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K. Spencer, Y. Chen, M. A. Hauser, S. Schmidt, W. K. Scott, N. Schnetz-Boutaud, A. Agarwal, E. A. Postel, M. A. Pericak-Vance, J. L. Haines; No Deletion of CFHL1 and CFHL3 Genes in Age-Related Macular Degeneration. Invest. Ophthalmol. Vis. Sci. 2007;48(13):4629.
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Age-related macular degeneration (AMD) impairs central vision and interferes with normal daily tasks for as many as 7.5 million Americans. Much progress has been made in identifying genetic risk factors for AMD, including both susceptibility variants and protective haplotypes in the complement factor H (CFH) gene on chromosome 1. Recently, deletion of the "CFH-like" genes CFHL1 and CFHL3 was found to be segregating with a particular CFH haplotype, and deletion of these genes was suggested to be protective for AMD (Hughes et al. 2006).
We genotyped 3 tag SNPs from the original CFH putative deletion-carrying haplotype that perfectly differentiate this haplotype (GAA at rs2019724, rs1831281, and rs3753396), and identified 20 homozygotes (8 cases and 12 controls) for the potential deletion out of our full dataset of 437 cases and 160 controls. Seven SNPs within the proposed deletion were genotyped in the full dataset with particular attention paid to lack of PCR amplification in individuals who may be homozygous for the deletion. We also amplified exon 2 of CFHL1 and exon 1 of CFHL3 in the 20 homozygotes and performed agarose gel electrophoresis, to determine whether this entire region had been deleted. Finally, we sequenced 13 of these individuals (4 cases and 9 controls) for 4 exons of CFHL1 and 5 exons of CFHL3 to ensure that the PCR amplicons were specific to the proper sequence.
For the 7 SNPs in this region, all 20 individuals homozygous for the proposed deletion yielded genotypes for all SNPs, with the exception of 1 individual who failed for 1 SNP. Additionally, all 20 individuals successfully produced PCR product observable by agarose gel electrophoresis for exon 2 of CFHL1 and exon 1 of CFHL3, and therefore do not have total deletions of these genes. Of the 13 people we sequenced for the additional exons of CFHL3 and CFHL1, all 13 produced high quality sequence for these exons. Eleven of the 13 were heterozygous for at least one SNP in these genes, demonstrating that these individuals have two copies of the genes.
Our data do not support a deletion of the CFHL1 and CFHL3 genes in individuals homozygous for this CFH haplotype. The functional protective variant(s) on this haplotype remain(s) to be determined.
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