An approach that can be used to identify rare variants is sequence analysis of candidate genes. Logical candidate genes that may harbor rare variants are genes at or near common variants that have been identified by previous GWASs, and genes involved in pathways that have been associated with the disease. Sequence analysis of the
CFH gene in AMD families identified several loss-of-function (frameshift, nonsense) variants that segregate with the disease.
78,79 Genomic sequencing of a high risk haplotype (H5) at the
CFH locus identified a coding variant, R1210C, that confers high risk of developing AMD,
80 The variant was identified in 40 of 2423 AMD patients but only in 1 of 1122 control individuals, indicating that it is a rare allele, but that it confers a high risk of developing AMD. Moreover, carriers of the R1210C variant have a younger age of onset than individuals who do not carry the allele.
80 Complement factor I (CFI), like CFH, is a main inhibitor of the alternative complement pathway, and, therefore, also represents an excellent candidate gene to harbor rare variants in AMD. Sequence analysis of the
CFI gene in 84 AMD patients identified a recurrent variant, G119R, in 3 affected individuals.
81 In a case-control cohort, the G119R variant was identified in 20 of 3567 AMD patients, while it was found in only 1 of 3938 control individuals. Thus, the G119R is a rare allele, but confers high risk of developing AMD (OR, 22.2; 95% CI, 3.0–164.5).
81 Cases with AMD carrying the G119R variant had significantly lower plasma CFI concentrations compared to controls and cases who did not carry the variant, and plasma samples of patients carrying the CFI G119R variant had a significantly lower capacity to degrade C3b compared to control individuals.
81 Sequence analysis of 681 candidate genes in 1676 AMD cases and 745 controls identified a significant burden of rare variants in the
CFI gene in patients compared to controls.
82 In addition, rare variants in the
C3 (K155Q) and the
C9 (P167S) genes have been associated with AMD.
82–84