An Extended Haplotype Within the CFH Gene Without Y402H is Associated With AMD Susceptibility in an Indian Cohort

Abstract

Purpose: : Age related macular degeneration (AMD) has been implicated to multiple variations in several complement factor genes. Association studies have demonstrated the involvement of a CFH polymorphism (Y402H) worldwide. Subsequent studies have proved that variations other than Y402H could also influence the risk of AMD. The present study aimed at identifying variations in chromosome 1 including the CFH gene, in an Indian cohort.

Methods: : The cohort comprised of unrelated AMD patients (n=250) and ethnically matched normal controls (n=250) enrolled based on AREDS criteria. Microarray analysis with the Affymetrix chip (version 6.0) conducted on a subset of patients and controls revealed >41,000 SNPs in chromosome 1, of which 357 SNPs were significantly associated with AMD (p<10^-3) after multiple corrections. The associated regions were replicated in an extended cohort using the Illumina Golden Gate assay. Since the SNPs in this region overlapped the CFH gene, we further screened this segment by resequencing a cohort of normal controls (n=20) for discovering new variations. These specific variations were further validated in the original cohort. Allele and genotype frequencies were computed and Hardy-Weinberg equilibrium analysis and odds ratios were calculated to assess the risk conferred by these SNPs. Linkage disequlibrium and haplotype analysis were done with the Haploview software.

Results: : A preliminary analysis of the chromosome 1 region overlapping CFH, exhibited 23 variations, of which only 4 SNPs exhibited a significant association. The region harbored by the rs800292 and rs2274700 SNPs were in strong LD (D’=0.8) and significantly associated with AMD. A risk haplotype was generated with these two SNPs including the Y402H variant (p=2.92x10^-7); the association was consistent even after exclusion of Y402H from this LD block (p=3.01x10^-4). However, haplotypes generated with variants flanking the rs800292 and rs2274700 SNPs did not indicate any significant risk to AMD (p=0.351).

Conclusions: : The results indicated a potential risk haplotype within an extended region of CFH (without Y402H) with AMD susceptibility in the Indian cohort.

Keywords: age-related macular degeneration • genetics • gene microarray