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Copy Number Variants (CNVs) are now recognized as playing a significant role in complex disease etiology. Age-related macular degeneration (AMD) is the most common cause of irreversible vision loss in the western world. While a number of genes and environmental factors have been associated with both risk and protection in AMD, the role of CNVs has remained largely unexplored. We analyzed the two major AMD risk-associated regions on chromosome 1q32 and 10q26 for CNVs using Multiplex Ligation-dependant Probe Amplification. The analysis targeted nine genes in these two key regions, including the Complement Factor H ( CFH ) gene, the 5 CFH-related ( CFHR ) genes representing a known copy number “hotspot”, the  F13B  gene as well as the  ARMS2  and  HTRA1  genes in 387 cases of late AMD and 327 controls. No copy number variation was detected at the  ARMS2  and  HTRA1  genes in the chromosome 10 region, nor for the  CFH  and  F13B  genes at the chromosome 1 region. However, significant association was identified for the  CFHR3-1  deletion in AMD cases (p = 2.38×10 −12 ) OR = 0.31, CI-0.95 (0.23–0.44), for both neovascular disease (nAMD) (p = 8.3×10 −9 ) OR = 0.36 CI-0.95 (0.25–0.52) and geographic atrophy (GA) (p = 1.5×10 −6 ) OR = 0.36 CI-0.95 (0.25–0.52) compared to controls. In addition, a significant association with deletion of  CFHR1-4  was identified only in patients who presented with bilateral GA (p = 0.02) (OR = 7.6 CI-0.95 1.38–41.8). This is the first report of a phenotype specific association of a CNV for a major subtype of AMD and potentially allows for pre-diagnostic identification of individuals most likely to proceed to this end stage of disease.

Comprehensive Analysis of Copy Number Variation of Genes at Chromosome 1 and 10 Loci Associated with Late Age Related Macular Degeneration