Simulating gene-environment interactions in complex human diseases

Genome Medicine

Volumn 2, Issue 3, 2010, Pages

  Peng, Bo ^a  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPUTER PROGRAM; ENVIRONMENTAL FACTOR; GENE INTERACTION; HUMAN; MATHEMATICAL MODEL; PRIORITY JOURNAL; REVIEW; SIMULATION;

EID: 78751680980     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/gm142     Document Type: Review

References (17)

1. Motsinger-Reif AA, Reif DM, Fanelli TJ, Ritchie MD. A comparison of analytical methods for genetic association studies. Genet Epidemiol 2008, 32:767-778. 10.1002/gepi.20345, 18561203.
2. Li D, Conti DV. Detecting gene-environment interactions using a combined case-only and case-control approach. Am J Epidemiol 2009, 169:497-504. 10.1093/aje/kwn339, 2732970, 19074774.
3. Wang T, Ho G, Ye K, Strickler H, Elston RC. A partial least-square approach for modeling gene-gene and gene-environment interactions when multiple markers are genotyped. Genet Epidemiol 2009, 33:6-15. 10.1002/gepi.20351, 2700837, 18615621.
4. Amato R, Pinelli M, D'Andrea D, Miele G, Nicodemi M, Raiconi G, Cocozza S. A novel approach to simulate gene-environment interactions in complex diseases. BMC Bioinformatics 2010, 11:8. 10.1186/1471-2105-11-8, 2824681, 20051127.
5. Isohanni M, Oja H, Moilanen I, Rantakallio P, Koiranen M. The relation between teenage smoking and drinking, with special reference to non-standard family background. Scand J Soc Med 1993, 21:24-30. 10.1177/140349489302100105, 8469940.
6. Moore JH, Hahn LW, Ritchie MD, Thornton TA, White BC. Routine discovery of complex genetic models using genetic algorithms. Appl Soft Comput 2004, 4:79-86.
7. Peng B, Amos CI, Kimmel M. Forward-time simulations of human populations with complex diseases. PLoS Genet 2007, 3:e47. 10.1371/journal.pgen.0030047, 1829403,1829403, 17381243.
8. Wright FA, Huang H, Guan X, Gamiel K, Jeffries C, Barry WT, Pardo-Manuel F, Sullivan PF, Wilhelmsen KC, Zou F. Simulating association studies: a data-based resampling method for candidate regions or whole genome scans. Bioinformatics 2007, 23:2581-2518. 10.1093/bioinformatics/btm386, 17785348.
9. Marchini J, Howie B, Myers S, McVean G, Donnelly P. A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet 2007, 39:906-913. 10.1038/ng2088, 17572673.
10. Li C, Li M. GWAsimulator: a rapid whole-genome simulation program. Bioinformatics 2008, 24:140-142. 10.1093/bioinformatics/btm549, 18006546.
11. Edwards TL, Bush WS, Turner SD, Dudek SM, Torstenson ES, Schmidt M, Martin E, Ritchie MD. Generating linkage disequilibrium patterns in data simulations using genomeSIMLA. Lect Notes Comput Sci 2008, 4973:24-35. full_text, 19779634.
12. Schaffner SF, Foo C, Gabriel S, Reich D, Daly MJ, Altshuler D. Calibrating a coalescent simulation of human genome sequence variation. Genome Res 2005, 15:1576-1583. 10.1101/gr.3709305, 1310645, 16251467.
13. Liang L, Zöllner S, Abecasis GR. GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics 2007, 23:1565-1567. 10.1093/bioinformatics/btm138, 17459963.
14. The International HapMap Consortium A haplotype map of the human genome. Nature 2005, 437:1299-1320. 10.1038/nature04226, 1880871, 16255080, The International HapMap Consortium.
15. Chen GK, Marjoram P, Wall JD. Fast and flexible simulation of DNA sequence data. Genome Res 2009, 19:136-142. 10.1101/gr.083634.108, 2612967, 19029539.
16. Chanda P, Sucheston L, Zhang A, Brazeau D, Freudenheim JL, Ambrosone C, Ramanathan M. AMBIENCE: a novel approach and efficient algorithm for identifying informative genetic and environmental associations with complex phenotypes. Genetics 2008, 180:1191-1210. 10.1534/genetics.108.088542, 2567367, 18780753.
17. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007, 81:559-575. 10.1086/519795, 1950838, 17701901.