Comparison of risk allele frequencies of single nucleotide polymorphisms associated with age-related macular degeneration in different ethnic groups
Abstract Background 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 purpose of this study was to determine the genetic causes o...
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| Format: | Article |
| Language: | English |
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BMC
2021-02-01
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| Series: | BMC Ophthalmology |
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| Online Access: | https://doi.org/10.1186/s12886-021-01830-9 |
| _version_ | 1819123545875152896 |
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| author | Hyun-Tae Shin Byung Woo Yoon Je Hyun Seo |
| author_facet | Hyun-Tae Shin Byung Woo Yoon Je Hyun Seo |
| author_sort | Hyun-Tae Shin |
| collection | DOAJ |
| description | Abstract Background 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 purpose of this study was to determine the genetic causes of differences in the prevalence of AMD among individuals of different races. Methods We 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. Results European, 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. Conclusion The 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. |
| first_indexed | 2024-12-22T07:10:04Z |
| format | Article |
| id | doaj.art-d79d1f83d9364094a6dd654e6c0e8dd2 |
| institution | Directory Open Access Journal |
| issn | 1471-2415 |
| language | English |
| last_indexed | 2024-12-22T07:10:04Z |
| publishDate | 2021-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Ophthalmology |
| spelling | doaj.art-d79d1f83d9364094a6dd654e6c0e8dd22022-12-21T18:34:33ZengBMCBMC Ophthalmology1471-24152021-02-0121111410.1186/s12886-021-01830-9Comparison of risk allele frequencies of single nucleotide polymorphisms associated with age-related macular degeneration in different ethnic groupsHyun-Tae Shin0Byung Woo Yoon1Je Hyun Seo2Veterans Medical Research Institute, Veterans Health Service Medical CenterDivision of Oncology, Department of Internal Medicine, Inje University Seoul Paik HospitalVeterans Medical Research Institute, Veterans Health Service Medical CenterAbstract Background 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 purpose of this study was to determine the genetic causes of differences in the prevalence of AMD among individuals of different races. Methods We 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. Results European, 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. Conclusion The 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.https://doi.org/10.1186/s12886-021-01830-9Age-related macular degenerationAllele frequencySingle nucleotide polymorphismGenetic risk scoresPrevalence |
| spellingShingle | Hyun-Tae Shin Byung Woo Yoon Je Hyun Seo Comparison of risk allele frequencies of single nucleotide polymorphisms associated with age-related macular degeneration in different ethnic groups BMC Ophthalmology Age-related macular degeneration Allele frequency Single nucleotide polymorphism Genetic risk scores Prevalence |
| title | Comparison of risk allele frequencies of single nucleotide polymorphisms associated with age-related macular degeneration in different ethnic groups |
| title_full | Comparison of risk allele frequencies of single nucleotide polymorphisms associated with age-related macular degeneration in different ethnic groups |
| title_fullStr | Comparison of risk allele frequencies of single nucleotide polymorphisms associated with age-related macular degeneration in different ethnic groups |
| title_full_unstemmed | Comparison of risk allele frequencies of single nucleotide polymorphisms associated with age-related macular degeneration in different ethnic groups |
| title_short | Comparison of risk allele frequencies of single nucleotide polymorphisms associated with age-related macular degeneration in different ethnic groups |
| title_sort | comparison of risk allele frequencies of single nucleotide polymorphisms associated with age related macular degeneration in different ethnic groups |
| topic | Age-related macular degeneration Allele frequency Single nucleotide polymorphism Genetic risk scores Prevalence |
| url | https://doi.org/10.1186/s12886-021-01830-9 |
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