Density of Common Complex Ocular Traits in the Aging Eye: Analysis of Secondary Traits in Genome-Wide Association Studies Albert O. Edwards1*, Sung J. Lee1, Brooke L. Fridley2, Nirubol Tosakulwong1 1 Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota, United States of America, 2 Division of Biostatistics, Mayo Clinic, Rochester, Minnesota, United States of America Abstract Genetic association studies are identifying genetic risks for common complex ocular traits such as age-related macular degeneration (AMD). The subjects used for discovery of these loci have been largely from clinic-based, case-control studies. Typically, only the primary phenotype (e.g., AMD) being studied is systematically documented and other complex traits (e.g., affecting the eye) are largely ignored. The purpose of this study was to characterize these other or secondary complex ocular traits present in the cases and controls of clinic-based studies being used for genetic study of AMD. The records of 100 consecutive new patients (of any diagnosis) age 60 or older for which all traits affecting the eye had been recorded systematically were reviewed. The average patient had 3.5 distinct diagnoses. A subset of 10 complex traits was selected for further study because they were common and could be reliably diagnosed. The density of these 10 complex ocular traits increased by 0.017 log-traits/year (P = 0.03), ranging from a predicted 2.74 at age 60 to 4.45 at age 90. Trait-trait association was observed only between AMD and primary vitreomacular traction (P = 0.0009). Only 1% of subjects age 60 or older had no common complex traits affecting the eye. Extrapolations suggested that a study of 2000 similar subjects would have sufficient power to detect genetic association with an odds ratio of 2.0 or less for 4 of these 10 traits. In conclusion, the high prevalence of complex traits affecting the aging eye and the inherent biases in referral patterns leads to the potential for confounding by undocumented secondary traits within case-control studies. In addition to the primary trait, other common ocular phenotypes should be systematically documented in genetic association studies so that adjustments for potential trait-trait associations and other bias can be made and genetic risk variants identified in secondary analyses. Citation: Edwards AO, Lee SJ, Fridley BL, Tosakulwong N (2008) Density of Common Complex Ocular Traits in the Aging Eye: Analysis of Secondary Traits in Genome-Wide Association Studies. PLoS ONE 3(6): e2510. doi:10.1371/journal.pone.0002510 Editor: Peter Heutink, Vrije Universiteit Medical Centre, Netherlands Received January 22, 2008; Accepted May 21, 2008; Published June 25, 2008 Copyright: 2008 Edwards et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The research was supported by EY014467, the Foundation Fighting Blindness, Owing Mills, MD, the American Health Assistance Foundation, Clarksburg, MD, unrestricted departmental grants from Research to Prevent Blindness, New York, NY, and the Mayo Clinic Foundation. The sole role of the sponsors was to provide funding. Competing Interests: The authors have declared that no competing interests exist. * E-mail: edwardslab@mayo.edu Introduction The eye has long been an excellent organ for studying hereditary diseases, in part, because the visual system enables use of our discriminating sense of vision to characterize phenotypes. Genetic association studies on age-related macular degeneration (AMD, Online Mendelian Inheritance of Man, OMIM, 603075), cataract (OMIM 601371), glaucoma (OMIM 137760), and other diseases are unraveling the genetic risks for common complex ocular traits [1–3]. Other common diseases such as epiretinal membranes are not known to be hereditary, but could influence study endpoints through biases in referral patterns or unknown genetic effects. Genetic association studies have proven a powerful method and important genetic risks have been identified for systemic age-related complex traits such as cancer and coronary artery disease [4,5]. Many of these studies use clinic- based case-control subjects ascertained for the presence or absence of the primary trait (e.g., AMD) and systematically document phenotypes on few, if any, other complex ocular traits [6–10]. The unavailability of phenotypes on other (secondary) ocular traits in a case-control study gives rise to a number of limitations. Because such clinic based studies are collected from a number of different subspecialty clinics, the inability to account for the diagnoses for which the patient presented could lead to undetected confounding of genetic results. Trait-trait associations that might confound the interpretation of association results, such as the reported increased risk of exudative AMD in eyes with posterior vitreous adherence to the macula or Fuchs endothelial dystrophy (OMIM 610158), cannot be assessed [11–14]. Genetic risks may alter the risk of related diseases, such as the common risk on chromosome 8q24 for cancer, and it is well established that Mendelian diseases can affect multiple tissues with diseases indistinguishable from the complex traits affecting the eye [4,15,16]. Such shared risks are likely to be missed in the absence of systematic phenotyping of common traits affecting an organ. Equally important to these potential problems is the inability to explore genotypes generated in genome-wide studies for associa- tion with secondary ocular traits or even the large number of biomorphic and biochemical variables such as axial length of the eye, corneal thickness, and retinal autofluorescence that influence disease progression [17–19]. Indeed, some common complex traits, biomorphic features, and biochemical endpoints might PLoS ONE | www.plosone.org 1 June 2008 | Volume 3 | Issue 6 | e2510