Statistical epistasis networks reduce the computational complexity of searching three-locus genetic models

Pacific Symposium on Biocomputing

Volumn , Issue , 2013, Pages 397-408

  Hu, Ting ^a   Andrew, Angeline S ^a   Karagas, Margaret R ^a   Moore, Jason H ^a  

^a DARTMOUTH MEDICAL SCHOOL   (United States)

Author keywords

Epistasis; GWAS; High order genetic interactions; MDR; Statistical epistasis networks

Indexed keywords

CLUSTERING ALGORITHMS;

BIOLOGICAL VALIDATIONS; COMPUTATIONAL CHALLENGES; EPISTASIS; GENETIC INTERACTION; GENOME-WIDE ASSOCIATION STUDIES; GWAS; HIGH-DIMENSIONAL DATA SPACE; NETWORK-BASED APPROACH;

DISEASES;

ALGORITHM; BIOLOGICAL MODEL; BIOLOGY; BLADDER TUMOR; COMPUTER PROGRAM; DATA MINING; EPISTASIS; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; GENETIC PREDISPOSITION; GENETICS; HUMAN; NUCLEIC ACID DATABASE; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL; STATISTICS AND NUMERICAL DATA; ARTICLE; STATISTICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATA MINING; DATABASES, NUCLEIC ACID; EPISTASIS, GENETIC; GENE REGULATORY NETWORKS; GENETIC PREDISPOSITION TO DISEASE; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE; URINARY BLADDER NEOPLASMS;

EID: 84891452334     PISSN: 23356928     EISSN: 23356936     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (37)

1. J. N. Hirschhorn and M. J. Daly, Nature Review Genetics 6, 95 (2005).
2. W. Y. S. Wang, B. J. Barratt, D. G. Clayton and J. A. Todd, Nature Review Genetics 6, 109 (2005).
3. J. Hardy and A. Singleton, New England Journal of Medicine 360, 1759 (2009).
4. T. A. Manolio, F. S. Collins, N. J. Cox, D. B. Goldstein, L. A. Hindorff and et al., Nature 461, 747 (2009).
5. J. H. Moore, Human Heredity 56, 73 (2003).
6. O. Carlborg and C. S. Haley, Nature Review Genetics 5, 618 (2004).
7. J. H. Moore and S. M. Williams, BioEssays 27, 637 (2005).
8. H. J. Cordell, Human Molecular Genetics 11, 2463 (2002).
9. H. J. Cordell, Nature Review Genetics 10, 392 (2009).
10. J. H. Moore and S. M. Williams, The American Journal of Human Genetics 85, 309 (2009).
11. J. Shendure and H. Ji, Nature Biotechnology 26, 1135 (2008).
12. J. H. Moore and M. D. Ritchie, Journal of the Amarican Medical Association 291, 1642 (2004).
13. J. H. Moore and B. C. White, Genetic Programming Theory and Practice IV, 969 (2005).
14. R. Nunkesser, T. Bernholt, H. Schwender, K. Ickstadt and I. Wegener, Bioinformatics 23, 3280 (2007).
15. J. H. Moore, F. W. Asselbergs and S. M. Williams, Bioinformatics 26, 445 (2010).
16. T. Hu, N. A. Sinnott-Armstrong, J. W. Kiralis, A. S. Andrew, M. R. Karagas and J. H. Moore, BMC Bioinformatics 12, p. 364 (2011).
17. R. Culverhouse, B. K. Suarez, J. Lin and T. Reich, American Journal of Human Genetics 70, 461 (2002).
18. W. Wongseree, A. Assawamakin, T. Piroonratana, S. Sinsomros, C. Limwongse and N. Chaiyaratana, BMC Bioinformatics 10, p. 294 (2009).
19. M. D. Ritchie, L. W. Hahn, N. Roodi, L. R. Bailey, W. D. Dupont, F. F. Parl and J. H. Moore, The American Journal of Human Genetics 69, 138 (2001).
20. L. W. Hahn, M. D. Ritchie and J. H. Moore, Bioinformatics 19, 376 (2003).
21. M. D. Ritchie, L. W. Hahn and J. H. Moore, Genetic Epidemiology 24, 150 (2003).
22. J. H. Moore, J. C. Gilbert, C.-T. Tsai, F.-T. Chiang, T. Holden, N. Barney and B. C. White, Journal of Theoretical Biology 241, 252 (2006).
23. M. R. Karagas, T. D. Tosteson, J. Blum, J. S. Morris, J. A. Baron and B. Klaue, Environmental Health Perspectives 106, 1047 (1998).
24. A. S. Andrew, H. H. Nelson, K. T. Kelsey, J. H. Moore, A. C. Meng, D. P. Casella, T. D. Tosteson, A. R. Schned and M. R. Karagas, Carcinogenesis 27, 1030 (2006).
25. A. Jakulin and I. Bratko, Lecture Notes in Artificial Intelligence 2838, 229 (2003).
26. D. Anastassiou, Molecular Systems Biology 3, p. 83 (2007).
27. J. H. Moore, N. Barney, C.-T. Tsai, F.-T. Chiang, J. Gui and B. C. White, Human Heredity 63, 120 (2007).
28. B. A. McKinney, J. E. Crowe, J. Guo and D. Tian, PLoS Genetics 5, p. e1000432 (2009).
29. D. B. West, Introduction to Graph Theory: Second edition (Prentice Hall, 2001).
30. A. S. Andrew, J. Gui, A. C. Sanderson, R. A. Mason, E. V. Morlock, A. R. Schned, K. T. Kelsey, C. J. Marsit, J. H. Moore and M. R. Karagas, Human Genetics 125, 527 (2009).
31. I. Kononenko, Lecture Notes in Computer Science 784, 171 (1994).
32. J. H. Moore and B. C. White, Lecture Notes in Computer Sceicne 4447, 166 (2007).
33. T. M. Cover and J. A. Thomas, Elements of Information Theory: Second Edition (Wiley, 2006).
34. A. K. Wong, C. Y. Park, C. S. Greene, L. A. Bongo, Y. Guan and O. G. Troyanskaya, Nucleic Acids Research 40, W484 (2012).
35. E. M. El-Omar, M. Carrington, W.-H. Chow, K. E. L. McCol, J. H. Bream, H. A. Young, J. Herrera, J. Lissowska, C.-C. Yuan, N. Rothman, G. Lanyon, M. Martin, J. F. Fraumeni Jr and C. S. Rabkin, Nature 404, 398 (2000).
36. M. C. Southey, M. A. Jenkins, L. Mead, J. Whitty, M. Trivett and et al., Journal Of Clinical Oncology 23, 6524 (2005).
37. S. Michiels, A. Laplanche, T. Boulet, P. Dessen, B. Guillonneau, A. Mejean, F. Desgrandchamps, M. Lathrop, A. Sarasin and S. Benhamou, Carcinogenesis 30, 763 (2009).