Biology-Driven Gene-Gene Interaction Analysis of Age-Related Cataract in the eMERGE Network

Genetic Epidemiology

Volumn 39, Issue 5, 2015, Pages 376-384

  Hall, Molly A ^a   Verma, Shefali S ^a   Wallace, John ^a   Lucas, Anastasia ^a   Berg, Richard L ^b   Connolly, John ^c   Crawford, Dana C ^d   Crosslin, David R ^e   de Andrade, Mariza ^f   Doheny, Kimberly F ^g   Haines, Jonathan L ^d   Harley, John B ^h   Jarvik, Gail P ^e,i   Kitchner, Terrie ^b   Kuivaniemi, Helena ^j   Larson, Eric B ^k   Carrell, David S ^k   Tromp, Gerard ^j   Vrabec, Tamara R ^j   Pendergrass, Sarah A ^j   Mccarty, Catherine A ^l   Ritchie, Marylyn D ^a,j   more..

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b MARSHFIELD CLINIC   (United States)

^c CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

^d CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^e UNIVERSITY OF WASHINGTON   (United States)

^f MAYO CLINIC   (United States)

^g JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^h UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

ⁱ UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^j GEISINGER HEALTH SYSTEM   (United States)

^k GROUP HEALTH RESEARCH INSTITUTE   (United States)

^l ESSENTIA INSTITUTE OF RURAL HEALTH   (United States)

more..

Author keywords

Association; Complex disease; Genetic interaction

Indexed keywords

AGE; BIOLOGICAL MODEL; BIOLOGY; CASE CONTROL STUDY; CATARACT; CELL ADHESION; COMPARATIVE STUDY; ELECTRONIC HEALTH RECORD; FEMALE; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; GENOTYPE ENVIRONMENT INTERACTION; HUMAN; MALE; MIDDLE AGED; POPULATION GROUP; PROCEDURES; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE; STATISTICAL ANALYSIS;

AGE FACTORS; CASE-CONTROL STUDIES; CATARACT; CELL ADHESION; COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; ELECTRONIC HEALTH RECORDS; FEMALE; GENE-ENVIRONMENT INTERACTION; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HUMANS; MALE; MIDDLE AGED; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; POPULATION GROUPS; SIGNAL TRANSDUCTION; SOFTWARE;

EID: 84934439962     PISSN: 07410395     EISSN: 10982272     Source Type: Journal    
DOI: 10.1002/gepi.21902     Document Type: Article

References (74)

1. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. 2012. An integrated map of genetic variation from 1092 human genomes. Nature 491(7422):56-65.
2. Apple DJ, Solomon KD, Tetz MR, Assia EI, Holland EY, Legler UF, Tsai JC, Castaneda VE, Hoggatt JP, Kostick AM. 1992. Posterior capsule opacification. Surv Ophthalmol 37(2):73-116.
3. Asbell PA, Dualan I, Mindel J, Brocks D, Ahmad M, Epstein S. 2005. Age-related cataract. Lancet 365(9459):599-609.
4. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT and others. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25-29.
5. Awasthi N, Guo S, Wagner BJ. 2009. Posterior capsular opacification: a problem reduced but not yet eradicated. Arch Ophthalmol 127(4):555-562.
6. Bao XL, Song H, Chen Z, Tang X. 2012. Wnt3a promotes epithelial-mesenchymal transition, migration, and proliferation of lens epithelial cells. Mol Vis 18:1983-1990.
7. Benedek GB. 1971. Theory of transparency of the eye. Appl Opt 10(3):459-473.
8. Black A, Wood J. 2005. Vision and falls. Clin Exp Optom 88(4):212-222.
9. Bush WS, Dudek SM, Ritchie MD. 2009. Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies. Pac Symp Biocomput 368-379.
10. Bush WS, McCauley JL, DeJager PL, Dudek SM, Hafler DA, Gibson RA, Matthews PM, Kappos L, Naegelin Y, Polman CH and others. 2011. A knowledge-driven interaction analysis reveals potential neurodegenerative mechanism of multiple sclerosis susceptibility. Genes Immun 12(5):335-340.
11. Cho HJ, Baek KE, Saika S, Jeong MJ, Yoo J. 2007. Snail is required for transforming growth factor-beta-induced epithelial-mesenchymal transition by activating PI3 kinase/Akt signal pathway. Biochem Biophys Res Commun 353(2):337-343.
12. Chong CC, Stump RJ, Lovicu FJ, McAvoy JW. 2009. TGFbeta promotes Wnt expression during cataract development. Exp Eye Res 88(2):307-313.
13. Cooper MA, Son AI, Komlos D, Sun Y, Kleiman NJ, Zhou R. 2008. Loss of ephrin-A5 function disrupts lens fiber cell packing and leads to cataract. Proc Natl Acad Sci USA 105(43):16620-16625.
14. Cordell HJ. 2009. Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 10(6):392-404.
15. Crawford DC, Crosslin DR, Tromp G, Kullo IJ, Kuivaniemi H, Hayes MG, Denny JC, Bush WS, Haines JL, Roden DM and others. 2014. eMERGEing progress in genomics-the first seven years. Front Genet 5:184.
16. Delaneau O, Zagury JF, Marchini J. 2013. Improved whole-chromosome phasing for disease and population genetic studies. Nat Methods 10(1):5-6.
17. Donaldson P, Kistler J, Mathias RT. 2001. Molecular solutions to mammalian lens transparency. News Physiol Sci 16:118-123.
18. Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, Nadeau JH. 2010. Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 11(6):446-450.
19. Ellwein LB, Urato CJ. 2002. Use of eye care and associated charges among the Medicare population: 1991-1998. Arch Ophthalmol 120(6):804-811.
20. Frazer KA, Murray SS, Schork NJ, Topol EJ. 2009. Human genetic variation and its contribution to complex traits. Nat Rev Genet 10(4):241-251.
21. Goodenough DA. 1992. The crystalline lens. A system networked by gap junctional intercellular communication. Semin Cell Biol 3(1):49-58.
22. Gong X, Li E, Klier G, Huang Q, Wu Y, Lei H, Kumar NM, Horwitz J, Gilula NB. 1997. Disruption of alpha3 connexin gene leads to proteolysis and cataractogenesis in mice. Cell 91(6):833-843.
23. Gottesman O, Kuivaniemi H, Tromp G, Faucett WA, Li R, Manolio TA, Sanderson SC, Kannry J, Zinberg R, Basford MA and others. 2013. The Electronic Medical Records and Genomics (eMERGE) Network: past, present, and future. Genet Med 15(10):761-771.
24. Grady BJ, Torstenson E, Dudek SM, Giles J, Sexton D, Ritchie MD. 2010. Finding unique filter sets in PLATO: a precursor to efficient interaction analysis in GWAS data. Pac Symp Biocomput 315-326.
25. Grady BJ, Torstenson ES, McLaren PJ, PI DEB, Haas DW, Robbins GK, Gulick RM, Haubrich R, Ribaudo H, Ritchie MD. 2011. Use of biological knowledge to inform the analysis of gene-gene interactions involved in modulating virologic failure with efavirenz-containing treatment regimens in ART-naive ACTG clinical trials participants. Pac Symp Biocomput 253-264.
26. Guarino M, Tosoni A, Nebuloni M. 2009. Direct contribution of epithelium to organ fibrosis: epithelial-mesenchymal transition. Hum Pathol 40(10):1365-1376.
27. Hejtmancik JF, Kantorow M. 2004. Molecular genetics of age-related cataract. Exp Eye Res 79(1):3-9.
28. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA. 2009. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci USA 106(23):9362-9367.
29. Howie BN, Donnelly P, Marchini J. 2009. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5(6):e1000529.
30. Huang WR, Fan XX, Tang X. 2011. SiRNA targeting EGFR effectively prevents posterior capsular opacification after cataract surgery. Mol Vis 17:2349-2355.
31. Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C and others. 2010. NetPath: a public resource of curated signal transduction pathways. Genome Biol 11(1):R3.
32. Kim D, Li R, Dudek SM, Frase AT, Pendergrass SA, Ritchie MD. 2014. Knowledge-driven genomic interactions: an application in ovarian cancer. BioData Min 7:20.
33. Licata L, Briganti L, Peluso D, Perfetto L, Iannuccelli M, Galeota E, Sacco F, Palma A, Nardozza AP, Santonico E and others. 2012. MINT, the molecular interaction database: 2012 update. Nucleic Acids Res 40(Database issue):D857-D861.
34. Liu X, Yu X, Zack DJ, Zhu H, Qian J. 2008. TiGER: a database for tissue-specific gene expression and regulation. BMC Bioinform 9:271.
35. Logan CY, Nusse R. 2004. The Wnt signaling pathway in development and disease. Annu Rev Cell Dev Biol 20:781-810.
36. Ma L, Brautbar A, Boerwinkle E, Sing CF, Clark AG, Keinan A. 2012. Knowledge-driven analysis identifies a gene-gene interaction affecting high-density lipoprotein cholesterol levels in multi-ethnic populations. PLoS Genet 8(5):e1002714.
37. Maher B. 2008. Personal genomes: the case of the missing heritability. Nature 456(7218):18-21.
38. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A and others. 2009. Finding the missing heritability of complex diseases. Nature 461(7265):747-753.
39. Martinez G, deIongh RU. 2010. The lens epithelium in ocular health and disease. Int J Biochem Cell Biol 42(12):1945-1963.
40. Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, deBono B, Garapati P, Hemish J, Hermjakob H, Jassal B and others. 2009. Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res 37(Database issue):D619-D622.
41. McCarty CA, Chapman-Stone D, Derfus T, Giampietro PF, Fost N. 2008. Community consultation and communication for a population-based DNA biobank: the Marshfield clinic personalized medicine research project. Am J Med Genet A 146A(23):3026-3033.
42. McCarty CA, Chisholm RL, Chute CG, Kullo IJ, Jarvik GP, Larson EB, Li R, Masys DR, Ritchie MD, Roden DM and others. 2011. The eMERGE Network: a consortium of biorepositories linked to electronic medical records data for conducting genomic studies. BMC Med Genomics 4:13.
43. Nusse R. 2005. Wnt signaling in disease and in development. Cell Res 15(1):28-32.
44. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. 1999. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27(1):29-34.
45. Peissig PL, Rasmussen LV, Berg RL, Linneman JG, McCarty CA, Waudby C, Chen L, Denny JC, Wilke RA, Pathak J and others. 2012. Importance of multi-modal approaches to effectively identify cataract cases from electronic health records. J Am Med Inform Assoc 19(2):225-234.
46. Pendergrass SA, Dudek SM, Crawford DC, Ritchie MD. 2010. Synthesis-view: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis. BioData Min 3:10.
47. Pendergrass SA, Frase A, Wallace J, Wolfe D, Katiyar N, Moore C, Ritchie MD. 2013a. Genomic analyses with biofilter 2.0: knowledge driven filtering, annotation, and model development. BioData Min 6(1):25.
48. Pendergrass SA, Verma SS, Holzinger ER, Moore CB, Wallace J, Dudek SM, Huggins W, Kitchner T, Waudby C, Berg R and others. 2013b. Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit. Pac Symp Biocomput 147-158.
49. Perez-Moreno M, Jamora C, Fuchs E. 2003. Sticky business: orchestrating cellular signals at adherens junctions. Cell 112(4):535-548.
50. Pontoriero GF, Smith AN, Miller LA, Radice GL, West-Mays JA, Lang RA. 2009. Co-operative roles for E-cadherin and N-cadherin during lens vesicle separation and lens epithelial cell survival. Dev Biol 326(2):403-417.
51. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D. 2006. Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38(8):904-909.
52. Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J and others. 2012. The Pfam protein families database. Nucleic Acids Res 40(Database issue):D290-D301.
53. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, deBakker PI, Daly MJ and others. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559-575.
54. Rasmussen LV, Peissig PL, McCarty CA, Starren J. 2012. Development of an optical character recognition pipeline for handwritten form fields from an electronic health record. J Am Med Inform Assoc 19(e1):e90-e95.
55. Ritchie MD. 2009. Using prior knowledge and genome-wide association to identify pathways involved in multiple sclerosis. Genome Med 1(6):65.
56. Ritchie MD. 2011. Using biological knowledge to uncover the mystery in the search for epistasis in genome-wide association studies. Ann Hum Genet 75(1):172-182.
57. Ritchie MD, Verma SS, Hall MA, Goodloe RJ, Berg RL, Carrell DS, Carlson CS, Chen L, Crosslin DR, Denny JC and others. 2014. Electronic medical records and genomics (eMERGE) network exploration in cataract: several new potential susceptibility loci. Mol Vis 20:1281-1295.
58. Roden DM, Pulley JM, Basford MA, Bernard GR, Clayton EW, Balser JR, Masys DR. 2008. Development of a large-scale de-identified DNA biobank to enable personalized medicine. Clin Pharmacol Ther 84(3):362-369.
59. Rowan S, Conley KW, Le TT, Donner AL, Maas RL, Brown NL. 2008. Notch signaling regulates growth and differentiation in the mammalian lens. Dev Biol 321(1):111-122.
60. Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. 2012. A travel guide to Cytoscape plugins. Nat Methods 9(11):1069-1076.
61. Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. 2001. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29(1):308-311.
62. Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, VanAuken K, Wang X, Shi X and others. 2011. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res 39(Database issue):D698-D704.
63. Sun X, Lu Q, Mukheerjee S, Crane PK, Elston R, Ritchie MD. 2014. Analysis pipeline for the epistasis search-statistical versus biological filtering. Front Genet 5:106.
64. Turner SD, Berg RL, Linneman JG, Peissig PL, Crawford DC, Denny JC, Roden DM, McCarty CA, Ritchie MD, Wilke RA. 2014a. Knowledge-driven multi-locus analysis reveals gene-gene interactions influencing HDL cholesterol level in two independent EMR-linked biobanks. PLoS ONE 6(5):e19586
65. Turner S, Armstrong LL, Bradford Y, Carlson CS, Crawford DC, Crenshaw AT, deAndrade M, Doheny KF, Haines JL, Hayes G and others. 2011b. Quality control procedures for genome-wide association studies. Curr Protoc Hum Genet Chapter 1(Unit1):19.
66. Verma SS dAM, Tromp G, Kuivaniemi H, Pugh E, Namjou B, Mukherjee S, Jarvik GP, Kottyan LC, Burt A and others. 2014. Imputation and quality control steps for combining multiple genome-wide datasets. Front Genet 5(370).
67. Wang Z, Xu W, San Lucas FA, Liu Y. 2013. Incorporating prior knowledge into Gene Network Study. Bioinformatics 29(20):2633-2640.
68. Wei CJ, Xu X, Lo CW. 2004. Connexins and cell signaling in development and disease. Annu Rev Cell Dev Biol 20:811-838.
69. White TW, Paul DL. 1999. Genetic diseases and gene knockouts reveal diverse connexin functions. Annu Rev Physiol 61:283-310.
70. White TW, Goodenough DA, Paul DL. 1998. Targeted ablation of connexin50 in mice results in microphthalmia and zonular pulverulent cataracts. J Cell Biol 143(3):815-825.
71. Yao K, Ye PP, Tan J, Tang XJ, Shen Tu XC. 2008. Involvement of PI3K/Akt pathway in TGF-beta2-mediated epithelial mesenchymal transition in human lens epithelial cells. Ophthalmic Res 40(2):69-76.
72. Yu X, Lin J, Zack DJ, Qian J. 2006. Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res 34(17):4925-4936.
73. Zuk O, Hechter E, Sunyaev SR, Lander ES. 2012. The mystery of missing heritability: genetic interactions create phantom heritability. Proc Natl Acad Sci USA 109(4):1193-1198.
74. Zuvich RL, Armstrong LL, Bielinski SJ, Bradford Y, Carlson CS, Crawford DC, Crenshaw AT, deAndrade M, Doheny KF, Haines JL and others. 2011. Pitfalls of merging GWAS data: lessons learned in the eMERGE network and quality control procedures to maintain high data quality. Genet Epidemiol 35(8):887-898.