Determination and Assessment of Extended Haplotypes Spanning the Chromosome 1q32 CFH-To-CFHR5 Locus

Abstract

Purpose: : Variations and haplotypes of the complement factor H (CFH) and the five CFH-related genes (CFHR-1 through CFHR-5) are significantly associated with the risk of developing complement-mediated diseases, including age-related macular degeneration (AMD). Due to the strong homology between these six genes, and substantial copy number variation within the 1q32 region, it has been difficult to determine the causal association of individual variants, genes, and haplotypes to disease. To address this deficiency, haplotypes encompassing CFH and the five CFHR genes were determined, and their association with AMD and other diseases assessed.

Methods: : Sixty-three SNPs in 1,073 white individuals were genotyped. The deletion status of the CFHR-3/CFHR-1 genes was assessed using SSCP and a novel qPCR assay developed to detect the CFHR-3/CFHR-1 deletion on single chromosomes. Genotypes were imputed and phased and haplotypes were subsequently constructed. Haplotype validity was confirmed in multiple three-generation families, including Utah CEPH families. Disease association was assessed by constructing haplotypes in a backwards step-wise selection method with individual SNPs, in 657 white siblings (average age = 83 yrs), who had normal maculas and the diagnosis of AREDS categories 2, 3, and neovascular AMD.

Results: : Nine major haplotypes (>1% frequency) within the 260kb region were identified; they are tagged by eight SNPs. The deletion status of the CFHR-3/CFHR-1 genes could be predicted with 97% specificity and 96% sensitivity based on the genotype of a single SNP. Fourteen percent of chromosomes in the discovery cohort contained this deletion. Haplotype fidelity was confirmed in large multi-generation families. Unique associations of six of the nine major haplotypes with different AMD risk phenotypes (both as a binary and quantitative trait) were found (p < 10^-7), after permutation testing correction and controlling for age, sex and smoking status. In addition, haplotype associations with other complement-mediated diseases were found.

Conclusions: : Haplotypes spanning the extended CFH-to-CFHR-5 locus and including CFHR-3/CFHR-1 deletion were determined. These 1q32 haplotypes will be valuable in refining our understanding of the causal association of individual gene variations and haplotypes in disease risk and protection.

Keywords: age-related macular degeneration • genetics