Identification of novel therapeutics for complex diseases from genome-wide association data

BMC Medical Genomics

Volumn 7, Issue SUPPL.1, 2014, Pages

  Grover, Mani P ^a   Ballouz, Sara ^b   Mohanasundaram, Kaavya A ^a   George, Richard A ^c   H Sherman, Craig D ^a   Crowley, Tamsyn M ^a,d   Wouters, Merridee A ^a  

^a DEAKIN UNIVERSITY   (Australia)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^c VICTOR CHANG CARDIAC RESEARCH INSTITUTE   (Australia)

^d CSIRO   (Australia)

Author keywords

Candidate gene; Complex disease; Drug database; Drug repositioning; Drug target; Genome wide association study

Indexed keywords

ALEGLITAZAR; ALITRETINOIN; ALPHA TOCOPHEROL; AMG 714; AVI 4126; BENAZEPRIL; BEZAFIBRATE; FENOLDOPAM; GEMFIBROZIL; GLATIRAMER; IMIPRAMINE; INFLIXIMAB; ISOSORBIDE MONONITRATE; LITHIUM SALT; METHOTREXATE; MONOCYTE CHEMOTACTIC PROTEIN 1; PALIFERMIN; PIG INSULIN; PIRENZEPINE; RAMIPRIL; REPAGLINIDE; ROSIGLITAZONE; RUXOLITINIB; SORAFENIB; SUNITINIB; TRILOSTANE; UNINDEXED DRUG; UROKINASE; VALSARTAN; ZAURATEGRAST;

ADVANCED CANCER; ARTICLE; BIOINFORMATICS; BIPOLAR DISORDER; CORONARY ARTERY DISEASE; CUSHING SYNDROME; DRUG DATABASE; DRUG IDENTIFICATION; DRUG INDICATION; DRUG TARGETING; GENE MAPPING; GENE TARGETING; GENETIC ASSOCIATION; GENETIC DATABASE; GENETIC IDENTIFICATION; HUMAN; HYPERLIPIDEMIA; HYPERTENSION; INSULIN DEPENDENT DIABETES MELLITUS; INTERMETHOD COMPARISON; KAPOSI SARCOMA; KIDNEY CARCINOMA; KNOWLEDGE BASE; MULTIPLE SCLEROSIS; NON INSULIN DEPENDENT DIABETES MELLITUS; ORAL MUCOSITIS; PEPTIC ULCER; PHARMACOGENOMICS; PHENOTYPE; PREDICTION; PRIORITY JOURNAL; PSORIASIS; RHEUMATOID ARTHRITIS; DISEASES; DRUG APPROVAL; DRUG DEVELOPMENT; FEASIBILITY STUDY; FOOD AND DRUG ADMINISTRATION; GENE LOCUS; GENETICS; MOLECULARLY TARGETED THERAPY; PROCEDURES; UNITED STATES;

DATABASES, PHARMACEUTICAL; DISEASE; DRUG APPROVAL; DRUG DISCOVERY; FEASIBILITY STUDIES; GENETIC LOCI; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MOLECULAR TARGETED THERAPY; UNITED STATES; UNITED STATES FOOD AND DRUG ADMINISTRATION;

EID: 84900449627     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-7-S1-S8     Document Type: Article

References (37)

1. Drug repositioning: identifying and developing new uses for existing drugs. Ashburn TT, Thor KB, Nat Rev Drug Discov 2004 3 673 683 10.1038/nrd1468 15286734 (Pubitemid 39173508)
2. PhRMA annual membership survey. Pharmaceutical Research and Manufacturers of America, Washington, DC 2013
3. The return of thalidomide: can birth defects be prevented? Lary J, Daniel K, Erickson J, Roberts H, Moore C, Drug Saf 1999 21 161 169 10.2165/00002018-199921030-00002 10487395 (Pubitemid 29427879)
4. New uses for old drugs. Chong CR, Sullivan DJ, Nature 2007 448 645 646 10.1038/448645a 17687303 (Pubitemid 47236844)
5. Drug target prediction and repositioning using an integrated network-based approach. Emig D, Ivliev A, Pustovalova O, Lancashire L, Bureeva S, Nikolsky Y, Bessarabova M, PLoS One 2013 8 60618 10.1371/journal.pone.0060618 23593264
6. Gene-Environment interactions and the etiology of common complex disease. Cooper RS, Ann Intern Med 2003 139 437 440 10.7326/0003-4819-139-5-Part-2- 200309021-00011 12965972 (Pubitemid 38120872)
7. Genetic mapping in human disease. Altshuler D, Daly MJ, Lander ES, Science 2008 322 881 888 10.1126/science.1156409 18988837
8. Use of genome-wide association studies for drug repositioning. Sanseau P, Agarwal P, Barnes MR, Pastinen T, Richards JB, Cardon LR, Mooser V, Nat Biotechnol 2012 30 317 320 10.1038/nbt.2151 22491277
9. Analysis of genome-wide association study data using the protein knowledge base. Ballouz S, Liu J, Oti M, Gaeta B, Fatkin D, Bahlo M, Wouters M, BMC Genet 2011 12 98 22077927
10. Prioritizing GWAS results: a review of statistical methods and recommendations for their application. Cantor RM, Lange K, Sinsheimer JS, Am J Hum Genet 2010 86 6 22 10.1016/j.ajhg.2009.11.017 20074509
11. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Wellcome Trust Case Control Consortium, Nature 2007 447 661 678 10.1038/nature05911 17554300 (Pubitemid 46889737)
12. POCUS: mining genomic sequence annotation to predict disease genes. Turner FS, Clutterbuck DR, Semple CAM, Genome Biol 2003 4 75 10.1186/gb-2003-4-11-r75 14611661
13. Web tools for the prioritization of candidate disease genes. Oti M, Ballouz S, Wouters MA, Methods Mol Biol 2011 760 189 206 10.1007/978-1-61779- 176-5-12 21779998
14. Computational tools for prioritizing candidate genes: boosting disease gene discovery. Moreau Y, Tranchevent L-C, Nat Rev Genet 2012 13 523 536 10.1038/nrg3253 22751426
15. Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies. Teber E, Liu J, Ballouz S, Fatkin D, Wouters M, BMC Bioinformatics 2009 10 Suppl 1 69 10.1186/1471-2105-10-S1-S69 19208173
16. Gentrepid V2. 0: a web server for candidate disease gene prediction. Ballouz S, Liu JY, George RA, Bains N, Liu A, Oti M, Gaeta B, Fatkin D, Wouters MA, BMC Bioinformatics 2013 14 249 10.1186/1471-2105-14-249 23947436
17. Candidate disease gene prediction using Gentrepid: application to a genome-wide association study on coronary artery disease. Ballouz S, Liu JY, Oti M, Gaeta B, Fatkin D, Bahlo M, Wouters MA (2013), Mol Genet Genomic Med 24498628
18. DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Nucleic Acids Res 2011 39 Suppl 1 1035 D1041 21059682
19. The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge. Hernandez-Boussard T, Whirl-Carrillo M, Hebert JM, Gong L, Owen R, Gong M, Gor W, Liu F, Truong C, Whaley R, Nucleic Acids Res 2008 36 Suppl 1 913 D918 18032438
20. Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery. Zhu F, Shi Z, Qin C, Tao L, Liu X, Xu F, Zhang L, Song Y, Liu X, Zhang J, Nucleic Acids Res 2012 40 1128 D1136 10.1093/nar/gkr797 21948793
21. Analysis of protein sequence and interaction data for candidate disease gene prediction. George RA, Liu JY, Feng LL, Bryson-Richardson RJ, Fatkin D, Wouters MA, Nucleic Acids Res 2006 34 130 e130 10.1093/nar/gkl707 17020920 (Pubitemid 44742463)
22. Beyond Mendel: an evolving view of human genetic disease transmission. Badano JL, Katsanis N, Nat Rev Genet 2002 3 779 789 12360236
23. GeneSeeker: extraction and integration of human disease-related information from web-based genetic databases. van Driel MA, Cuelenaere K, Kemmeren PPCW, Leunissen JAM, Brunner HG, Vriend G, Nucleic Acids Res 2005 33 Suppl 2 758 W761 15980578
24. ToppGene suite for gene list enrichment analysis and candidate gene prioritization. Chen J, Bardes EE, Aronow BJ, Jegga AG, Nucleic Acids Res 2009 37 Suppl 2 305 W311 19465376
25. ENDEAVOUR update: a web resource for gene prioritization in multiple species. Tranchevent LC, Barriot R, Yu S, Van Vooren S, Van Loo P, Coessens B, De Moor B, Aerts S, Moreau Y, Nucleic Acids Res 2008 36 Suppl 2 377 W384 18508807
26. Human disease genes. Jimenez-Sanchez G, Childs B, Valle D, Nature 2001 409 853 855 10.1038/35057050 11237009 (Pubitemid 32165343)
27. g: Profiler - a web server for functional interpretation of gene lists (2011 update). Reimand J, Arak T, Vilo J, Nucleic Acids Res 2011 39 Suppl 2 307 W315 21646343
28. Predicting protein druggability. Hajduk PJ, Huth JR, Tse C, Drug Discov Today 2005 10 1675 1682 10.1016/S1359-6446(05)03624-X 16376828 (Pubitemid 41817616)
29. How many drug targets are there? Overington JP, Al-Lazikani B, Hopkins AL, Nat Rev Drug Discov 2006 5 993 996 10.1038/nrd2199 17139284 (Pubitemid 44835126)
30. The druggable genome. Hopkins AL, Groom CR, Nat Rev Drug Discov 2002 1 727 730 10.1038/nrd892 12209152 (Pubitemid 37361545)
31. Druggability of human disease genes. Sakharkar MK, Sakharkar KR, Pervaiz S, Int J Biochem Cell Biol 2007 39 1156 1164 10.1016/j.biocel.2007.02.018 17446117 (Pubitemid 46830908)
32. Knockouts model the 100 best-selling drugs - will they model the next 100? Zambrowicz BP, Sands AT, Nat Rev Drug Discov 2003 2 38 51 10.1038/nrd987 12509758 (Pubitemid 37361623)
33. The Quest for the Cure: The Science, Stories and Struggles Behind the Next Generation of Medicines. Stockwell B, Columbia University Press 2011
34. TARGETgene: a tool for identification of potential therapeutic targets in cancer. Wu CC, D'Argenio D, Asgharzadeh S, Triche T, PLoS One 2012 7 43305 10.1371/journal.pone.0043305 22952662
35. Integrative systems biology approaches to identify and prioritize disease and drug candidate genes. Kaimal V, Sardana D, Bardes EE, Gudivada RC, Chen J, Jegga AG, Methods Mol Biol 2011 700 241 259 10.1007/978-1-61737-954-3-16 21204038
36. Exploiting drug-disease relationships for computational drug repositioning. Dudley JT, Deshpande T, Butte AJ, Brief Bioinform 2011 12 303 311 10.1093/bib/bbr013 21690101
37. Predictive methods in drug repurposing: gold mine or just a bigger haystack? Cavalla D, Drug Discov Today 2012 23270784