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Comparisons of multi-marker association methods to detect association between a candidate region and disease.

ABSTRACT: The joint use of information from multiple markers may be more effective to reveal association between a genomic region and a trait than single marker analysis. In this article, we compare the performance of seven multi-marker methods. These methods include (1) single marker analysis (either the best-scoring single nucleotide polymorphism in a candidate region or a combined test based on Fisher's method); (2) fixed effects regression models where the predictors are either the observed genotypes in the region, principal components that explain a proportion of the genetic variation, or predictors based on Fourier transformation for the genotypes; and (3) variance components analysis. In our simulation studies, we consider genetic models where the association is due to one, two, or three markers, and the disease-causing markers have varying allele frequencies. We use information from either all the markers in a region or information only from tagging markers. Our simulation results suggest that when there is one disease-causing variant, the best-scoring marker method is preferred whereas the variance components method and the principal components method work well for more common disease-causing variants. When there is more than one disease-causing variant, the principal components method seems to perform well over all the scenarios studied. When these methods are applied to analyze associations between all the markers in or near a gene and disease status for an inflammatory bowel disease data set, the analysis based on the principal components method leads to biologically more consistent discoveries than other methods.

SUBMITTER: Ballard DH

PROVIDER: S-EPMC3158797 | biostudies-literature | 2010 Apr

REPOSITORIES: biostudies-literature

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Comparisons of multi-marker association methods to detect association between a candidate region and disease.

Ballard David H DH Cho Judy J Zhao Hongyu H

Genetic epidemiology 20100401 3

The joint use of information from multiple markers may be more effective to reveal association between a genomic region and a trait than single marker analysis. In this article, we compare the performance of seven multi-marker methods. These methods include (1) single marker analysis (either the best-scoring single nucleotide polymorphism in a candidate region or a combined test based on Fisher's method); (2) fixed effects regression models where the predictors are either the observed genotypes ...[more]

PMID: 19810024

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Project description:BackgroundDespite the increasing popularity of multi-model comparison studies and their ability to inform policy recommendations, clear guidance on how to conduct multi-model comparisons is not available. Herein, we present guidelines to provide a structured approach to comparisons of multiple models of interventions against infectious diseases. The primary target audience for these guidelines are researchers carrying out model comparison studies and policy-makers using model comparison studies to inform policy decisions.MethodsThe consensus process used for the development of the guidelines included a systematic review of existing model comparison studies on effectiveness and cost-effectiveness of vaccination, a 2-day meeting and guideline development workshop during which mathematical modellers from different disease areas critically discussed and debated the guideline content and wording, and several rounds of comments on sequential versions of the guidelines by all authors.ResultsThe guidelines provide principles for multi-model comparisons, with specific practice statements on what modellers should do for six domains. The guidelines provide explanation and elaboration of the principles and practice statements as well as some examples to illustrate these. The principles are (1) the policy and research question - the model comparison should address a relevant, clearly defined policy question; (2) model identification and selection - the identification and selection of models for inclusion in the model comparison should be transparent and minimise selection bias; (3) harmonisation - standardisation of input data and outputs should be determined by the research question and value of the effort needed for this step; (4) exploring variability - between- and within-model variability and uncertainty should be explored; (5) presenting and pooling results - results should be presented in an appropriate way to support decision-making; and (6) interpretation - results should be interpreted to inform the policy question.ConclusionThese guidelines should help researchers plan, conduct and report model comparisons of infectious diseases and related interventions in a systematic and structured manner for the purpose of supporting health policy decisions. Adherence to these guidelines will contribute to greater consistency and objectivity in the approach and methods used in multi-model comparisons, and as such improve the quality of modelled evidence for policy.

Dataset Information

Comparisons of multi-marker association methods to detect association between a candidate region and disease.

Publications

Comparisons of multi-marker association methods to detect association between a candidate region and disease.

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