Dataset Information

Identifying significant gene-environment interactions using a combination of screening testing and hierarchical false discovery rate control.

ABSTRACT: Although gene-environment (G× E) interactions play an important role in many biological systems, detecting these interactions within genome-wide data can be challenging due to the loss in statistical power incurred by multiple hypothesis correction. To address the challenge of poor power and the limitations of existing multistage methods, we recently developed a screening-testing approach for G× E interaction detection that combines elastic net penalized regression with joint estimation to support a single omnibus test for the presence of G× E interactions. In our original work on this technique, however, we did not assess type I error control or power and evaluated the method using just a single, small bladder cancer data set. In this paper, we extend the original method in two important directions and provide a more rigorous performance evaluation. First, we introduce a hierarchical false discovery rate approach to formally assess the significance of individual G× E interactions. Second, to support the analysis of truly genome-wide data sets, we incorporate a score statistic-based prescreening step to reduce the number of single nucleotide polymorphisms prior to fitting the first stage penalized regression model. To assess the statistical properties of our method, we compare the type I error rate and statistical power of our approach with competing techniques using both simple simulation designs as well as designs based on real disease architectures. Finally, we demonstrate the ability of our approach to identify biologically plausible SNP-education interactions relative to Alzheimer's disease status using genome-wide association study data from the Alzheimer's Disease Neuroimaging Initiative (ADNI).

SUBMITTER: Frost HR

PROVIDER: S-EPMC5108431 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Identifying significant gene-environment interactions using a combination of screening testing and hierarchical false discovery rate control.

Frost H Robert HR Shen Li L Saykin Andrew J AJ Williams Scott M SM Moore Jason H JH

Genetic epidemiology 20160831 7

Although gene-environment (G× E) interactions play an important role in many biological systems, detecting these interactions within genome-wide data can be challenging due to the loss in statistical power incurred by multiple hypothesis correction. To address the challenge of poor power and the limitations of existing multistage methods, we recently developed a screening-testing approach for G× E interaction detection that combines elastic net penalized regression with joint estimation to suppo ...[more]

PMID: 27578615

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Project description:MOTIVATION:Most de novo motif identification methods optimize the motif model first and then separately test the statistical significance of the motif score. In the first stage, a motif abundance parameter needs to be specified or modeled. In the second stage, a Z-score or P-value is used as the test statistic. Error rates under multiple comparisons are not fully considered. METHODOLOGY:We propose a simple but novel approach, fdrMotif, that selects as many binding sites as possible while controlling a user-specified false discovery rate (FDR). Unlike existing iterative methods, fdrMotif combines model optimization [e.g. position weight matrix (PWM)] and significance testing at each step. By monitoring the proportion of binding sites selected in many sets of background sequences, fdrMotif controls the FDR in the original data. The model is then updated using an expectation (E)- and maximization (M)-like procedure. We propose a new normalization procedure in the E-step for updating the model. This process is repeated until either the model converges or the number of iterations exceeds a maximum. RESULTS:Simulation studies suggest that our normalization procedure assigns larger weights to the binding sites than do two other commonly used normalization procedures. Furthermore, fdrMotif requires only a user-specified FDR and an initial PWM. When tested on 542 high confidence experimental p53 binding loci, fdrMotif identified 569 p53 binding sites in 505 (93.2%) sequences. In comparison, MEME identified more binding sites but in fewer ChIP sequences than fdrMotif. When tested on 500 sets of simulated 'ChIP' sequences with embedded known p53 binding sites, fdrMotif, compared to MEME, has higher sensitivity with similar positive predictive value. Furthermore, fdrMotif is robust to noise: it selected nearly identical binding sites in data adulterated with 50% added background sequences and the unadulterated data. We suggest that fdrMotif represents an improvement over MEME. AVAILABILITY:C code can be found at: http://www.niehs.nih.gov/research/resources/software/fdrMotif/.

Dataset Information

Identifying significant gene-environment interactions using a combination of screening testing and hierarchical false discovery rate control.

Publications

Identifying significant gene-environment interactions using a combination of screening testing and hierarchical false discovery rate control.

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