the frequency of specific haplotypes, C-B, A-B-DRB1, and A-C-B-DRB1, used in donor search. It was ascertained whether the haplotype frequencies estimated by maximum likelihood estimation (MLE) would be equivalent to the frequencies found in the present family study
We identified 44 HLA-A, 75 HLA-B, 29 HLA-C, and 42 HLA-DRB1 alleles and found A*24:02 to be 36.48%, the highest in Japanese population; it is distributed in approximately 60% of the population

Summary

Introduction

The human leukocyte antigen (HLA) gene family is characterized by extreme degree of genetic polymorphism and linkage disequilibrium (LD). The varieties in polymorphism and LD patterns of HLA gene family show a tendency to be unique in each ethnic group [1, 2]. HLA antigens have been known to play an important role in immune responses. In hematopoietic stem cell transplantation (HSCT), HLA matching between donors and recipients lowers the risk of graft rejection and graft-versus-host disease (GVHD) [3, 4]. Morishima et al suggested that the genetic difference derived from HLA haplotype is associated with acute GVHD in allogeneic HSCT [5]. HLA haplotype cannot be excluded from consideration during donor selection because of potential contribution from proteins encoded by non-HLA genes inherited with HLA genes

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Results

Conclusion