About this Journal Submit a Manuscript Table of Contents
Journal of Ophthalmology
Volume 2010 (2010), Article ID 861291, 9 pages
http://dx.doi.org/10.1155/2010/861291
Research Article

Identification of Diabetic Retinopathy Genes through a Genome-Wide Association Study among Mexican-Americans from Starr County, Texas

1Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, P.O. Box 20186, Houston, TX 77225, USA
2Valley Retina Institute, McAllen, TX 78503, USA
3Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
4Division of Endocrinology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
5Department of Human Genetics, The University of Chicago, Chicago, IL 60637, USA

Received 18 December 2009; Revised 22 May 2010; Accepted 14 July 2010

Academic Editor: Kavita Hegde

Copyright © 2010 Yi-Ping Fu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. A. Foster and S. Resnikoff, “The impact of Vision 2020 on global blindness,” Eye, vol. 19, no. 10, pp. 1133–1135, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  2. Centers for Disease Control and Prevention, National Diabetes Fact Sheet: General Information and National Estimates on Diabetes in the United States, 2005, Department of Health and Human Services, Centers for Disease Control and Prevention, Atlanta, Ga, USA, 2005.
  3. J. B. Saaddine, A. A. Honeycutt, K. M. V. Narayan, X. Zhang, R. Klein, and J. P. Boyle, “Projection of diabetic retinopathy and other major eye diseases among people with diabetes mellitus: United States, 2005–2050,” Archives of Ophthalmology, vol. 126, no. 12, pp. 1740–1747, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  4. H. C. Looker, J. Krakoff, W. C. Knowler, P. H. Bennett, R. Klein, and R. L. Hanson, “Longitudinal studies of incidence and progression of diabetic retinopathy assessed by retinal photography in Pima Indians,” Diabetes Care, vol. 26, no. 2, pp. 320–326, 2003. View at Publisher · View at Google Scholar · View at Scopus
  5. M. C. Leske, S.-Y. Wu, A. Hennis, L. Hyman, B. Nemesure, L. Yang, and A. P. Schachat, “Hyperglycemia, blood pressure, and the 9-year incidence of diabetic retinopathy: the Barbados Eye Studies,” Ophthalmology, vol. 112, no. 5, pp. 799–805, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  6. L. Cikamatana, P. Mitchell, E. Rochtchina, S. Foran, and J. J. Wang, “Five-year incidence and progression of diabetic retinopathy in a defined older population: the Blue Mountains Eye Study,” Eye, vol. 21, no. 4, pp. 465–471, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  7. R. Singh, K. Ramasamy, C. Abraham, V. Gupta, and A. Gupta, “Diabetic retinopathy: an update,” Indian Journal of Ophthalmology, vol. 56, no. 3, pp. 179–188, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. M. I. Harris, R. Klein, C. C. Cowie, M. Rowland, and D. D. Byrd-Holt, “Is the risk of diabetic retinopathy greater in non-Hispanic blacks and Mexican Americans than in non-Hispanic whites with type 2 diabetes? A U.S. population study,” Diabetes Care, vol. 21, no. 8, pp. 1230–1235, 1998. View at Publisher · View at Google Scholar · View at Scopus
  9. N. Emanuele, J. Sacks, R. Klein, D. Reda, R. Anderson, W. Duckworth, and C. Abraira, “Ethnicity, race, and baseline retinopathy correlates in the Veterans Affairs Diabetes Trial,” Diabetes Care, vol. 28, no. 8, pp. 1954–1958, 2005. View at Publisher · View at Google Scholar · View at Scopus
  10. “Clustering of long-term complications in families with diabetes in the diabetes control and complications trial. The Diabetes Control and Complications Trial Research Group,” Diabetes, vol. 46, no. 11, pp. 1829–1839, 1997. View at Scopus
  11. M. Rema, G. Saravanan, R. Deepa, and V. Mohan, “Familial clustering of diabetic retinopathy in South Indian Type 2 diabetic patients,” Diabetic Medicine, vol. 19, no. 11, pp. 910–916, 2002. View at Publisher · View at Google Scholar · View at Scopus
  12. D. M. Hallman, J. C. Huber Jr., V. H. Gonzalez, B. E. K. Klein, R. Klein, and C. L. Hanis, “Familial aggregation of severity of diabetic retinopathy in Mexican Americans from Starr County, Texas,” Diabetes Care, vol. 28, no. 5, pp. 1163–1168, 2005. View at Publisher · View at Google Scholar · View at Scopus
  13. N. H. Arar, B. I. Freedman, and B. I. Freedman, “Heritability of the severity of diabetic retinopathy: the FIND-Eye study,” Investigative Ophthalmology and Visual Science, vol. 49, no. 9, pp. 3839–3845, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  14. K. M. Warpeha and U. Chakravarthy, “Molecular genetics of microvascular disease in diabetic retinopathy,” Eye, vol. 17, no. 3, pp. 305–311, 2003. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  15. K. Uhlmann, P. Kovacs, Y. Boettcher, H.-P. Hammes, and R. Paschke, “Genetics of diabetic retinopathy,” Experimental and Clinical Endocrinology and Diabetes, vol. 114, no. 6, pp. 275–294, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  16. G. Imperatore, R. L. Hanson, D. J. Pettitt, S. Kobes, P. H. Bennett, and W. C. Knowler, “Sib-pair linkage analysis for susceptibility genes for microvascular complications among Pima Indians with 2 diabetes,” Diabetes, vol. 47, no. 5, pp. 821–830, 1998. View at Publisher · View at Google Scholar · View at Scopus
  17. H. C. Looker, R. G. Nelson, E. Chew, R. Klein, B. E. K. Klein, W. C. Knowler, and R. L. Hanson, “Genome-wide linkage analyses to identify loci for diabetic retinopathy,” Diabetes, vol. 56, no. 4, pp. 1160–1166, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  18. D. M. Hallman, E. Boerwinkle, V. H. Gonzalez, B. E. K. Klein, R. Klein, and C. L. Hanis, “A genome-wide linkage scan for diabetic retinopathy susceptibility genes in Mexican Americans with type 2 diabetes from Starr County, Texas,” Diabetes, vol. 56, no. 4, pp. 1167–1173, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  19. “A catalog of published genome-wide association studies,” http://www.genome.gov/26525384.
  20. M. G. Hayes, A. Pluzhnikov, and A. Pluzhnikov, “Identification of type 2 diabetes genes in Mexican Americans through genome-wide association studies,” Diabetes, vol. 56, no. 12, pp. 3033–3044, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  21. R. L. Hanson, C. Bogardus, and C. Bogardus, “A search for variants associated with young-onset type 2 diabetes in American Indians in a 100K genotyping array,” Diabetes, vol. 56, no. 12, pp. 3045–3052, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  22. E. Rampersaud, C. M. Damcott, and C. M. Damcott, “Identification of novel candidate genes for type 2 diabetes from a genome-wide association scan in the old order amish: evidence for replication from diabetes-related quantitative traits and from independent populations,” Diabetes, vol. 56, no. 12, pp. 3053–3062, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  23. J. C. Florez, A. K. Manning, and A. K. Manning, “A 100K genome-wide association scan for diabetes and related traits in the Framingham Heart Study: replication and integration with other genome-wide datasets,” Diabetes, vol. 56, no. 12, pp. 3063–3074, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  24. E. Boerwinkle, C. A. Brown, and C. A. Brown, “Multi-center genetic study of hypertension: the Family blood pressure program (FBPP),” Hypertension, vol. 39, no. 1, pp. 3–9, 2002. View at Publisher · View at Google Scholar · View at Scopus
  25. H. Matsuzaki, S. Dong, and S. Dong, “Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays,” Nat Methods, vol. 1, no. 2, pp. 109–111, 2004. View at Scopus
  26. D. L. Nicolae, X. Wu, K. Miyake, and N. J. Cox, “GEL: a novel genotype calling algorithm using empirical likelihood,” Bioinformatics, vol. 22, no. 16, pp. 1942–1947, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  27. “Diabetic retinopathy study. Report number 6. Design, methods, and baseline results. Report number 7. A modification of the airlie house classification of diabetic retinopathy. prepared by the diabetic retinopathy,” Investigative Ophthalmology and Visual Science, vol. 21, no. 1, part 2, pp. 1–226, 1981. View at Scopus
  28. R. Klein, B. E. K. Klein, and Y. L. Magli, “An alternative method of grading diabetic retinopathy,” Ophthalmology, vol. 93, no. 9, pp. 1183–1187, 1986. View at Scopus
  29. “Grading diabetic retinopathy from stereoscopic color fundus photographs—an extension of the Modified Airlie House classification. ETDRS report number 10. Early Treatment Diabetic Retinopathy Study research group,” Ophthalmology, vol. 98, supplement 5, pp. 786–806, 1991.
  30. S. Purcell, B. Neale, and B. Neale, “PLINK: a tool set for whole-genome association and population-based linkage analyses,” American Journal of Human Genetics, vol. 81, no. 3, pp. 559–575, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  31. B. Devlin and K. Roeder, “Genomic control for association studies,” Biometrics, vol. 55, no. 4, pp. 997–1004, 1999. View at Scopus
  32. Y. Li, C. J. Willer, J. Ding, P. Scheet, and G. R. Abecasis, “Rapid markov chain haplotyping and genotype inference,” submitted.
  33. Y. Li and G. R. Abecasis, “Mach 1.0: rapid haplotype reconstruction and missing genotype inference,” American Journal of Human Genetics, vol. S79, p. 2290, 2006.
  34. Y. S. Aulchenko, S. Ripke, A. Isaacs, and C. M. van Duijn, “GenABEL: an R library for genome-wide association analysis,” Bioinformatics, vol. 23, no. 10, pp. 1294–1296, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  35. Y. S. Aulchenko, M. V. Struchalin, and C. M. van Duijn, “ProbABEL package for genome-wide association analysis of imputed data,” BMC Bioinformatics, vol. 11, article 134, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  36. L. B. Piller, Y. P. Fu, V. H. Gonzalez, B. E. K. Klein, R. Klein, and C. L. Hanis, Prevalence and incidence of diabetic retinopathy of Mexican-Americans with type 2 diabetes from Starr county, Texas.
  37. K. A. Frazer, D. G. Ballinger, and D. G. Ballinger, “A second generation human haplotype map of over 3.1 million SNPs,” Nature, vol. 449, no. 7164, pp. 851–861, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  38. N. Ban, Y. Yamada, and Y. Yamada, “Activating transcripton factor-2 is a positive regulator in CaM kinase IV-induced human insulin gene expression,” Diabetes, vol. 49, no. 7, pp. 1142–1148, 2000. View at Scopus
  39. A. Kobielak, H. A. Pasolli, and E. Fuchs, “Mammalian formin-1 participates in adherens junctions and polymerization of linear actin cables,” Nature Cell Biology, vol. 6, no. 1, pp. 21–30, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  40. B. L. Goode and M. J. Eck, “Mechanism and function of formins in the control of actin assembly,” Annual Review of Biochemistry, vol. 76, pp. 593–627, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  41. Y. Kamei, Y. Takeda, K. Teramoto, O. Tsutsumi, Y. Taketani, and K. Watanabe, “Human NB-2 of the contactin subgroup molecules: chromosomal localization of the gene (CNTN5) and distinct expression pattern from other subgroup members,” Genomics, vol. 69, no. 1, pp. 113–119, 2000. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  42. M. G. Larson, L. D. Atwood, and L. D. Atwood, “Framingham Heart Study 100K project: genome-wide associations for cardiovascular disease outcomes,” BMC Medical Genetics, vol. 8, supplement 1, article S5, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  43. K. Ohtani, Y. Suzuki, and Y. Suzuki, “The membrane-type collectin CL-P1 is a scavenger receptor on vascular endothelial cells,” Journal of Biological Chemistry, vol. 276, no. 47, pp. 44222–44228, 2001. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  44. J. Cai and M. Boulton, “The pathogenesis of diabetic retinopathy: old concepts and new questions,” Eye, vol. 16, no. 3, pp. 242–260, 2002. View at Publisher · View at Google Scholar · View at Scopus
  45. J. Marchini, B. Howie, S. Myers, G. McVean, and P. Donnelly, “A new multipoint method for genome-wide association studies by imputation of genotypes,” Nature Genetics, vol. 39, no. 7, pp. 906–913, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  46. S. R. Browning, “Missing data imputation and haplotype phase inference for genome-wide association studies,” Human Genetics, vol. 124, no. 5, pp. 439–450, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  47. M. Via, C. Gignoux, and E. G. Burchard, “The 1000 genomes project: new opportunities for research and social challenges,” Genome Medicine, vol. 2, no. 1, p. 3, 2010.
  48. M. Nothnagel, D. Ellinghaus, S. Schreiber, M. Krawczak, and A. Franke, “A comprehensive evaluation of SNP genotype imputation,” Human Genetics, vol. 125, no. 2, pp. 163–171, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  49. Y.-F. Pei, J. Li, L. Zhang, C. J. Papasian, and H.-W. Deng, “Analyses and comparison of accuracy of different genotype imputation methods,” PLoS ONE, vol. 3, no. 10, Article ID e3551, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  50. K. Yoshioka, T. Takemura, and S. Hattori, “Tubulointerstitial nephritis antigen: primary structure, expression and role in health and disease,” Nephron, vol. 90, no. 1, pp. 1–7, 2002. View at Publisher · View at Google Scholar · View at Scopus
  51. D. Gong, X. Chen, and X. Chen, “Quantitative proteomic profiling identifies new renal targets of copper(II)-selective chelation in the reversal of diabetic nephropathy in rats,” Proteomics, vol. 9, no. 18, pp. 4309–4320, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  52. R. J. Wordinger, G. Zode, and A. F. Clark, “Focus on Molecules: gremlin,” Experimental Eye Research, vol. 87, no. 2, pp. 78–79, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  53. D. W. P. Lappin, C. Hensey, R. McMahon, C. Godson, and H. R. Brady, “Gremlins, glomeruli and diabetic nephropathy,” Current Opinion in Nephrology and Hypertension, vol. 9, no. 5, pp. 469–472, 2000. View at Publisher · View at Google Scholar · View at Scopus
  54. V. Dolan, M. Murphy, P. Alarcon, H. R. Brady, and C. Hensey, “Gremlin—a putative pathogenic player in progressive renal disease,” Expert Opinion on Therapeutic Targets, vol. 7, no. 4, pp. 523–526, 2003. View at Publisher · View at Google Scholar · View at Scopus
  55. R. Kane, L. Stevenson, C. Godson, A. W. Stitt, and C. O'Brien, “Gremlin gene expression in bovine retinal pericytes exposed to elevated glucose,” British Journal of Ophthalmology, vol. 89, no. 12, pp. 1638–1642, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  56. M. S. Roy, D. M. Hallman, Y.-P. Fu, M. Machado, and C. L. Hanis, “Assessment of 193 candidate genes for retinopathy in African Americans with type 1 diabetes,” Archives of Ophthalmology, vol. 127, no. 5, pp. 605–612, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  57. A. D. Skol, L. J. Scott, G. R. Abecasis, and M. Boehnke, “Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies,” Nature Genetics, vol. 38, no. 2, pp. 209–213, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus