A statistical procedure to map high-order epistasis for ccomplex traits

Briefings in Bioinformatics

Volumn 14, Issue 3, 2013, Pages 302-314

  Pang, Xiaoming ^a   Wang, Zhong ^b   Yap, John S ^c   Wang, Jianxin ^d   Zhu, Junjia ^e,g   Bo, Wenhao ^d   Lv, Yafei ^d   Xu, Fang ^d   Zhou, Tao ^d   Peng, Shaofeng ^d   Shen, Dengfeng ^d   Wu, Rongling ^d,f  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

^b DALIAN UNIVERSITY OF TECHNOLOGY   (China)

^c UNIVERSITY OF FLORIDA   (United States)

^d BEIJING FORESTRY UNIVERSITY   (China)

^e PENNSYLVANIA STATE UNIVERSITY   (United States)

^f UNIVERSITY OF WASHINGTON   (United States)

^g PENN STATE COLLEGE OF MEDICINE   (United States)

Author keywords

EM algorithm; Epistasis; High order interactions; Quantitative trait loci

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; EM ALGORITHM; EPISTASIS; HIGH-ORDER INTERACTIONS; QUANTITATIVE TRAIT LOCUS; VALIDATION STUDY;

EM ALGORITHM; EPISTASIS; HIGH-ORDER INTERACTIONS; QUANTITATIVE TRAIT LOCI;

COMPUTER SIMULATION; EPISTASIS, GENETIC; MODELS, GENETIC; QUANTITATIVE TRAIT LOCI;

EID: 84878499945     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbs027     Document Type: Article

References (60)

1. Whitlock MC, Phillips PC, Moore BG, et al. Multiple fitness peaks and epistasis. Ann Rev Ecol Syst 1995;26:601-29.
2. Wolf JB, Brodie EE III, Wade MJ. Epistasis and the Evolutionary Process. Oxford: Oxford University Press, 2000.
3. Carlborg O, Haley CS. Epistasis: too often neglected in ccomplex trait studies? Nat RevGenet 2004;5:618-25.
4. Phillips PC. Epistasis - the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 2008;9:855-67.
5. Moore J, Williams S. Epistasis and its implications for personal genetics export. AmJHum Genet 2009;85:309-20.
6. Huang LS, Sternberg PW. Genetic dissection of developmental pathways. Methods Cell Biol 1995;48:97-122.
7. Wu RL, Ma CM, Lin M, et al. A general framework for analyzing the genetic architecture of developmental characteristics. Genetics 2004;166:1541-51.
8. Imielinski M, Belta C. Deep epistasis in human metabolism. CHAOS 2010;20:026104.
9. Martin MP, Gao X, Lee JH, et al. Epistatic interaction between KIR3DS1 and HLA-B delays the progression to AIDS. Nat Genet 2003;3:429-34.
10. Gabutero E, Moore C, Mallal S, et al. Interaction between allelic variation in IL12B and CCR5 affects the development of AIDS. AIDS 2007;21:65-9.
11. Hinkley T, Martins J, Chappey C, et al. A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase. Nat Genet 2011;43:487-9.
12. Lukens LN, Doebley J. Epistatic and environmental interactions for quantitative trait loci involved in maize evolution. Genet Res 1999;74:291-302.
13. Nunkesser R, Bernholt T, Schwender H, et al. Detecting high-order interactions of single nucleotide polymorphisms using genetic programming. Bioinformatics 2009;23:3280-8.
14. Ritchie MD, Hahn LW, Roodi N, et al. Multifactordimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. AmJHum Genet 2001;69:138-47.
15. McMullen MD, Byrne PF, Snook ME, et al. Quantitative trait loci and metabolic pathways. Proc Natl Acad Sci U S A 1998;95:1996-2000.
16. Stich B, Yu J, Melchinger AE, et al. Power to detect higher-order epistatic interactions in a metabolic pathway using a new mapping strategy. Genetics 2007;176:563-70.
17. Gutierrez J. A developmental systems perspective on epistasis: Computational exploration of mutational interactions in model developmental regulatory networks. PLoS One 2009;4(9):e6823.
18. Pettersson M, Besnier F, Siegel PB, et al. Replication and explorations of high-order epistasis using a large advanced intercross line pedigree. PLoS Genet 2011;7(7):e1002180.
19. Wang Z, Liu T, Lin Z, et al. A general model for multilocus epistatic interactions in case-ccontrol studies. PLoS One 2010;5(8):e11384.
20. Lander ES, Botstein D. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 1989;121:185-99.
21. Zeng Z-B. Precision mapping of quantitative trait loci. Genetics 1994;136:1457-68.
22. Xu S. Estimating polygenic effects using markers of the entire genome. Genetics 2003;163:789-801.
23. Wu RL, Ma CX, Casella C. StatisticalGenetics ofQuantitative Traits: Linkage,Maps, andQTL. New York: Springer-Verlag, 2007.
24. Kao C-H, Zeng Z-B. Modeling epistasis of quantitative trait loci using Cockerham's model. Genetics 2002;160:1243-61.
25. Shah SH, Schmidt MA, Mei H, et al. Searching for epistatic interactions in nuclear families using conditional linkage analysis. BMCGenetics 2005;6(Suppl 1):S148.
26. Li Y, Berg A, Chang MN, et al. A statistical model for genetic mapping of viral infection by integrating epidemiological behavior. Statist Appl Genet Mol Biol 2009;8(1): Article 38.
27. Yi NJ, Shriner D, Bcanerjee S, et al. An efficient Bayesian model selection approach for interacting QTL models with many effects. Genetics 2007;176:1865-77.
28. Hansen TF, Wagner GP. Epistasis and the mutation load: a measurement-theoretical approach. Genetics 2001;158: 477-85.
29. Beerenwinkel S, Pachter L, Sturmfels B, et al. Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evol Biol 2007;7:60.
30. Imielinski M, Belta C. Exploiting the pathway structure of metabolism to reveal high-order epistasis. BMC Syst Biol 2008;2:40.
31. Huang N, Parco A, Mew T, et al. RFLP mapping of isozymes, RAPD and QTLs for grain shape, brown planthopper resistance in a doubled haploid rice population. Mol Breed 1997;3:105-13.
32. Bateson W. Mendel's Principles of Heredity. Cambridge, UK: Cambridge University Press, 1909.
33. Steen KV. Travelling the world of gene-gene interactions. Brief Bioinform 2012;13: 1-19.
34. Elliger CA, Chan BG, Waiss AC, et al. C-glycosylflavonesf rom Zeamaye that inhibit ineect development. Phytochemistry 1980;19:293-7.
35. Franken P, Niesbach-Klosgen U, Weydemann U, et al. The duplicated chalcone synthase genes C2 and Whp (white pollen) of Zea mays are independently regulated; evidence for translational ccontrol of Whp expression by the anthocyanin ntensifying gene in. EMBO J 1991;10: 2605-12.
36. Grotewold E, Peterson T. Isolation and characterization of a maize gene encoding chalcone flavonone isomerase. Mol Gen Genet 1994;242:1-8.
37. Styles ED, Ceska O. Genetic ccontrol of 3-hydroxy- and 3-deoxy-flavonoids in Zea mays. Phytochemistry 1975;14: 413-5.
38. Heller W, Forkmann G. Biosynthesis of flavonoids. In: Harborne JB, (ed). The Flavonoids: Advances in Research Since 1986. London: Chapman & Hall, 1994;499-535.
39. Marrs KA, Alfenito MR, Lloyd AM, et al. A glutathione S-transferase involved in vacuolar transfer encoded by the maize gene Bronze-2. Nature 1995;375:397-400.
40. Fisher RA. The correlations between relatives on the supposition of Mendelian inheritance. Trans RSoc Edinb 1918; 52:399-433.
41. Mather K, Jinks JL. Biometrical Genetics. 3rd edn. London: Chapman & Hall, 1982.
42. Churchill GA, Doerge RW. Empirical threshold values for quantitative trait mapping. Genetics 1994;138:963-71.
43. Wang CG, Wang Z, Luo JT, et al. A model for transgenerational imprinting variation in ccomplex traits. PLoS One 2010;5(7):e11396.
44. Dupuis J, Siegmund D. Statistical methods for mapping quantitative trait loci from a dense set of markers. Genetics 1999;151:373-86.
45. Piepho H-P. A quick method for computing approximate thresholds for quantitative trait loci detection. Genetics 2001; 157:425-32.
46. Chang MR, Wu RL, Wu S, et al. Score statistics of quantitative trait locus mapping. Stat Appl Genet Mol Biol 2009; 8(1):Article 16.
47. Wu JS, Zhang B, Cui YH, et al. Genetic mapping of developmental instability: Design, model and algorithm. Genetics 2007;176:1187-96.
48. Senthilvel S, Vinod KK, Senthilvel P, etal. QTL and QTL environment effects on agronomic and nitrogen acquisition traits in rice. J Integ Plant Biol 2008;50:1108-17.
49. Bartual R, Lacasa A, Marsal JI, etal. Epistasis in the resistance of pepper to phytophthora stem blight (Phytophthora capsici L.) and its significance in the prediction of double cross performances. Euphytica 1994;72:149-52.
50. Wu RL. Detecting epistatic genetic variance with a clonally replicated design: models for low- vs. Mapping high-order epistasis for ccomplex traits 313 high-order nonallelic interaction. TheorAppl Genet 1996;93: 102-09.
51. Yan JQ, Zhu J, He CX, et al. Molecular dissection of developmental behavior of plant height in rice (Oryza sativa L.). Genetics 1998;150:1257-65.
52. Zhao W, Zhu J, Gallo-Meagher M, et al. A unified statistical model for functional mapping of genotype by environment interactions for ontogenetic development. Genetics 2004; 168:1751-62.
53. Gayan J, Gonzalez-Perez A, Bermudo F, et al. A method for detecting epistasis in genome-wide studies using caseccontrol multi-locus association analysis. BMC Genomics 2007;9:360.
54. Huang X, Wei X, Sang T, et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 2010;42:961-7.
55. Marchini J, Donnelly P, Cardon LR. Genome-wide strategies for detecting multiple loci that influence ccomplex diseases. Nat Genet 2005;37:413-7.
56. Wang WY, Barratt BJ, Clayton DG, et al. Genome-wide association studies: theoretical and practical concerns. Nat Rev Genet 2005;6:109-18.
57. Wan X, Yang C, Yang Q, etal. Predictive rule inference for epistatic interaction detection in genome-wide association studies. Bioinformatics 2010;26:30-7.
58. Hlavacek WS, Faeder JR. The ccomplexity of cell signaling and the need for a new mechanics. Sci Signal 2009;2(81): pe46.
59. Weng GZ, Bhalla US, Iyengar R. Ccomplexity in biological signaling systems export. Science 1999;284:92-6.
60. Li JH, Das K, Fu G, et al. Bayesian lasso for genome-wide association studies. Bioinformatics 2011;27: 516-23.