SPOT: A web-based tool for using biological databases to prioritize SNPs after a genome-wide association study

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Saccone, Scott F ^a   Bolze, Raphael ^b   Thomas, Prasanth ^b   Quan, Jiaxi ^a   Mehta, Gaurang ^b   Deelman, Ewa ^b   Tischfield, Jay A ^c   Rice, John P ^a  

^a WASHINGTON UNIVERSITY   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^c Rutgers University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER GRAPHICS; COMPUTER MODEL; COMPUTER NETWORK; COMPUTER PROGRAM; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC DATABASE; HUMAN COMPUTER INTERACTION; MOLECULAR BIOLOGY; ONLINE SYSTEM; PRIORITY JOURNAL; RESEARCH PRIORITY; SINGLE NUCLEOTIDE POLYMORPHISM; WEB BROWSER; GENOMICS; INTERNET;

DATABASES, GENETIC; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; INTERNET; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE;

EID: 77954283427     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq513     Document Type: Article

References (61)

1. Chanock,S.J., Manolio,T., Boehnke,M., Boerwinkle,E., Hunter,D.J., Thomas,G., Hirschhorn,J.N., Abecasis,G., Altshuler,D., Bailey-Wilson,J.E. et al. (2007) Replicating genotype-phenotype associations. Nature, 447, 655-660.
2. Cantor,R.M., Lange,K. and Sinsheimer,J.S. (2010) Prioritizing GWAS results: a review of statistical methods and recommendations for their application. Am. J. Hum. Genet., 86, 6-22.
3. Saccone,S.F., Bierut,L.J., Chesler,E.J., Kalivas,P.W., Lerman,C., Saccone,N.L., Uhl,G.R., Li,C.Y., Philip,V.M., Edenberg,H.J. et al. (2009) Supplementing high-density SNP microarrays for additional coverage of disease-related genes: addiction as a paradigm. PLoS ONE, 4, e5225.
4. Saccone,S.F., Saccone,N.L., Swan,G.E., Madden,P.A., Goate,A.M., Rice,J.P. and Bierut,L.J. (2008) Systematic biological prioritization after a genome-wide association study: an application to nicotine dependence. Bioinformatics, 24, 1805-1811.
5. Roeder,K., Bacanu,S.A., Wasserman,L. and Devlin,B. (2006) Using linkage genome scans to improve power of association in genome scans. Am. J. Hum. Genet., 78, 243-252.
6. Frazer,K.A., Ballinger,D.G., Cox,D.R., Hinds,D.A., Stuve,L.L., Gibbs,R.A., Belmont,J.W., Boudreau,A., Hardenbol,P., Leal,S.M. et al. (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature, 449, 851-861.
7. Barrett,J.C., Fry,B., Maller,J. and Daly,M.J. (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21, 263-265.
8. Sayers,E.W., Barrett,T., Benson,D.A., Bolton,E., Bryant,S.H., Canese,K., Chetvernin,V., Church,D.M., Dicuccio,M., Federhen,S. et al. (2010) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 38, D5-D16.
9. Ramensky,V., Bork,P. and Sunyaev,S. (2002) Human non-synonymous SNPs: server and survey. Nucleic Acids Res., 30, 3894-3900.
10. Adzhubei,I.A., Schmidt,S., Peshkin,L., Ramensky,V.E., Gerasimova,A., Bork,P., Kondrashov,A.S. and Sunyaev,S.R. (2010) A method and server for predicting damaging missense mutations. Nat. Methods, 7, 248-249.
11. Loots,G. and Ovcharenko,I. (2007) ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes. Bioinformatics, 23, 122-124.
12. Nicolae,D.L., Gamazon,E., Zhang,W., Duan,S., Dolan,M.E. and Cox,N.J. (2010) Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. PLoS Genet., 6, e1000888.
13. Barnes,M.R. and Plumpton,M. (2007) Predictive functional analysis of polymorphisms: an overview. In In Barnes,M.R. (ed.), Bioinformatics for Geneticists, 2nd edn. John Wiley & Sons, Ltd, West Sussex, England, pp. 249-280.
14. Barnes,M.R. and Derwent,P.S. (2007) Needle in a haystack? Dealing with 500,000 SNP genome scans. In Barnes,M.R. (ed.), Bioinformatics for Geneticists, 2nd edn. John Wiley & Sons, Ltd, West Sussex, England, pp. 447-493.
15. Howard,H.J., Horaitis,O., Cotton,R.G., Vihinen,M., Dalgleish,R., Robinson,P., Brookes,A.J., Axton,M., Hoffmann,R. and Tuffery-Giraud,S. (2010) The Human Variome Project (HVP) 2009 Forum "Towards Establishing Standards". Hum. Mutat., 31, 366-367.
16. Dickson,S.P., Wang,K., Krantz,I., Hakonarson,H. and Goldstein,D.B. (2010) Rare variants create synthetic genome-wide associations. PLoS Biol., 8, e1000294.
17. Kitsios,G.D. and Zintzaras,E. (2009) Genome-wide association studies: hypothesis-"free" or "engaged"? Trans. Res., 154, 161-164.
18. Clayton,D.G., Walker,N.M., Smyth,D.J., Pask,R., Cooper,J.D., Maier,L.M., Smink,L.J., Lam,A.C., Ovington,N.R., Stevens,H.E. et al. (2005) Population structure, differential bias and genomic control in a large-scale, case-control association study. Nat. Genet., 37, 1243-1246.
19. Hampe,J., Franke,A., Rosenstiel,P., Till,A., Teuber,M., Huse,K., Albrecht,M., Mayr,G., De La Vega,F.M., Briggs,J. et al. (2007) A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat. Genet., 39, 207-211.
20. Ng,S.B., Buckingham,K.J., Lee,C., Bigham,A.W., Tabor,H.K., Dent,K.M., Huff,C.D., Shannon,P.T., Jabs,E.W., Nickerson,D.A. et al. (2010) Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet., 42, 30-35.
21. Portugal,G.S. and Gould,T.J. (2008) Genetic variability in nicotinic acetylcholine receptors and nicotine addiction: converging evidence from human and animal research. Behav. Brain Res., 193, 1-16.
22. Wacholder,S., Chanock,S., Garcia-Closas,M., El Ghormli,L. and Rothman,N. (2004) Assessing the probability that a positive report is false: an approach for molecular epidemiology studies. J. Natl Cancer Inst., 96, 434-442.
23. Goldstein,D.B. (2009) Common genetic variation and human traits. N. Engl. J. Med., 360, 1696-1698.
24. Furberg,H., Kim,Y., Dackor,J., Boerwinkle,E., Franceschini,N., Ardissino,D., Bernardinelli,L., Mannucci,P.M., Mauri,F., Merlini,P.A. et al. (2010) Genome-wide meta-analyses identify multiple loci associated with smoking behavior. Nat. Genet., 42, 441-447.
25. Thorgeirsson,T.E., Gudbjartsson,D.F., Surakka,I., Vink,J.M., Amin,N., Geller,F., Sulem,P., Rafnar,T., Esko,T., Walter,S. et al. (2010) Sequence variants at CHRNB3-CHRNA6 and CYP2A6 affect smoking behavior. Nat. genet., 42, 448-453.
26. Liu,J.Z., Tozzi,F., Waterworth,D.M., Pillai,S.G., Muglia,P., Middleton,L., Berrettini,W., Knouff,C.W., Yuan,X., Waeber,G. et al. (2010) Meta-analysis and imputation refines the association of 15q25 with smoking quantity. Nat. Genet., 42, 436-440.
27. Hirschhorn,J.N. (2009) Genomewide association studies-illuminating biologic pathways. N. Engl. J. Med., 360, 1699-1701.
28. Saccone,S.F., Hinrichs,A.L., Saccone,N.L., Chase,G.A., Konvicka,K., Madden,P.A., Breslau,N., Johnson,E.O., Hatsukami,D., Pomerleau,O. et al. (2007) Cholinergic nicotinic receptor genes implicated in a nicotine dependence association study targeting 348 candidate genes with 3713 SNPs. Hum. Mol. Genet., 16, 36-49.
29. Bierut,L.J., Madden,P.A., Breslau,N., Johnson,E.O., Hatsukami,D., Pomerleau,O.F., Swan,G.E., Rutter,J., Bertelsen,S., Fox,L. et al. (2007) Novel genes identified in a high-density genome wide association study for nicotine dependence. Hum. Mol. Genet., 16, 24-35.
30. Saccone,N.L., Wang,J.C., Breslau,N., Johnson,E.O., Hatsukami,D., Saccone,S.F., Grucza,R.A., Sun,L., Duan,W., Budde,J. et al. (2009) The CHRNA5-CHRNA3-CHRNB4 nicotinic receptor subunit gene cluster affects risk for nicotine dependence in African-Americans and in European-Americans. Cancer Res., 69, 6848-6856.
31. Pillai,S.G., Ge,D., Zhu,G., Kong,X., Shianna,K.V., Need,A.C., Feng,S., Hersh,C.P., Bakke,P., Gulsvik,A. et al. (2009) A genome-wide association study in chronic obstructive pulmonary disease (COPD): identification of two major susceptibility loci. PLoS Genet., 5, e1000421.
32. Caporaso,N., Gu,F., Chatterjee,N., Sheng-Chih,J., Yu,K., Yeager,M., Chen,C., Jacobs,K., Wheeler,W., Landi,M.T. et al. (2009) Genome-wide and candidate gene association study of cigarette smoking behaviors. PLoS ONE, 4, e4653.
33. Stevens,V.L., Bierut,L.J., Talbot,J.T., Wang,J.C., Sun,J., Hinrichs,A.L., Thun,M.J., Goate,A. and Calle,E.E. (2008) Nicotinic receptor gene variants influence susceptibility to heavy smoking. Cancer Epidemiol. Biomarkers Prev., 17, 3517-3525.
34. Hung,R.J., McKay,J.D., Gaborieau,V., Boffetta,P., Hashibe,M., Zaridze,D., Mukeria,A., Szeszenia-Dabrowska,N., Lissowska,J., Rudnai,P. et al. (2008) A susceptibility locus for lung cancer maps to nicotinic acetylcholine receptor subunit genes on 15q25. Nature, 452, 633-637.
35. Chanock,S.J. and Hunter,D.J. (2008) Genomics: when the smoke clears. Nature, 452, 537-538.
36. Berrettini,W., Yuan,X., Tozzi,F., Song,K., Francks,C., Chilcoat,H., Waterworth,D., Muglia,P. and Mooser,V. (2008) alpha-5/alpha-3 nicotinic receptor subunit alleles increase risk for heavy smoking. Mol. Psychiatry, 13, 368-373.
37. Bosker,F.J., Hartman,C.A., Nolte,I.M., Prins,B.P., Terpstra,P., Posthuma,D., van Veen,T., Willemsen,G., Derijk,R.H., de Geus,E.J. et al. (2010) Poor replication of candidate genes for major depressive disorder using genome-wide association data. Mol. Psychiatry., [Epub ahead of print].
38. Hindorff,L.A., Sethupathy,P., Junkins,H.A., Ramos,E.M., Mehta,J.P., Collins,F.S. and Manolio,T.A. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl Acad. Sci. USA, 106, 9362-9367.
39. Kumar,P., Henikoff,S. and Ng,P.C. (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc., 4, 1073-1081.
40. Manolio,T.A., Collins,F.S., Cox,N.J., Goldstein,D.B., Hindorff,L.A., Hunter,D.J., McCarthy,M.I., Ramos,E.M., Cardon,L.R., Chakravarti,A. et al. (2009) Finding the missing heritability of complex diseases. Nature, 461, 747-753.
41. Hardy,J. and Singleton,A. (2009) Genomewide association studies and human disease. N. Engl J. Med., 360, 1759-1768.
42. Thorisson,G.A., Muilu,J. and Brookes,A.J. (2009) Genotype-phenotype databases: challenges and solutions for the post-genomic era. Nat. Rev. Genet., 10, 9-18.
43. Xu,Z. and Taylor,J.A. (2009) SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies. Nucleic Acids Res., 37, W600-W605.
44. Lee,P.H. and Shatkay,H. (2007) F-SNP: computationally predicted functional SNPs for disease association studies. Nucleic Acids Res., 36, D820-D824.
45. Yuan,H.Y., Chiou,J.J., Tseng,W.H., Liu,C.H., Liu,C.K., Lin,Y.J., Wang,H.H., Yao,A., Chen,Y.T. and Hsu,C.N. (2006) FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Res., 34, W635-W641.
46. Mi,H., Dong,Q., Muruganujan,A., Gaudet,P., Lewis,S. and Thomas,P.D. (2010) PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res., 38, D204-D210.
47. Yue,P., Melamud,E. and Moult,J. (2006) SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics, 7, 166.
48. Sandelin,A., Wasserman,W.W. and Lenhard,B. (2004) ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res., 32, W249-W252.
49. Hubbard,T.J., Aken,B.L., Ayling,S., Ballester,B., Beal,K., Bragin,E., Brent,S., Chen,Y., Clapham,P., Clarke,L. et al. (2008) Ensembl 2009. Nucleic Acids Res., 37, D690-D697.
50. Cartegni,L., Wang,J., Zhu,Z., Zhang,M.Q. and Krainer,A.R. (2003) ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res., 31, 3568-3571.
51. Goren,A., Ram,O., Amit,M., Keren,H., Lev-Maor,G., Vig,I., Pupko,T. and Ast,G. (2006) Comparative analysis identifies exonic splicing regulatory sequences-the complex definition of enhancers and silencers. Mol. cell, 22, 769-781.
52. Wang,Z., Rolish,M.E., Yeo,G., Tung,V., Mawson,M. and Burge,C.B. (2004) Systematic identification and analysis of exonic splicing silencers. Cell, 119, 831-845.
53. Wong,Y.H., Lee,T.Y., Liang,H.K., Huang,C.M., Wang,T.Y., Yang,Y.H., Chu,C.H., Huang,H.D., Ko,M.T. and Hwang,J.K. (2007) KinasePhos 2.0: a web server for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns. Nucleic Acids Res., 35, W588-W594.
54. Ryan,M., Diekhans,M., Lien,S., Liu,Y. and Karchin,R. (2009) LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics, 25, 1431-1432.
55. Zhang,X.H. and Chasin,L.A. (2004) Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev., 18, 1241-1250.
56. Fairbrother,W.G., Yeh,R.F., Sharp,P.A. and Burge,B. (2002) Predictive identification of exonic splicing enhancers in human genes. Science, 297, 1007-1013.
57. Reumers,J., Maurer-Stroh,S., Schymkowitz,J. and Rousseau,F. (2006) SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinformatics, 22, 2183-2185.
58. Monigatti,F., Gasteiger,E., Bairoch,A. and Jung,E. (2002) The Sulfinator: predicting tyrosine sulfation sites in protein sequences. Bioinformatics, 18, 769-770.
59. Rhead,B., Karolchik,D., Kuhn,R.M., Hinrichs,A.S., Zweig,A.S., Fujita,P.A., Diekhans,M., Smith,K.E., Rosenbloom,K.R., Raney,B.J. et al. (2009) The UCSC genome browser database: update 2010. Nucleic Acids Res., 38, D613-D619.
60. The UniProt Consortium. (2010) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res., 38, D142-D148.
61. Johnson,A.D., Handsaker,R.E., Pulit,S.L., Nizzari,M.M., O'Donnell,C.J. and de Bakker,P.I. (2008) SNAP: a web-based tool for identification and annotation of proxy SNPs using HapMap. Bioinformatics, 24, 2938-2939.