Abstract
Diabetic retinopathy (DR) is a common clinical expression of diabetes mellitus-induced vasculopathy and is a major cause of vision loss. Significant gaps remain in our understanding of the molecular pathoetiology of DR, and it is hoped that human genetic approaches can reveal novel targets especially since DR is a heritable trait. Previous studies have focused on genetic risk factors of DR but their results have been mixed. In this study, we hypothesized that the use of the extreme phenotype design will increase the power of a genomewide search for “protective” genetic variants. We enrolled a small yet atypical cohort of 43 diabetics who did not develop DR a decade or more after diagnosis (cases), and 64 diabetics with DR (controls), all of similar ethnic background (Saudi). Whole-exome sequencing of the entire cohort was followed by statistical analysis employing combined multivariate and collapsing methods at the gene level, to identify genes that are enriched for rare variants in cases vs. controls. Three genes (NME3, LOC728699, and FASTK) reached gene-based genome-wide significance at the 10−08 threshold (p value = 1.55 × 10−10, 6.23 × 10−10, 3.21 × 10−08, respectively). Our results reveal novel candidate genes whose increased rare variant burden appears to protect against DR, thus highlighting them as attractive candidate targets, if replicated by future studies, for the treatment and prevention of DR. Extreme phenotype design when implemented in sequencing-based genome-wide case–control studies has the potential to reveal novel candidates with a smaller cohort size compared to standard study designs.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Abhary S, Hewitt AW, Burdon KP, Craig JE (2009) A systematic meta-analysis of genetic association studies for diabetic retinopathy. Diabetes 58:2137–2147
Arar NH, Freedman BI, Adler SG, Iyengar SK, Chew EY, Davis MD, Satko SG, Bowden DW, Duggirala R, Elston RC (2008) Heritability of the severity of diabetic retinopathy: the FIND-Eye study. Invest Ophthalmol Vis Sci 49:3839–3845
Barnett IJ, Lee S, Lin X (2013) Detecting rare variant effects using extreme phenotype sampling in sequencing association studies. Genet Epidemiol 37:142–151
Cheung N, Mitchell P, Wong TY (2010) Diabetic retinopathy. Lancet 376:124–136. doi:10.1016/S0140-6736(09)62124-3
Cohen JC, Kiss RS, Pertsemlidis A, Marcel YL, McPherson R, Hobbs HH (2004) Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 305:869–872
Emond MJ, Louie T, Emerson J, Zhao W, Mathias RA, Knowles MR, Wright FA, Rieder MJ, Tabor HK, Nickerson DA (2012) Exome sequencing of extreme phenotypes identifies DCTN4 as a modifier of chronic Pseudomonas aeruginosa infection in cystic fibrosis. Nat Genet 44:886–889
Group EDPR (2004) The prevalence of diabetic retinopathy among adults in the United States. Arch Ophthalmol 122:552
Hietala K, Forsblom C, Summanen P, Groop P-H (2008) Heritability of proliferative diabetic retinopathy. Diabetes 57:2176–2180
Hosseini SM, Boright AP, Sun L, Canty AJ, Bull SB, Klein BE, Klein R, Paterson AD, Group DER (2015) The association of previously reported polymorphisms for microvascular complications in a meta-analysis of diabetic retinopathy. Hum Genet 134:247–257
Kuo JZ, Wong TY, Rotter JI (2014) Challenges in elucidating the genetics of diabetic retinopathy. JAMA ophthalmology 132:96–107
Li B, Leal SM (2008) Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 83:311–321
Li D, Lewinger JP, Gauderman WJ, Murcray CE, Conti D (2011) Using extreme phenotype sampling to identify the rare causal variants of quantitative traits in association studies. Genet Epidemiol 35:790–799
Li B, Liu DJ, Leal SM (2013) Identifying rare variants associated with complex traits via sequencing. Curr Protoc Hum Genet 1.26. 1–1.26. 22. doi:10.1002/0471142905.hg0126s78
Löbbert RW, Winterpacht A, Seipel B, Zabel BU (1996) Molecular cloning and chromosomal assignment of the human homologue of the rat cGMP-inhibited phosphodiesterase 1 (PDE3A)—A gene involved in fat metabolism located at 11p15. 1. Genomics 37:211–218
Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A (2009) Finding the missing heritability of complex diseases. Nature 461:747–753
McAuley AK, Wang JJ, Dirani M, Connell PP, Lamoureux E, Hewitt AW (2014) Replication of genetic loci implicated in diabetic retinopathy. Invest Ophthalmol Vis Sci 55:1666–1671
McCarthy JJ, McLeod HL, Ginsburg GS (2013) Genomic medicine: a decade of successes, challenges, and opportunities. Sci Transl Med 5:189sr4–189sr4
Mohamed Q, Gillies MC, Wong TY (2007) Management of diabetic retinopathy: a systematic review. JAMA 298:902–916
Murray CJ, Vos T, Lozano R, Naghavi M, Flaxman AD, Michaud C, Ezzati M, Shibuya K, Salomon JA, Abdalla S (2013) Disability-adjusted life years (DALYs) for 291 diseases and injuries in 21 regions, 1990–2010: a systematic analysis for the global burden of disease study 2010. Lancet 380:2197–2223
Petrovič D (2013) Candidate genes for proliferative diabetic retinopathy. Biomed Res Int 2013. doi:10.1155/2013/540416
Rose R, Liu H, Palmer D, Maurice D (1997) Cyclic AMP-mediated regulation of vascular smooth muscle cell cyclic AMP phosphodiesterase activity. Br J Pharmacol 122:233–240
Roy MS, Klein R, O’Colmain BJ, Klein BE, Moss SE, Kempen JH (2004) The prevalence of diabetic retinopathy among adult type 1 diabetic persons in the United States. Arch Ophthalmol 122:546–551. doi:10.1001/archopht.122.4.546
Shamoon H, Duffy H, Fleischer N, Engel S, Saenger P, Strelzyn M, Litwak M, Wylierosett J, Farkash A, Geiger D (1993) The effect of intensive treatment of diabetes on the development and progression of long-term complications in insulin-dependent diabetes-mellitus. N Engl J Med 329:977–986
Shi G, Rao D (2011) Optimum designs for next-generation sequencing to discover rare variants for common complex disease. Genet Epidemiol 35:572–579
Tian Q, Taupin J, Elledge S, Robertson M, Anderson P (1995) Fas-activated serine/threonine kinase (FAST) phosphorylates TIA-1 during Fas-mediated apoptosis. J Exp Med 182:865–874
Visscher PM, Brown MA, McCarthy MI, Yang J (2012) Five years of GWAS discovery. Am J Hum Genet 90:7–24
Wild S, Roglic G, Green A, Sicree R, King H (2004) Global prevalence of diabetes estimates for the year 2000 and projections for 2030. Diabetes Care 27:1047–1053
Acknowledgments
This work was supported in part by KACST 10-BIO1356-20 (FSA).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
Corina Shtir is employed by Thermo Fisher Scientific that manufactures the platform used in this study for whole-exome sequencing.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Shtir, C., Aldahmesh, M.A., Al-Dahmash, S. et al. Exome-based case–control association study using extreme phenotype design reveals novel candidates with protective effect in diabetic retinopathy. Hum Genet 135, 193–200 (2016). https://doi.org/10.1007/s00439-015-1624-8
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00439-015-1624-8