Analysis of risk allele frequencies of single nucleotide polymorphisms related to open-angle glaucoma in different ethnic groups
Abstract Background The prevalence of open-angle glaucoma (OAG) varies from 0.5% to 7.0% among populations of diverse ancestry, suggesting the existence of genetic differences. The purposes of this study were to provide insights into genetic causes of OAG, which can result in prevalence and phenotyp...
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| Format: | Article |
| Language: | English |
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BMC
2021-03-01
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| Series: | BMC Medical Genomics |
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| Online Access: | https://doi.org/10.1186/s12920-021-00921-2 |
| _version_ | 1819172421915115520 |
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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 open-angle glaucoma (OAG) varies from 0.5% to 7.0% among populations of diverse ancestry, suggesting the existence of genetic differences. The purposes of this study were to provide insights into genetic causes of OAG, which can result in prevalence and phenotype differences among populations of diverse ancestry for OAG, and to compare allele frequencies of intraocular pressure (IOP) elevation-related SNPs in OAG among Koreans and other ethnic groups. Methods We collected the data on a total of 135 OAG-associated single nucleotide polymorphisms (SNPs) from a genome-wide association studies (GWAS) catalog. The population-level allele frequencies of these SNPs were derived based on the 1000 Genomes Project and Korean Reference Genome Database. We used Fisher's exact test to assess whether the effect allele at a given SNP was significantly enriched or depleted. Results European, American, and South Asian populations showed similar heatmap patterns, while African, East Asian, and Korean populations had distinct patterns. Korean population presented different profiles compared to other groups; rs1579050 (FMNL2 gene), rs2024211 (CAV2;CAV1), and rs8141433 (GNB1L;TXNRD2 gene), which are known to be associated with IOP variation, were enriched in Americans, Europeans, and Africans, and depleted in Koreans. These can be the candidates for the causative genes of differences in the prevalence of IOP variation in OAG according to ethnic groups. Conclusions Differences in allele frequencies associated with IOP related SNPs between Koreans and other ethnicities were observed, which may explain the high prevalence of OAG with normal IOP predominantly in Koreans and East Asians. |
| first_indexed | 2024-12-22T20:06:55Z |
| format | Article |
| id | doaj.art-5bf6d88437bf46e9bc74faa3d4c5e916 |
| institution | Directory Open Access Journal |
| issn | 1755-8794 |
| language | English |
| last_indexed | 2024-12-22T20:06:55Z |
| publishDate | 2021-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Genomics |
| spelling | doaj.art-5bf6d88437bf46e9bc74faa3d4c5e9162022-12-21T18:14:06ZengBMCBMC Medical Genomics1755-87942021-03-0114111810.1186/s12920-021-00921-2Analysis of risk allele frequencies of single nucleotide polymorphisms related to open-angle glaucoma in different ethnic groupsHyun-Tae Shin0Byung Woo Yoon1Je Hyun Seo2Veterans Health Service Medical Center, Veterans Medical Research InstituteDivision of Oncology, Department of Internal Medicine, Inje University Seoul Paik HospitalVeterans Health Service Medical Center, Veterans Medical Research InstituteAbstract Background The prevalence of open-angle glaucoma (OAG) varies from 0.5% to 7.0% among populations of diverse ancestry, suggesting the existence of genetic differences. The purposes of this study were to provide insights into genetic causes of OAG, which can result in prevalence and phenotype differences among populations of diverse ancestry for OAG, and to compare allele frequencies of intraocular pressure (IOP) elevation-related SNPs in OAG among Koreans and other ethnic groups. Methods We collected the data on a total of 135 OAG-associated single nucleotide polymorphisms (SNPs) from a genome-wide association studies (GWAS) catalog. The population-level allele frequencies of these SNPs were derived based on the 1000 Genomes Project and Korean Reference Genome Database. We used Fisher's exact test to assess whether the effect allele at a given SNP was significantly enriched or depleted. Results European, American, and South Asian populations showed similar heatmap patterns, while African, East Asian, and Korean populations had distinct patterns. Korean population presented different profiles compared to other groups; rs1579050 (FMNL2 gene), rs2024211 (CAV2;CAV1), and rs8141433 (GNB1L;TXNRD2 gene), which are known to be associated with IOP variation, were enriched in Americans, Europeans, and Africans, and depleted in Koreans. These can be the candidates for the causative genes of differences in the prevalence of IOP variation in OAG according to ethnic groups. Conclusions Differences in allele frequencies associated with IOP related SNPs between Koreans and other ethnicities were observed, which may explain the high prevalence of OAG with normal IOP predominantly in Koreans and East Asians.https://doi.org/10.1186/s12920-021-00921-2Open-angle glaucomaAllele frequencySingle nucleotide polymorphismIntraocular pressurePrevalenceNormal-tension glaucoma |
| spellingShingle | Hyun-Tae Shin Byung Woo Yoon Je Hyun Seo Analysis of risk allele frequencies of single nucleotide polymorphisms related to open-angle glaucoma in different ethnic groups BMC Medical Genomics Open-angle glaucoma Allele frequency Single nucleotide polymorphism Intraocular pressure Prevalence Normal-tension glaucoma |
| title | Analysis of risk allele frequencies of single nucleotide polymorphisms related to open-angle glaucoma in different ethnic groups |
| title_full | Analysis of risk allele frequencies of single nucleotide polymorphisms related to open-angle glaucoma in different ethnic groups |
| title_fullStr | Analysis of risk allele frequencies of single nucleotide polymorphisms related to open-angle glaucoma in different ethnic groups |
| title_full_unstemmed | Analysis of risk allele frequencies of single nucleotide polymorphisms related to open-angle glaucoma in different ethnic groups |
| title_short | Analysis of risk allele frequencies of single nucleotide polymorphisms related to open-angle glaucoma in different ethnic groups |
| title_sort | analysis of risk allele frequencies of single nucleotide polymorphisms related to open angle glaucoma in different ethnic groups |
| topic | Open-angle glaucoma Allele frequency Single nucleotide polymorphism Intraocular pressure Prevalence Normal-tension glaucoma |
| url | https://doi.org/10.1186/s12920-021-00921-2 |
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