Rare variants and loci for age-related macular degeneration in the Ohio and Indiana Amish

Andrea R Waksmunski,Jessica N Cooke Bailey,William K Scott,Laura Caywood,Robert P Igo,Renee Laux,Larry D Adams,Jonathan L Haines,Dwight Stambolian,Sarada Fuzzell,Yeunjoo E Song,Margaret A Pericak-Vance,Denise Fuzzell,Michael Prough

doi:10.1007/s00439-019-02050-4

Abstract

Age-related macular degeneration (AMD) is a leading cause of blindness in the world. While dozens of independent genomic variants are associated with AMD, about one-third of AMD heritability is still unexplained. To identify novel variants and loci for AMD, we analyzed Illumina HumanExome chip data from 87 Amish individuals with early or late AMD, 79 unaffected Amish individuals, and 15 related Amish individuals with unknown AMD affection status. We retained 37,428 polymorphic autosomal variants across 175 samples for association and linkage analyses. After correcting for multiple testing (n = 37,428), we identified four variants significantly associated with AMD: rs200437673 (LCN9, p = 1.50 × 10−11), rs151214675 (RTEL1, p = 3.18 × 10−8), rs140250387 (DLGAP1, p = 4.49 × 10−7), and rs115333865 (CGRRF1, p = 1.05 × 10−6). These variants have not been previously associated with AMD and are not in linkage disequilibrium with the 52 known AMD-associated variants reported by the International AMD Genomics Consortium based on physical distance. Genome-wide significant linkage peaks were observed on chromosomes 8q21.11–q21.13 (maximum recessive HLOD = 4.03) and 18q21.2–21.32 (maximum dominant HLOD = 3.87; maximum recessive HLOD = 4.27). These loci do not overlap with loci previously linked to AMD. Through gene ontology enrichment analysis with ClueGO in Cytoscape, we determined that several genes in the 1-HLOD support interval of the chromosome 8 locus are involved in fatty acid binding and triglyceride catabolic processes, and the 1-HLOD support interval of the linkage region on chromosome 18 is enriched in genes that participate in serine-type endopeptidase inhibitor activity and the positive regulation of epithelial to mesenchymal transition. These results nominate novel variants and loci for AMD that require further investigation.

Highlights

Age-related macular degeneration (AMD) is the third leading cause of vision loss in the world (Ayoub and Patel 2009)
Using ROADTRIPS and kinship coefficients derived from the relationships detailed in the allconnecting path pedigree, we identified four novel variants associated with AMD in the Amish
Since we analyzed exome chip data, we recognize that these variants may not be the functional variants underlying these loci and that we might be observing their association signals because they are in linkage disequilibrium with the true functional variants for AMD

Summary

Introduction

Age-related macular degeneration (AMD) is the third leading cause of vision loss in the world (Ayoub and Patel 2009). It is characterized by the deterioration of the central field of vision due to the accumulation of lipid deposits (drusen), inflammation, and neurodegeneration in the macula (Fritsche et al 2014). More than half of AMD heritability is explained by 52 independent common and rare genetic variants across 34 genomic loci (Fritsche et al 2016). About half of AMD heritability is unaccounted for by known genetic polymorphisms and may be partially resolved with the identification of rare variants (Manolio et al 2009)

Methods

Results

Conclusion