Comparison of risk allele frequencies of single nucleotide polymorphisms associated with age-related macular degeneration in different ethnic groups

Hyun-Tae Shin,Byung Woo Yoon,Je Hyun Seo

doi:10.1186/s12886-021-01830-9

Abstract

BackgroundThe prevalence of age-related macular degeneration (AMD) varies from 6.8 to 18.3% for all forms of AMD and from 0.6 to 2.6% for late AMD according to race, suggesting the existence of genetic differences among races. The purpose of this study was to determine the genetic causes of differences in the prevalence of AMD among individuals of different races.MethodsWe collected 138 AMD-associated single nucleotide polymorphisms (SNPs) from a genome-wide association studies catalog. Their population-level allele frequencies were derived based on the 1000 Genomes Project and Korean Reference Genome Database. We used Fisher’s exact tests to assess whether the effect allele at a given SNP was significantly enriched or depleted in the database.ResultsEuropean, American, and South Asian populations showed similar heatmap patterns, whereas East Asian, and Korean populations had distinct patterns. Korean populations exhibited patterns that were different from those of the other groups; rs5754227 (SYN3), rs1626340 (TGFBR1/COL15A1), rs3750846(ARMS2/HTRA1), and rs9564692 (B3GALTL) were enriched, whereas rs2230199 (C3) and rs73036519 (EXOC3L2/MARK4) were depleted in Koreans; these SNPs are associated with late AMD. The genetic risk score calculated from allele frequencies was not less in East Asians than in Europeans.ConclusionThe prevalence of AMD is lower in Asians than in Europeans. However, our study showed that genetic risk scores in East Asians were similar to those in Europeans, which may explain why the global projected number of people with AMD by 2040 is in largest for East Asians, including Koreans.

Highlights

The prevalence of age-related macular degeneration (AMD) varies from 6.8 to 18.3% for all forms of AMD and from 0.6 to 2.6% for late AMD according to race, suggesting the existence of genetic differences among races
The single nucleotide polymorphisms (SNPs) were identified in 17 European populations, four East Asian populations, and three South Asian populations; three studies were performed in mixed ethnic populations
After collecting 138 AMD-associated SNPs, we determined the effect allele frequencies (EAFs) for each of the continental groups and for Koreans based on genotype information from the 1000 Genomes Project and Korean Reference Genome Database (KRGDB) (Supplementary Table S1)

Summary

Introduction

The prevalence of age-related macular degeneration (AMD) varies from 6.8 to 18.3% for all forms of AMD and from 0.6 to 2.6% for late AMD according to race, suggesting the existence of genetic differences among races. Age-related macular degeneration (AMD) is the leading cause of visual impairment in developed countries [1, 2], in people older than 60 years. In Europe, the prevalence of early AMD increases from 3.5% in those aged 55–59 years to 17.9% in those aged 85 years; for late AMD, the prevalence increases from 0.1 to 9.8% [6]. For Asian AMD, the prevalence rates of early and late AMD were found to range from 1.4 to 17.3% and 0.1 to 7.3%, respectively, with a higher prevalence in elderly groups [7, 8]. The number of people affected is expected to increase dramatically during the coming decades as Asian populations age, and it is estimated that there will be more Asians with AMD than in the rest of the world combined by 2040 [2]

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