From Interaction to Co-Association -A Fisher r-To-z Transformation-Based Simple Statistic for Real World Genome-Wide Association Study

PLoS ONE

Volumn 8, Issue 7, 2013, Pages

  Yuan, Zhongshang ^a   Liu, Hong ^b   Zhang, Xiaoshuai ^a   Li, Fangyu ^a   Zhao, Jinghua ^c   Zhang, Furen ^b   Xue, Fuzhong ^a  

^a SHANDONG UNIVERSITY   (China)

^b SHANDONG PROVINCIAL HOSPITAL AFFILIATED TO SHANDONG FIRST MEDICAL UNIVERSITY   (China)

^c INSTITUTE OF METABOLIC SCIENCE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CALCULATION; CARD6 GENE; CONTROLLED STUDY; FISHER R TO Z TRANSFORMATION BASED SIMPLE STATISTIC; GENE; GENE INTERACTION; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; GSDMB GENE; IFNG GENE; LEPROSY; LRRK2 GENE; NOD2 GENE; PARK2 GENE; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; STATISTICAL MODEL; TNFSF15 GENE; ZPBP2 GENE;

ALGORITHMS; COMPUTER SIMULATION; EPISTASIS, GENETIC; GENOME-WIDE ASSOCIATION STUDY; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; MODELS, STATISTICAL; POLYMORPHISM, SINGLE NUCLEOTIDE; SAMPLE SIZE;

EID: 84880839472     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0070774     Document Type: Article

References (27)

1. Haines JL, Hauser MA, Schmidt S, Scott WK, Olson LM, et al. (2005) Complement factor H variant increases the risk of age-related macular degeneration. Science 308: 419-421.
2. Gibson G, (2010) Hints of hidden heritability in GWAS. Nat Genet 42: 558-560.
3. Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, et al. (2009) Finding the missing heritability of complex diseases. Nature 461: 747-753.
4. Eichler EE, Flint J, Gibson G, Kong A, Leal SM, et al. (2010) Missing heritability and strategies for finding the underlying causes of complex disease. Nature Reviews Genetics 11: 446-450.
5. Gibson G, (2012) Rare and common variants: twenty arguments. Nature Reviews Genetics 13: 135-145.
6. Peng Q, Zhao J, Xue F, (2009) A gene-based method for detecting gene-gene co-association in a case-control association study. European Journal of Human Genetics 18: 582-587.
7. Yuan Z, Gao Q, He Y, Zhang X, Li F, et al. (2012) Detection for gene-gene co-association via kernel canonical correlation analysis. BMC genetics 13: 83.
8. Cordell HJ, (2009) Detecting gene-gene interactions that underlie human diseases. Nature Reviews Genetics 10: 392-404.
9. Kam-Thong T, Czamara D, Tsuda K, Borgwardt K, Lewis CM, et al. (2010) EPIBLASTER-fast exhaustive two-locus epistasis detection strategy using graphical processing units. European Journal of Human Genetics 19: 465-471.
10. Kang G, Yue W, Zhang J, Cui Y, Zuo Y, et al. (2008) An entropy-based approach for testing genetic epistasis underlying complex diseases. Journal of theoretical biology 250: 362-374.
11. Rajapakse I, Perlman MD, Martin PJ, Hansen JA, Kooperberg C, (2012) Multivariate Detection of Gene-Gene Interactions. Genetic epidemiology 36: 622-630.
12. Ueki M, Cordell HJ, (2012) Improved statistics for genome-wide interaction analysis. PLoS Genetics 8: e1002625.
13. Wan X, Yang C, Yang Q, Xue H, Fan X, et al. (2010) BOOST: A fast approach to detecting gene-gene interactions in genome-wide case-control studies. American journal of human genetics 87: 325.
14. Wu X, Dong H, Luo L, Zhu Y, Peng G, et al. (2010) A novel statistic for genome-wide interaction analysis. PLoS genetics 6: e1001131.
15. Zhao J, Jin L, Xiong M, (2006) Test for interaction between two unlinked loci. American journal of human genetics 79: 831.
16. Greenland S, Pearl J, Robins JM, (1999) Causal diagrams for epidemiologic research. Epidemiology 10: 37-48.
17. Zhang X, Yang X, Yuan Z, Liu Y, Li F, et al. (2013) A PLSPM-Based Test Statistic for Detecting Gene-Gene Co-Association in Genome-Wide Association Study with Case-Control Design. PloS one 8: e62129.
18. Armitage P, (1955) Tests for linear trends in proportions and frequencies. Biometrics 11: 375-386.
19. Fisher RA, (1915) Frequency distribution of the values of the correlation coefficient in samples from an indefinitely large population. Biometrika 10: 507-521.
20. Fisher RA, (1921) On the "Probable Error" of a Coefficient of Correlation Deduced from a Small Sample. Metron 1: 3-32.
21. Wellek S, Ziegler A, (2008) A genotype-based approach to assessing the association between single nucleotide polymorphisms. Human Heredity 67: 128-139.
22. Gaiano N, Kohtz JD, Turnbull DH, Fishell G, (1999) A method for rapid gain-of-function studies in the mouse embryonic nervous system. Nature neuroscience 2: 812-819.
23. Winklhofer KF, Tatzelt J, Haass C, (2008) The two faces of protein misfolding: gain-and loss-of-function in neurodegenerative diseases. The EMBO journal 27: 336-349.
24. Zhang F, Huang W, Chen S, Sun L, Liu H, et al. (2009) Genomewide association study of leprosy. New England Journal of Medicine 361: 2609-2618.
25. Su Z, Marchini J, Donnelly P, (2011) HAPGEN2: simulation of multiple disease SNPs. Bioinformatics 27: 2304-2305.
26. Bouzigon E, Corda E, Aschard H, Dizier M, Boland A, et al. (2008) Effect of 17q21 variants and smoking exposure in early-onset asthma. New England Journal of Medicine 359: 1985-1994.
27. Moffatt MF, Kabesch M, Liang L, Dixon AL, Strachan D, et al. (2007) Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature 448: 470-473.