Kernel canonical correlation analysis for assessing gene–gene interactions and application to ovarian cancer

Manolio TA, Collins FS, Cox NJ et al: Finding the missing heritability of complex diseases. Nature 2009; 461: 747–753.

Moore JH : The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered 2003; 56: 73–82.

Thomas DC, Haile RW, Duggan D : Recent developments in genomewide association scans: a workshop summary and review. Am J Hum Genet 2005; 77: 337–345.

Wang WYS, Barratt BJ, Clayton DG, Todd JA : Genome-wide association studies: theoretical and practical concerns. Nat Rev Genet 2005; 6: 109–118.

Thornton-Wells TA, Moore JH, Haines JL : Genetics, statistics and human disease: analytical retooling for complexity. Trends Genet 2004; 20: 640–647.

Zhao J, Jin L, Xiong M : Test for interaction between two unlinked loci. Am J Hum Genet 2006; 79: 831–845.

Peng Q, Zhao J, Xue F : A gene-based method for detecting gene-gene co-association in a case-control association study. Eur J Hum Genet 2010; 18: 582–587.

Hotelling H : Relations between two sets of variates. Biometrika 1936; 28: 321–377.

Schölkopf B, Smola A : Learning with kernels : support vector machines, regularization, optimization, and beyond. The MIT Press, 2002.

Scholkopf B, Smola A, Muller KR : Nonlinear component analysis as a kernel eigenvalue problem. Neural Comput 1998; 10: 1299–1319.

Schaid DJ : Genomic similarity and kernel methods I: advancements by building on mathematical and statistical foundations. Hum Hered 2010; 70: 109–131.

Wu MC, Lee S, Cai TX, Li Y, Boehnke M, Lin XH : Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet 2011; 89: 82–93.

Wu MC, Kraft P, Epstein MP et al: Powerful SNP-set analysis for case-control genome-wide association studies. Am J Hum Genet 2010; 86: 929–942.

Li S, Cui Y : Gene-centric gene-gene interaction: a model-based kernel machine method. Ann Appl Stat 2012; 6: 1134–1161.

Lawley DN : Tests of significance in canonical analysis. Biometrika 1959; 46: 59–66.

Hinkley D, Wang H-L : A trimmed jackknife. J Roy Stat Soc Ser B 1980; 42: 347–356.

Efron B : Large-scale simultaneous hypothesis testing: the choice of a null hypothesis. J Am Stat Assoc 2004; 99: 96–104.

Scheet P, Stephens M : A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 2006; 78: 629–644.

Montana G : HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients. Bioinformatics 2005; 21: 4309–4311.

Zhang F, Wagener D : An approach to incorporate linkage disequilibrium structure into genomic association analysis. J Genet Genomics 2008; 35: 381–385.

Rajapakse I, Perlman MD, Martin PJ, Hansen JA, Kooperberg C : Multivariate detection of gene-gene interactions. Genet Epidemiol 2012; 36: 622–630.

White KL, Schildkraut JM, Palmieri RT et al: Ovarian cancer risk associated with inherited inflammation-related variants. Cancer Res 2012; 72: 1064–1069.

Fridley BL, Jenkins GD, Tsai YY et al: Gene set analysis of survival following ovarian cancer implicates macrolide binding and intracellular signaling genes. Cancer Epidemiol Biomarkers Prev 2012; 21: 529–536.

Permuth-Wey J, Chen YA, Tsai YY et al: Inherited variants in mitochondrial biogenesis genes may influence epithelial ovarian cancer risk. Cancer Epidemiol Biomarkers Prev 2011; 20: 1131–1145.

Permuth-Wey J, Kim D, Tsai YY et al: LIN28B polymorphisms influence susceptibility to epithelial ovarian cancer. Cancer Res 2011; 71: 3896–3903.

Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR : MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 2010; 34: 816–834.

Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D : Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 2006; 38: 904–909.

Neale BM, Sham PC : The future of association studies: gene-based analysis and replication. Am J Hum Genet 2004; 75: 353–362.

Diaconis P, Freedman D : Asymptotics of graphical projection pursuit. Ann Stat 1984; 12: 793–815.

Engels EA, Wu X, Gu J, Dong Q, Liu J, Spitz MR : Systematic evaluation of genetic variants in the inflammation pathway and risk of lung cancer. Cancer Res 2007; 67: 6520–6527.

Schaid DJ, McDonnell SK, Hebbring SJ, Cunningham JM, Thibodeau SN : Nonparametric tests of association of multiple genes with human disease. Am J Hum Genet 2005; 76: 780–793.

Witten DM, Tibshirani RJ : Extensions of sparse canonical correlation analysis with applications to genomic data. Stat Appl Genet Mol Biol 2009; 8: Article28.

Waaijenborg S, Zwinderman AH : Sparse canonical correlation analysis for identifying, connecting and completing gene-expression networks. BMC Bioinform 2009; 10: 315.

Yamanishi Y, Vert JP, Nakaya A, Kanehisa M : Extraction of correlated gene clusters from multiple genomic data by generalized kernel canonical correlation analysis. Bioinformatics 2003; 19 ((Suppl 1):): i323–i330.

Yamamoto M, Sugiyama T, Murakmi H, Sakaori F : Correlation analysis of principal components from two populations. Comput Stat Data Anal 2007; 51: 4707–4716.