DNA samples were obtained from whole blood and stored in our blood repository. The following six common single-nucleotide polymorphisms (SNPs) associated with AMD were evaluated: (1) complement factor H (
CFH)
Y402H (rs1061170) in exon 9 of the
CFH gene on 1q31, with change 1277T>C, resulting in a substitution of histidine for tyrosine at codon 402 of the
CFH protein; (2)
CFH rs1410996 which is an independently associated SNP variant within intron 14 of
CFH; (3)
LOC387715 A69S (rs10490924 in the LOC387715/HTRA1 region of chromosome 10), a nonsynonymous coding SNP variant in exon 1 of
LOC387715, resulting in a substitution of the amino acid serine for alanine at codon 69; (4) complement factor 2 or
C2 E318D (rs9332739), the nonsynonymous coding SNP variant in exon 7 of
C2 resulting in the amino acid glutamic acid changing to aspartic acid at codon 318; (5) complement factor B or
CFB R32Q (rs641153), the nonsynonymous coding SNP variant in exon 2 of
CFB resulting in the amino acid glutamine changing to arginine at codon 32, (6) complement factor 3 or
C3 R102G (rs2230199), the nonsynonymous coding SNP variant in exon 3 of
C3 resulting in the amino acid glycine to arginine at codon 102. For the genetic variant on chromosome 10,
LOC387715A69S (
ARMS2), it remains uncertain whether the gene
HTRA1 adjacent to it may in fact be the AMD susceptibility gene on 10q26
9 10 11 ; but the relevant SNPs in these two genes have been reported to be nearly perfectly correlated. Thus, although the other SNP is a promising candidate variant, rs10490924 can be considered a surrogate for the causal variant that resides in this region. For the
C2/CFB genes, there are two independent associations to the
C2/CFB locus, but because of linkage disequilibrium we do not know which of the two genes or both are functionally affected. Genotyping was performed with primer mass extension and MALDI-TOF MS analysis on a gene-analysis system (MassEXTEND; Sequenom, San Diego, CA) at the Broad Institute Center for Genotyping and Analysis (Cambridge, MA).