Development of a Genotype Assay for Age-Related Macular Degeneration

Abstract

Purpose: To develop a genotype assay to assess associations with common and rare age-related macular degeneration (AMD) risk variants, to calculate an overall genetic risk score (GRS), and to identify potential misdiagnoses with inherited macular dystrophies that mimic AMD.Design: Case-control study.Participants: Individuals (n ¼ 4740) from 5 European cohorts. Methods: We designed single-molecule molecular inversion probes for target selection and used next generation sequencing to sequence 87 single nucleotide polymorphisms (SNPs), coding and splice-site regions of 10 AMD-(related) genes (ARMS2, C3, C9, CD46, CFB, CFH, CFI, HTRA1, TIMP3, and SLC16A8), and 3 genes that cause inherited macular dystrophies (ABCA4, CTNNA1, and PRPH2). Genetic risk scores for common AMD risk variants were calculated based on effect size and genotype of 52 AMD-associated variants. Frequency of rare variants was compared between late AMD patients and control individuals with logistic regression analysis.Main Outcome Measures: Genetic risk score, association of genetic variants with AMD, and genotypeephenotype correlations.Results: We observed high concordance rates between our platform and other genotyping platforms for the 69 successfully genotyped SNPs (>96%) and for the rare variants (>99%). We observed a higher GRS for patients with late AMD compared with patients with early/intermediate AMD (P < 0.001) and individuals without AMD (P < 0.001). A higher proportion of pathogenic variants in the CFH (odds ratio [OR] ¼ 2.88; P ¼ 0.006), CFI (OR ¼ 4.45; P ¼ 0.005), and C3 (OR ¼ 6.56; P ¼ 0.0003) genes was observed in late AMD patients compared with control individuals. In 9 patients, we identified pathogenic variants in the PRPH2, ABCA4, and CTNNA1 genes, which allowed reclassification of these patients as having inherited macular dystrophy.Conclusions: This study reports a genotype assay for common and rare AMD genetic variants, which can identify individuals at intermediate to high genetic risk of late AMD and enables differential diagnosis of AMDmimicking dystrophies. Our study supports sequencing of CFH, CFI, and C3 genes because they harbor rare high-risk variants. Carriers of these variants could be amendable for new treatments for AMD that currently are under development. Ophthalmology 2020;-:1e14

Quantitative multiplex profiling of the complement system to diagnose complement‐mediated diseases

“…Each complement deficiency had been confirmed previously by genetic analysis, ELISA or radial immunodiffusion. Patients with AMD were screened by means of exome chip genotyping, 43 exome sequencing 44 and single‐molecule molecular inversion probes combined with next‐generation sequencing 45 . Additionally, we included three cases with a suspected but undiagnosed deficiency.…”

The complement system in age-related macular degeneration

“…Most of these genetic risk factors have been confirmed in independent studies [70,72]. Although polymorphisms in the CFH and ARMS2/HTRA1 genes bear the highest single attributable risk scores for a single risk allele, additional genetic variants have been associated to AMD: in or near genes of the complement system (CFB, CFI, C2, C3); genes involved in ECM remodelling as Collagen Type VIII Alpha 1 Chain (COL8A1) and Tissue Inhibitor of Metalloproteinases 3 (TIMP3); genes involved in cholesterol metabolism as ATP-binding cassette transporter (ABCA1), Apolipoprotein E (APOE), Cholesteryl ester transfer protein (CETP), Lipase C, Hepatic Type (LIPC) and genes in less well-defined pathways, e.g., Rho GTPase Activating Protein 21 (ARHGAP21) and Beta 3-Glucosyltransferase (B3GALTL) [73]. The odds ratios of the representative SNPs in these genes typically fall into the range of 1.1-3.0, with a majority < 2; thus, each locus only has small to moderate contribution to the risk of the disease.…”

Catenin α 1 mutations cause familial exudative vitreoretinopathy by overactivating Norrin/β-catenin signaling

“…Saskens et al identified mutations in CTNNA1 that cause butterfly-shaped pigment dystrophy (35). Very recently, a missense CTNNA1 mutation was identified in an age-related macular degeneration (AMD) patient (36). Furthermore, Alexander et al identified four mutations in CTNNA1 that cause macular pattern dystrophy (37).…”