Genome-wide analysis of copy number variants in age-related macular degeneration

Kacie J Meyer; Lea K Davis; Emily I Schindler; John S Beck; Danielle S Rudd; A Jason Grundstad; Todd E Scheetz; Terry A Braun; John H Fingert; Wallace L Alward; Young H Kwon; James C Folk; Stephen R Russell; Thomas H Wassink; Edwin M Stone; Val C Sheffield

doi:10.1007/s00439-010-0904-6

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Genome-wide analysis of copy number variants in age-related macular degeneration

Journal article

Open access

Peer reviewed

Genome-wide analysis of copy number variants in age-related macular degeneration

Kacie J Meyer, Lea K Davis, Emily I Schindler, John S Beck, Danielle S Rudd, A Jason Grundstad, Todd E Scheetz, Terry A Braun, John H Fingert, Wallace L Alward, …

Human genetics, Vol.129(1), pp.91-100

01/2011

DOI: 10.1007/s00439-010-0904-6

PMCID: PMC3613489

PMID: 20981449

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Abstract

Age-related macular degeneration (AMD) is a complex genetic disease, with many loci demonstrating appreciable attributable disease risk. Despite significant progress toward understanding the genetic and environmental etiology of AMD, identification of additional risk factors is necessary to fully appreciate and treat AMD pathology. In this study, we investigated copy number variants (CNVs) as potential AMD risk variants in a cohort of 400 AMD patients and 500 AMD-free controls ascertained at the University of Iowa. We used three publicly available copy number programs to analyze signal intensity data from Affymetrix GeneChip SNP Microarrays. CNVs were ranked based on prevalence in the disease cohort and absence from the control group; high interest CNVs were subsequently confirmed by qPCR. While we did not observe a single-locus "risk CNV" that could account for a major fraction of AMD, we identified several rare and overlapping CNVs containing or flanking compelling candidate genes such as NPHP1 and EFEMP1. These and other candidate genes highlighted by this study deserve further scrutiny as sources of genetic risk for AMD.

Choroidal Neovascularization - epidemiology

Genetic Predisposition to Disease

Genome-Wide Association Study

Prevalence

Membrane Proteins - genetics

Extracellular Matrix Proteins - genetics

Humans

Risk Factors

Male

DNA Copy Number Variations - genetics

Macular Degeneration - genetics

Adaptor Proteins, Signal Transducing - genetics

Aged, 80 and over

Macular Degeneration - epidemiology

Female

Iowa - epidemiology

Aged

Polymorphism, Single Nucleotide

Choroidal Neovascularization - genetics

Cohort Studies

Details

Title: Subtitle: Genome-wide analysis of copy number variants in age-related macular degeneration
Creators: Kacie J Meyer - Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA 52242, USA
Lea K Davis
Emily I Schindler
John S Beck
Danielle S Rudd
A Jason Grundstad
Todd E Scheetz
Terry A Braun
John H Fingert
Wallace L Alward
Young H Kwon
James C Folk
Stephen R Russell
Thomas H Wassink
Edwin M Stone
Val C Sheffield
Resource Type: Journal article
Publication Details: Human genetics, Vol.129(1), pp.91-100
DOI: 10.1007/s00439-010-0904-6
PMID: 20981449
PMCID: PMC3613489
NLM abbreviation: Hum Genet
ISSN: 1432-1203
eISSN: 1432-1203
Publisher: Germany
Grant note: R01 EY011298 / NEI NIH HHS T32 GM008629 / NIGMS NIH HHS R01 MH080128 / NIMH NIH HHS R01 EY016822 / NEI NIH HHS R01-EY-016822 / NEI NIH HHS T32GM008629 / NIGMS NIH HHS R01 EY010564 / NEI NIH HHS
Language: English
Date published: 01/2011
Academic Unit: Roy J. Carver Department of Biomedical Engineering; Electrical and Computer Engineering; Molecular Physiology and Biophysics; Psychiatry; Stead Family Department of Pediatrics; Iowa Neuroscience Institute; Medical Genetics and Genomics; Ophthalmology and Visual Sciences
Record Identifier: 9983979970802771

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