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Practical and theoretical considerations in study design for detecting gene-gene interactions using MDR and GMDR approaches.

Chen GB, Xu Y, Xu HM, Li MD, Zhu J, Lou XY - PLoS ONE (2011)

Bottom Line: To provide empirical guidelines for planning such studies and data analyses, we investigated the performance of the multifactor dimensionality reduction (MDR) and generalized MDR (GMDR) methods under various experimental scenarios.However, the two methods performed similarly when the accuracy was outside this range or the sample was significantly larger.We conclude that with adjustment of a covariate, GMDR performs better than MDR and a sample size of 1000∼2000 is reasonably large for detecting gene-gene interactions in the range of effect size reported by the current literature; whereas larger sample size is required for more subtle interactions with accuracy <0.56.

View Article: PubMed Central - PubMed

Affiliation: Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.

ABSTRACT
Detection of interacting risk factors for complex traits is challenging. The choice of an appropriate method, sample size, and allocation of cases and controls are serious concerns. To provide empirical guidelines for planning such studies and data analyses, we investigated the performance of the multifactor dimensionality reduction (MDR) and generalized MDR (GMDR) methods under various experimental scenarios. We developed the mathematical expectation of accuracy and used it as an indicator parameter to perform a gene-gene interaction study. We then examined the statistical power of GMDR and MDR within the plausible range of accuracy (0.50∼0.65) reported in the literature. The GMDR with covariate adjustment had a power of >80% in a case-control design with a sample size of ≥2000, with theoretical accuracy ranging from 0.56 to 0.62. However, when the accuracy was <0.56, a sample size of ≥4000 was required to have sufficient power. In our simulations, the GMDR outperformed the MDR under all models with accuracy ranging from 0.56∼0.62 for a sample size of 1000-2000. However, the two methods performed similarly when the accuracy was outside this range or the sample was significantly larger. We conclude that with adjustment of a covariate, GMDR performs better than MDR and a sample size of 1000∼2000 is reasonably large for detecting gene-gene interactions in the range of effect size reported by the current literature; whereas larger sample size is required for more subtle interactions with accuracy <0.56.

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Conditional genotype and score distributions.(A): Conditional genotype distribution; (B): Conditional score distribution without covariate adjustment; and (C): Conditional score distribution with covariate adjustment. The parameters used in our simulations under the balanced case-control design are:  = 2000, MAF = 0.5,  = -5.30,  = 2.5,  = 1, and .
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pone-0016981-g001: Conditional genotype and score distributions.(A): Conditional genotype distribution; (B): Conditional score distribution without covariate adjustment; and (C): Conditional score distribution with covariate adjustment. The parameters used in our simulations under the balanced case-control design are:  = 2000, MAF = 0.5,  = -5.30,  = 2.5,  = 1, and .

Mentions: To demonstrate the method, we offer the theoretical genotype distribution for a checkerboard model scenario, as commonly employed in this type of interaction study [14], [44], [45]. In the following sections, we consider a penetrance function containing only one covariate, but when necessary, it can easily be extended by incorporating more covariates and other effects; e.g., gene × environment factors. We assume a balanced case-control design with 2000 unrelated subjects, MAF = 0.5, , , , and a covariate . Under such assumptions, the trait is expected to have a heritability of 0.043 (according to the definition of Culverhouse et al. [44]), and there are two differential risk genotypic groups with their expected penetrances of 0.073 and 0.221 (0.005 and 0.057 if the covariate is excluded), which can be calculated from Equation (5) through numerical solution. After applying these equations, we obtain the expected genotype distribution for the case-control sample, as presented in Figure 1A (see Text S1 for details on calculating this distribution). Such an approach of generating the conditional genotype distribution is flexible and can be applied easily to other scenarios. When no covariate is considered, as assumed in the MDR approach [46], the genotype distribution becomes a simpler form.


Practical and theoretical considerations in study design for detecting gene-gene interactions using MDR and GMDR approaches.

Chen GB, Xu Y, Xu HM, Li MD, Zhu J, Lou XY - PLoS ONE (2011)

Conditional genotype and score distributions.(A): Conditional genotype distribution; (B): Conditional score distribution without covariate adjustment; and (C): Conditional score distribution with covariate adjustment. The parameters used in our simulations under the balanced case-control design are:  = 2000, MAF = 0.5,  = -5.30,  = 2.5,  = 1, and .
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3046176&req=5

pone-0016981-g001: Conditional genotype and score distributions.(A): Conditional genotype distribution; (B): Conditional score distribution without covariate adjustment; and (C): Conditional score distribution with covariate adjustment. The parameters used in our simulations under the balanced case-control design are:  = 2000, MAF = 0.5,  = -5.30,  = 2.5,  = 1, and .
Mentions: To demonstrate the method, we offer the theoretical genotype distribution for a checkerboard model scenario, as commonly employed in this type of interaction study [14], [44], [45]. In the following sections, we consider a penetrance function containing only one covariate, but when necessary, it can easily be extended by incorporating more covariates and other effects; e.g., gene × environment factors. We assume a balanced case-control design with 2000 unrelated subjects, MAF = 0.5, , , , and a covariate . Under such assumptions, the trait is expected to have a heritability of 0.043 (according to the definition of Culverhouse et al. [44]), and there are two differential risk genotypic groups with their expected penetrances of 0.073 and 0.221 (0.005 and 0.057 if the covariate is excluded), which can be calculated from Equation (5) through numerical solution. After applying these equations, we obtain the expected genotype distribution for the case-control sample, as presented in Figure 1A (see Text S1 for details on calculating this distribution). Such an approach of generating the conditional genotype distribution is flexible and can be applied easily to other scenarios. When no covariate is considered, as assumed in the MDR approach [46], the genotype distribution becomes a simpler form.

Bottom Line: To provide empirical guidelines for planning such studies and data analyses, we investigated the performance of the multifactor dimensionality reduction (MDR) and generalized MDR (GMDR) methods under various experimental scenarios.However, the two methods performed similarly when the accuracy was outside this range or the sample was significantly larger.We conclude that with adjustment of a covariate, GMDR performs better than MDR and a sample size of 1000∼2000 is reasonably large for detecting gene-gene interactions in the range of effect size reported by the current literature; whereas larger sample size is required for more subtle interactions with accuracy <0.56.

View Article: PubMed Central - PubMed

Affiliation: Institute of Bioinformatics, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China.

ABSTRACT
Detection of interacting risk factors for complex traits is challenging. The choice of an appropriate method, sample size, and allocation of cases and controls are serious concerns. To provide empirical guidelines for planning such studies and data analyses, we investigated the performance of the multifactor dimensionality reduction (MDR) and generalized MDR (GMDR) methods under various experimental scenarios. We developed the mathematical expectation of accuracy and used it as an indicator parameter to perform a gene-gene interaction study. We then examined the statistical power of GMDR and MDR within the plausible range of accuracy (0.50∼0.65) reported in the literature. The GMDR with covariate adjustment had a power of >80% in a case-control design with a sample size of ≥2000, with theoretical accuracy ranging from 0.56 to 0.62. However, when the accuracy was <0.56, a sample size of ≥4000 was required to have sufficient power. In our simulations, the GMDR outperformed the MDR under all models with accuracy ranging from 0.56∼0.62 for a sample size of 1000-2000. However, the two methods performed similarly when the accuracy was outside this range or the sample was significantly larger. We conclude that with adjustment of a covariate, GMDR performs better than MDR and a sample size of 1000∼2000 is reasonably large for detecting gene-gene interactions in the range of effect size reported by the current literature; whereas larger sample size is required for more subtle interactions with accuracy <0.56.

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