Deciphering the association of intronic single nucleotide polymorphisms of crystallin gene family with congenital cataract
Purpose: Introns play an important role in gene regulation and expression. Single nucleotide polymorphisms (SNPs) in introns have the potential to cause disease and alter the genotype–phenotype association. Hence, this study aimed to decipher the association of SNPs in the introns of the crystallin...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Wolters Kluwer Medknow Publications
2021-01-01
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| Series: | Indian Journal of Ophthalmology |
| Subjects: | |
| Online Access: | http://www.ijo.in/article.asp?issn=0301-4738;year=2021;volume=69;issue=8;spage=2064;epage=2070;aulast=Nair |
| _version_ | 1819086735775105024 |
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| author | Vidya Nair Rajkumar Sankaranarayanan Abhay Raghukant Vasavada |
| author_facet | Vidya Nair Rajkumar Sankaranarayanan Abhay Raghukant Vasavada |
| author_sort | Vidya Nair |
| collection | DOAJ |
| description | Purpose: Introns play an important role in gene regulation and expression. Single nucleotide polymorphisms (SNPs) in introns have the potential to cause disease and alter the genotype–phenotype association. Hence, this study aimed to decipher the association of SNPs in the introns of the crystallin gene in congenital cataracts. Methods: SNPs in the introns of crystallin gene family – CRYAA (rs3788059), CRYAB (rs2070894), CRYBA4 (rs2071861), and CRYBB2 (rs5752083, rs5996863) – were genotyped in 248 participants consisting of 141 congenital cataracts and 107 healthy controls by allele-specific oligonucleotide polymerase chain reaction method. Around 10% of samples for each SNPs were sequenced to confirm the genotypes. The allele, genotype, and haplotype frequency were evaluated by the SHEsis online tool. Results: Using dominant model, the “A” allele of rs3788059 was found to have an increased risk toward congenital cataract development whereas the “G” allele was found to be protective (AA + AG vs. GG; odds ratio [OR] 95% confidence interval [CI] = 3.73 [1.71, 8.15], P = 0.0009). The “A” allele of both rs2070894 (AA + AG vs. GG; OR [95% CI] = 0.49 [0.29, 0.84], P = 0.012) and rs5752083 (AA + AC vs. CC; OR [95% CI] = 0.25 [0.08, 0.76], P = 0.016) were suggested to have a protective role by the dominant model. The A-C-T haplotype (rs2071861, rs5752083, and rs5996863) was found to be a significant risk factor for the development of congenital cataract. Conclusion: Intronic SNPs in crystallin genes may play a role in the predisposition toward congenital cataract. However, the present findings need to be replicated in a large cohort with more number of samples. |
| first_indexed | 2024-12-21T21:24:59Z |
| format | Article |
| id | doaj.art-96c64c39397e40728f9ce7ed8e3cc117 |
| institution | Directory Open Access Journal |
| issn | 0301-4738 1998-3689 |
| language | English |
| last_indexed | 2024-12-21T21:24:59Z |
| publishDate | 2021-01-01 |
| publisher | Wolters Kluwer Medknow Publications |
| record_format | Article |
| series | Indian Journal of Ophthalmology |
| spelling | doaj.art-96c64c39397e40728f9ce7ed8e3cc1172022-12-21T18:49:47ZengWolters Kluwer Medknow PublicationsIndian Journal of Ophthalmology0301-47381998-36892021-01-016982064207010.4103/ijo.IJO_3062_20Deciphering the association of intronic single nucleotide polymorphisms of crystallin gene family with congenital cataractVidya NairRajkumar SankaranarayananAbhay Raghukant VasavadaPurpose: Introns play an important role in gene regulation and expression. Single nucleotide polymorphisms (SNPs) in introns have the potential to cause disease and alter the genotype–phenotype association. Hence, this study aimed to decipher the association of SNPs in the introns of the crystallin gene in congenital cataracts. Methods: SNPs in the introns of crystallin gene family – CRYAA (rs3788059), CRYAB (rs2070894), CRYBA4 (rs2071861), and CRYBB2 (rs5752083, rs5996863) – were genotyped in 248 participants consisting of 141 congenital cataracts and 107 healthy controls by allele-specific oligonucleotide polymerase chain reaction method. Around 10% of samples for each SNPs were sequenced to confirm the genotypes. The allele, genotype, and haplotype frequency were evaluated by the SHEsis online tool. Results: Using dominant model, the “A” allele of rs3788059 was found to have an increased risk toward congenital cataract development whereas the “G” allele was found to be protective (AA + AG vs. GG; odds ratio [OR] 95% confidence interval [CI] = 3.73 [1.71, 8.15], P = 0.0009). The “A” allele of both rs2070894 (AA + AG vs. GG; OR [95% CI] = 0.49 [0.29, 0.84], P = 0.012) and rs5752083 (AA + AC vs. CC; OR [95% CI] = 0.25 [0.08, 0.76], P = 0.016) were suggested to have a protective role by the dominant model. The A-C-T haplotype (rs2071861, rs5752083, and rs5996863) was found to be a significant risk factor for the development of congenital cataract. Conclusion: Intronic SNPs in crystallin genes may play a role in the predisposition toward congenital cataract. However, the present findings need to be replicated in a large cohort with more number of samples.http://www.ijo.in/article.asp?issn=0301-4738;year=2021;volume=69;issue=8;spage=2064;epage=2070;aulast=Naircrystallincongenital cataractintronicsnp genotyping |
| spellingShingle | Vidya Nair Rajkumar Sankaranarayanan Abhay Raghukant Vasavada Deciphering the association of intronic single nucleotide polymorphisms of crystallin gene family with congenital cataract Indian Journal of Ophthalmology crystallin congenital cataract intronic snp genotyping |
| title | Deciphering the association of intronic single nucleotide polymorphisms of crystallin gene family with congenital cataract |
| title_full | Deciphering the association of intronic single nucleotide polymorphisms of crystallin gene family with congenital cataract |
| title_fullStr | Deciphering the association of intronic single nucleotide polymorphisms of crystallin gene family with congenital cataract |
| title_full_unstemmed | Deciphering the association of intronic single nucleotide polymorphisms of crystallin gene family with congenital cataract |
| title_short | Deciphering the association of intronic single nucleotide polymorphisms of crystallin gene family with congenital cataract |
| title_sort | deciphering the association of intronic single nucleotide polymorphisms of crystallin gene family with congenital cataract |
| topic | crystallin congenital cataract intronic snp genotyping |
| url | http://www.ijo.in/article.asp?issn=0301-4738;year=2021;volume=69;issue=8;spage=2064;epage=2070;aulast=Nair |
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