Detection of SNP epistasis effects of quantitative traits using an extended Kempthorne model

Physiological Genomics

Volumn 28, Issue 1, 2006, Pages 46-52

  Mao, Yongcai ^a   London, Nicole R ^a   Ma, Li ^a   Dvorkin, Daniel ^a   Da, Yang ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Hardy Weinberg disequilibrium; Linkage disequilibrium; Quantitative trait; Single nucleotide polymorphism

Indexed keywords

CONFERENCE PAPER; EPISTASIS; GENE FREQUENCY; GENETIC TRAIT; HERITABILITY; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE TRAIT; SINGLE NUCLEOTIDE POLYMORPHISM; ARTICLE; BIOLOGICAL MODEL; COMPARATIVE STUDY; COMPUTER SIMULATION; GENE LINKAGE DISEQUILIBRIUM; GENETIC EPISTASIS; QUANTITATIVE TRAIT LOCUS; SAMPLE SIZE; STATISTICAL MODEL;

COMPUTER SIMULATION; EPISTASIS, GENETIC; LINEAR MODELS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SAMPLE SIZE;

EID: 34247848075     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00096.2006     Document Type: Conference Paper

References (24)

1. Affymetrix. Microarray Bulletin. April 2005.
2. Cambien F, Poirier O, Nicaud V, Herrmann SM, Mallet C, Ricard S, Behague I, Hallet V, Blanc H, Loukaci V, Thillet J, Evans A, Ruidavets JB, Arveiler D, Luc G, Tiret L. Sequence diversity in 36 candidate genes for cardiovascular disorders. Am J Hum Genet 65: 183-191, 1999.
3. Carlborg O, Haley CS. Epistasis: too often neglected in complex trait studies? Nat Rev Genet 5: 618-625, 2004.
4. Cheverud JM. Detecting epistasis among quantitative trait loci. In: Epistasis and the Evolutionary Process, edited by Wolf J, Brodie E III, and Wade M. New York: Oxford Univ. Press, 2000, p. 58-81.
5. Cockerham CC. An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present. Genetics 859-882: 1954.
6. Fisher RA. The correlation between relatives on the supposition of Mendelian inheritance. Trans Roy Soc Edinburgh 52: 399-433, 1918.
7. Freudenberg-Hua Y, Freudenberg J, Kluck N, Cichon S, Propping P, Nothen MM. Single nucleotide variation analysis in 65 candidate genes for CNS disorders in a representative sample of the European population. Genome Res 13: 2271-2276, 2003.
8. Haga H, Yamada R, Ohnishi Y, Nakamura Y, Tanaka T. Gene-based SNP discovery as part of the Japanese Millennium Genome Project: identification of 190,562 genetic variations in the human genome. Single-nucleotide polymorphism. J Hum Genet 47: 605-610, 2002.
9. Kao CH, Zeng ZB. Modeling epistasis of quantitative trait loci using Cockerham's model. Genetics 160: 1243-1261, 2002.
10. Kempthorne O. The correlation between relatives in a random mating population. Proc R Soc Lond B Biol Sci 143: 102-113, 1954.
11. Lander E, Kruglyak L. Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet 11: 241-247, 1995.
12. Li W, Reich J. A complete enumeration and classification of two-locus disease models. Hum Hered 50: 334-349, 2000.
13. London N, Da Y. Statistical power and sample size requirement for QTL detection. In: Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, edited by Valente BD, Rossi de Morais O, and Ventura RV. Belo Horizonte, Brazil: Instituto Pruciência, 2006, vol. 22, article no. 18.
14. Mao Y, Da Y. Statistical power and sample size for QTL detection using flanking markers under the f-2 design. In: Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, edited by Valente BD, Rossi de Morais O, and Ventura RV. Belo Horizonte, Brazil: Instituto Pruciência, 2006, vol. 23, article no. 19.
15. Mao Y, Da Y. Statistical power for detecting epistasis QTL effects under the F-2 design. Genet Sel Evol 37: 129-150, 2005.
16. Moore JH. The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered 56: 73-82, 2003.
17. Purcell S, Sham PC. Epistasis in quantitative trait locus linkage analysis: interaction or main effect? Behav Genet 34: 143-152, 2004.
18. Searle SR. Linear Models. New York: John Wiley & Sons, 1997, p. 112, 200.
19. Segre D, Deluna A, Church GM, Kishony R. Modular epistasis in yeast metabolism. Nat Genet 37: 77-83, 2004.
20. Stephens JC, Schneider JA, Tanguay DA, Choi J, Acharya T, Stanley SE, Jiang R, Messer CJ, Chew A, Han JH, Duan J, Carr JL, Lee MS, Koshy B, Kumar AM, Zhang G, Newell WR, Windemuth A, Xu C, Kalbfleisch TS, Shaner SL, Arnold K, Schulz V, Drysdale CM, Nandabalan K, Judson RS, Ruano G, Vovis GF. Haplotype variation and linkage disequilibrium in 313 human genes. Science 293: 489-493, 2001.
21. Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C. Global mapping of the yeast genetic interaction network. Science 303: 808-813, 2004.
22. Weir BS. Genetic Data Analysis II. Sunderland, MA: Sinauer Associates, 1996.
23. Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, Afshari C, Paules RS. Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol 8: 625-637, 2001.
24. Zhu X, Yan D, Cooper RS, Luke A, Ikeda MA, Chang YP, Weder A, Chakravarti A. Linkage disequilibrium and haplotype diversity in the genes of the renin-angiotensin system: findings from the family blood pressure program. Genome Res 13: 173-181, 2003.