Nonlinear tests for genomewide association studies.
As millions of single-nucleotide polymorphisms (SNPs) have been identified and high-throughput genotyping technologies have been rapidly developed, large-scale genomewide association studies are soon within reach. However, since a genomewide association study involves a large number of SNPs it is therefore nearly impossible to ensure a genomewide significance level of 0.05 using the available statistics, although the multiple-test problems can be alleviated, but not sufficiently, by the use of tagging SNPs. One strategy to circumvent the multiple-test problem associated with genome-wide association tests is to develop novel test statistics with high power. In this report, we introduce several nonlinear tests, which are based on nonlinear transformation of allele or haplotype frequencies. We investigate the power of the nonlinear test statistics and demonstrate that under certain conditions, some nonlinear test statistics have much higher power than the standard chi2-test statistic. Type I error rates of the nonlinear tests are validated using simulation studies. We also show that a class of similarity measure-based test statistics is based on the quadratic function of allele or haplotype frequencies, and thus they belong to nonlinear tests. To evaluate their performance, the nonlinear test statistics are also applied to three real data sets. Our study shows that nonlinear test statistics have great potential in association studies of complex diseases.
Zhao
Jinying
J
Human Genetics Center, University of Texas Health Science Center, Houston 77030, USA.
Jin
Li
L
Xiong
Momiao
M
D000217:Acyltransferases / Q000235:genetics; D000483:Alleles; D002394:Catechol O-Methyltransferase / Q000235:genetics; D003198:Computer Simulation; D004938:Esophageal Neoplasms / Q000201:enzymology / Q000235:genetics; D005260:Female; D005787:Gene Frequency; D015894:Genome, Human; D006239:Haplotypes; D006801:Humans; D008297:Male; D020778:Matrix Metalloproteinase 2 / Q000235:genetics; D008565:Membrane Proteins / Q000235:genetics; D015233:Models, Statistical; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D012559:Schizophrenia / Q000201:enzymology / Q000235:genetics
D008565:Membrane Proteins; D002394:Catechol O-Methyltransferase; D000217:Acyltransferases; C488097:ZDHHC8 protein, human; D020778:Matrix Metalloproteinase 2