Format

Send to

Choose Destination
Hum Genet. 2019 Oct;138(10):1171-1182. doi: 10.1007/s00439-019-02050-4. Epub 2019 Jul 31.

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

Author information

1
Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA.
2
Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA.
3
Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA.
4
John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.
5
Department of Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA.
6
Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA. jonathan.haines@case.edu.
7
Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH, USA. jonathan.haines@case.edu.
8
Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH, USA. jonathan.haines@case.edu.

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.

PMID:
31367973
DOI:
10.1007/s00439-019-02050-4

Supplemental Content

Full text links

Icon for Springer
Loading ...
Support Center