First Author: X.Lumi SLOVENIA
Co Author(s): D. Jevsinek Skok M. M. Jelen A. Zupan E. Bosjancic M. Ravnik-Glavac D. Glavac
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To investigate the distribution of genotypes within 42 single nucleotide polymorphisms (SNPs) associated with proliferative vitreoretinopathy (PVR) in Slovenian (SLO) population and compare genotype frequencies with frequencies in some other European populations within 1000 genome project.
Eye Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia and Department of Molecular Genetics, Faculty of Medicine, University of Ljubljana, Slovenia.
A total of 96 healthy controls and 113 patients, who developed PVR grade C1 or more within three months after the surgery for rhegmatogenous retinal detachment were enrolled in our study. Data on genotype distributions of 42 SNPs from 503 European individuals was obtained from the Ensembl database, release 83. Firstly, genotype distributions of 42 SNPs were compared between 96 healthy SLO controls and 503 European individuals. SNPs, which exhibited a statically significant difference in their distribution, were additionally evaluated on 3 European subpopulations: 99 Utah residents with Northern and Western European ancestry (CEU), 91 residents from Britain in England and Scotland (GBR), and 107 Iberian residents from Spain (IBS) and between GBR and IBS, respectively. Finally, genotype distributions in 4 SNPs (rs17561 (IL1A), rs2069763 (IL2) and rs1800629 (TNF)) were compared between 96 healthy controls and 113 patients with PVR.
Among 42 SNPs investigated between SLO and European population, significant differences in genotype distributions were found in 10 SNPs. Distributions of genotype rs315952 (IL1RN) varied between SLO and CEU (p = 0.037), SLO and GBR (p = 0.005) and SLO and IBS (p = 0.0008), while the differences between GBR and IBS were not observed. Distributions of genotype rs1891467 (TGFB2) varied between SLO and CEU (p = 0.011), SLO and GBR (p = 0.001) and SLO and IBS (p = 0.022), as well as between GBR and IBS (p = 0.0001). Differences in the distribution of genotypes for the SNP rs3024498 (IL10) were observed between SLO and GBR (p = 0.0049), SLO and IBS (p = 0.013) and between GBR and IBS (p = 0.0006). For the SNP rs3138056 (NFKB1A), differences between SLO and CEU (p = 0.0075) and between SLO and IBS (p = 0.0078) were observed. Differences in the distributions of genotypes for the SNP rs3138045 (NFKB1A) were observed between SLO and IBS (p = 0.012) and GBR and IBS (p = 0.025), while the distributions of genotypes for the SNP rs7656613 (PDGFRA) differed between SLO and CEU (p = 0.035) and SLO and GBR (p = 0.011).
Our study revealed that genotype distributions in 10 of 42 investigated SNPs vary significantly among Europeans in comparison to genotype distributions among PVR patients and Slovenian healthy controls. We did replicate associations with PVR in only three of investigated SNPs: rs1800795 of the IL-6 gene, rs1800871 in the vicinity of the IL10 and rs1800471 of the TGFB1. Polymorphisms that fail to replicate should be checked for interactions with other polymorphisms, particularly when samples are collected from groups with distinct ethnic backgrounds or different geographic regions.