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

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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.

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Acknowledgments

We are grateful to the patients and their families for participating in this study. We thank Dr. Kai Wang for helpful discussion. Alcon Research, Ltd. (Ft. Worth, TX) provided funds for the purchase of the SNP genotyping chips used in this study. This work was supported by the following grants and organizations: National Institutes of Health Predoctoral Training Grant T32GM008629 (L.K.D.); National Institutes of Health grants R01-EY-010564 (V.C.S.) and R01-EY-016822 (E.M.S.); the Carver Endowment for Molecular Ophthalmology (E.M.S. and V.C.S.); and Research to Prevent Blindness (Department of Ophthalmology, University of Iowa, Career Development Awards to T.E.S. and J.H.F., and the Lew Wasserman Award to W.L.M.A.); and Foundation Fighting Blindness. V.C.S. and E.M.S. are investigators of the Howard Hughes Medical Institute.

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Authors and Affiliations

  1. Interdisciplinary Genetics Program, University of Iowa, Iowa City, IA, USA

    Kacie J. Meyer, Emily I. Schindler, Danielle S. Rudd, Todd E. Scheetz, Terry A. Braun, John H. Fingert, Thomas H. Wassink, Edwin M. Stone & Val C. Sheffield

  2. Department of Psychiatry, University of Illinois, Chicago, IL, USA

    Lea K. Davis

  3. Department of Pediatrics, University of Iowa, Iowa City, IA, USA

    John S. Beck & Val C. Sheffield

  4. Center for Bioinformatics and Computational Biology, University of Iowa, Iowa City, IA, USA

    A. Jason Grundstad, Todd E. Scheetz & Terry A. Braun

  5. Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, IA, USA

    Todd E. Scheetz, Terry A. Braun, John H. Fingert, Wallace L. Alward, Young H. Kwon, James C. Folk, Stephen R. Russell & Edwin M. Stone

  6. Department of Psychiatry, University of Iowa, 500 Newton Road, 1-191 MEB, Iowa City, IA, 52242, USA

    Thomas H. Wassink

  7. Howard Hughes Medical Institute, University of Iowa, Iowa City, IA, USA

    Edwin M. Stone & Val C. Sheffield

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  1. Kacie J. Meyer
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Correspondence to Thomas H. Wassink.

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K. J. Meyer and L. K. Davis contributed equally to this work.

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Meyer, K.J., Davis, L.K., Schindler, E.I. et al. Genome-wide analysis of copy number variants in age-related macular degeneration. Hum Genet 129, 91–100 (2011). https://doi.org/10.1007/s00439-010-0904-6

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