Association of genetic profiles to Crohn's disease by linear combinations of single nucleotide polymorphisms

Artificial Intelligence in Medicine

Volumn 46, Issue 2, 2009, Pages 131-138

  D'Addabbo, Annarita ^a   Latiano, Anna ^b   Palmieri, Orazio ^b   Creanza, Maria Teresa ^a   Maglietta, Rosalia ^a   Annese, Vito ^b   Ancona, Nicola ^a  

^a INSTITUTE OF INTELLIGENT SYSTEMS FOR AUTOMATION   (Italy)

^b CASA SOLLIEVO DELLA SOFFERENZA HOSPITAL   (Italy)

Author keywords

Crohn's disease; Regularized least square classifiers; Single nucleotide polymorphisms

Indexed keywords

ASSOCIATION MEASURES; COMPLEX DISEASE; COMPLEX TRAITS; CROHN'S DISEASE; GENE VARIANTS; GENE-GENE INTERACTIONS; GENERAL METHODS; GENETIC MARKERS; LINEAR COMBINATIONS; ODDS RATIOS; OVER-COMPLETE; REGULARIZED LEAST SQUARE CLASSIFIERS; SCREENING PROGRAMS; SINGLE NUCLEOTIDE POLYMORPHISMS; UNIVARIATE ANALYSIS; WEIGHTING VECTORS;

CLASSIFIERS; CURVE FITTING; DATA STORAGE EQUIPMENT; LEARNING SYSTEMS; NUCLEOTIDES;

POLYMORPHISM;

CASPASE RECRUITMENT DOMAIN PROTEIN 15; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; MONOCYTE CHEMOTACTIC PROTEIN 1; NON RECEPTOR PROTEIN TYROSINE PHOSPHATASE 22; TUMOR NECROSIS FACTOR ALPHA;

ARTICLE; CONTROLLED STUDY; CROHN DISEASE; GENE LOCUS; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC RISK; GENETIC SCREENING; GENETIC SUSCEPTIBILITY; HUMAN; MAJOR CLINICAL STUDY; MARKER GENE; METHODOLOGY; PHENOTYPE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL; SUPPORT VECTOR MACHINE;

CROHN DISEASE; EPISTASIS, GENETIC; GENE EXPRESSION PROFILING; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 67349164301     PISSN: 09333657     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.artmed.2008.07.012     Document Type: Article

References (27)

1. Chakravarti A. Single nucleotide polymorphisms: ... to a future of genetic medicine. Nature 409 (2001) 822-823
2. Miki Y., Swensen J., Shattuck-Eidens D., Futreal P.A., Harshman K., Tavtigian S.,., et al. A strong candidate for the breast and ovarian-cancer susceptibility gene BRCA1. Science 266 (1994) 66-71
3. Wooster R., Bignell G., Lancaster J., Swift S., Seal S., Mangion J.,., et al. Identification of the breast cancer susceptibility gene BRCA2. Nature 378 (1995) 789-792
4. Easton D.F., Pooley K.A., Dunning A.M., Pharoah P.D.P., Thompson D., Ballinger D.G.,., et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447 (2007) 1087-1093
5. Hunter D.J., Kraft P., Jacobs K.B., Cox D.G., Yeager M., Hankinson S.E.,., et al. A genome-wide association study identifies alleles in FGFR2 associated with risk of sporadic postmenopausal breast cancer. Nat Genet 39 (2007) 870-874
6. Gaya D.R., Russll R.K., Nimmo E.R., and Satsangi J. New genes in inflammatory bowel disease: lessons from complex diseases. Lancet 367 (2006) 1271-1284
7. Nadeau J.H., and Topol E.J. The genetics of health. Nat Genet 38 (2006) 1095-1098
8. Lewis C.M. Genetic association studies: design, analysis and interpretation. Brief Bioinform 3 2 (2002) 146-153
9. Hageman G.S., Anderson D.H., Johnson L.V., Hancox L.S., Taiber A.J., Hardisty L.I.,., et al. A common haplotype in the complement regulatory gene factor H(HF1/CFH) predisposes individuals to age-related macular degeneration. Proc Natl Acad Sci USA 102 20 (2005) 7227-7232
10. The Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447 7145 (2007) 661-678
11. Risch N.J. Searcing for genetic determinants in the new millennium. Nature 405 6788 (2000) 847-856
12. Good P. Permutation tests: a practical guide to resampling methods for testing hypothesis (1994), Springer Verlag, New York
13. Storey J.D., and Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100 16 (2003) 9440-9445
14. Shanahan F. Crohn's disease. Lancet 359 (2002) 62-69
15. Podolsky D.K. Inflammatory bowel disease. N Engl J Med 347 6 (2002) 417-429
16. Rifkin R., Yeo G., and Poggio T. Regularized least squares classification. In: Suykens J.A.K., Horvath G., Basu S., Micchelli C., and Vandewalle J. (Eds). Advances in learning theory: methods, model and applications, NATO science series. III. Computer and systems sciences 190 (2003), IOS Press, Amsterdam 131-153
17. Maglietta R., D'Addabbo A., Piepoli A., Perri F., Liuni S., Pesole G.,., et al. Selection of relevant genes in cancer diagnosis based on their prediction accuracy. Artif. Intell. Med. 40 (2007) 29-44
18. Daubechies I. Ten lectures on wavelets. CBMS-NSF regional conferences series in applied mathematics (1992), SIAM, Philadelphia, PA
19. Ancona N., and Stramaglia S. An invariance property of predictors in kernel-induced hypothesis spaces. Neural Comput 18 (2006) 749-759
20. Lunetta K.L., Hayward L.B., Segal J., and Van Eerdewegh P. Screening large-scale association study data: exploiting interactions using random forests. BMC Genet 5 1 (2004) 32
21. D'Addabbo A., Latiano A., Palmieri O., Maglietta R., Annese V., and Ancona N. Regularized least squares cancer classifiers predict Crohn's disease from profiles of single nucleotide polymorphisms. Ann Hum Genet 71 4 (2007) 537-549
22. Nagelkerke N., Smits J., Le Cessie S., and Van Houwelingen H. Testing goodness-of-fit of the logistic regression model in case-control studies using sample reweighting. Stat Med 24 (2005) 121-130
23. Heidema A.G., Boer J.M., Nagelkerke N., Mariman E.C., van der A D.L., and Feskens E.J. The challange for genetic epidemiologists: how to analyze large numbers of SNPs in relation to complex diseases. BMC Genet 7 (2006) 23
24. Papoulis A. Probability, random variables, and stochastic processes (1985), McGraw-Hill International Student Edition, London
25. Ancona N., Maglietta R., D'Addabbo A., Liuni S., and Pesole G. Regularized least squares cancer classifiers from DNA microarray data. BMC Bioinform 6 Suppl 4 (2005) S2
26. Paschou P., Ziv E., Burchard E.G., Choudhry S., Rodriguez-Cintron W., Mahoney M.W.,., et al. PCA-correlated SNPs for structure identification in worldwide human populations. PLoS Genet 3 9 (2007) e160
27. Maglietta R., Piepoli A., Catalano D., Licciulli F., Carella M., Liuni S.,., et al. Statistical assessment of functional categories of genes deregulated in pathological conditions by using microarray data. Bioinformatics 23 16 (2007) 2063-2072