A multi-marker test based on family data in genome-wide association study

Document Type

Article

Publication Date

9-25-2007

Abstract

Background: Complex diseases are believed to be the results of many genes and environmental factors. Hence, multi-marker methods that can use the information of markers from different genes are appropriate for mapping complex disease genes. There already have been several multi-marker methods proposed for case-control studies. In this article, we propose a multi-marker test called a Multi-marker Pedigree Disequilibrium Test (MPDT) to analyze family data from genome-wide association studies. If the parental phenotypes are available, we also propose a two-stage test in which a genomic screening test is used to select SNPs, and then the MPDT is used to test the association of the selected SNPs. Results: We use simulation studies to evaluate the performance of the MPDT and the two-stage approach. The results show that the MPDT constantly outperforms the single marker transmission/disequilibrium test (TDT) 1. Comparing the power of the two-stage approach with that of the one-stage approach, which approach is more powerful depends on the value of the prevalence; when the prevalence is no less than 10%, the two-stage approach may be more powerful than the one-stage approach. Otherwise, the one-stage approach is more powerful. Conclusion: The proposed MPDT, is more powerful than the single marker TDT. When the parental phenotypes are available and the prevalence is no less than 10%, the proposed two-stage approach is more powerful than the one-stage approach. © 2007 Zhang et al; licensee BioMed Central Ltd.

Publication Title

BMC Genetics

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