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

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

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
JournalHuman Genetics
DOIs
StateAccepted/In press - Jan 1 2019

Fingerprint

Amish
Macular Degeneration
Chromosomes, Human, Pair 18
Chromosomes, Human, Pair 8
Gene Ontology
Serine Proteinase Inhibitors
Epithelial-Mesenchymal Transition
Linkage Disequilibrium
Blindness
Genomics

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Waksmunski, A. R., Igo, R. P., Song, Y. E., Cooke Bailey, J. N., Laux, R., Fuzzell, D., ... Haines, J. L. (Accepted/In press). Rare variants and loci for age-related macular degeneration in the Ohio and Indiana Amish. Human Genetics. https://doi.org/10.1007/s00439-019-02050-4

Rare variants and loci for age-related macular degeneration in the Ohio and Indiana Amish. / Waksmunski, Andrea R.; Igo, Robert P.; Song, Yeunjoo E.; Cooke Bailey, Jessica N.; Laux, Renee; Fuzzell, Denise; Fuzzell, Sarada; Adams, Larry D.; Caywood, Laura; Prough, Michael; Stambolian, Dwight; Scott, William K; Pericak-Vance, Margaret A; Haines, Jonathan L.

In: Human Genetics, 01.01.2019.

Research output: Contribution to journalArticle

Waksmunski, AR, Igo, RP, Song, YE, Cooke Bailey, JN, Laux, R, Fuzzell, D, Fuzzell, S, Adams, LD, Caywood, L, Prough, M, Stambolian, D, Scott, WK, Pericak-Vance, MA & Haines, JL 2019, 'Rare variants and loci for age-related macular degeneration in the Ohio and Indiana Amish', Human Genetics. https://doi.org/10.1007/s00439-019-02050-4
Waksmunski, Andrea R. ; Igo, Robert P. ; Song, Yeunjoo E. ; Cooke Bailey, Jessica N. ; Laux, Renee ; Fuzzell, Denise ; Fuzzell, Sarada ; Adams, Larry D. ; Caywood, Laura ; Prough, Michael ; Stambolian, Dwight ; Scott, William K ; Pericak-Vance, Margaret A ; Haines, Jonathan L. / Rare variants and loci for age-related macular degeneration in the Ohio and Indiana Amish. In: Human Genetics. 2019.
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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.",
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