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This article is part of the supplement: Genetic Analysis Workshop 15: Gene Expression Analysis and Approaches to Detecting Multiple Functional Loci

Open Access Proceedings

A comparison of founder-only and all-pedigree-members genotype-expression association by regression analysis

Young Ju Suh1, Hye-Soon Lee23, Franak Batliwalla2 and Wentian Li2*

Author Affiliations

1 BK21 Research Division of Medicine and Department of Preventive Medicine, School of Medicine, Ewha Womans University, Seoul 158-710, Korea

2 The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System, 350 Community Drive, Manhasset, New York 11030 USA

3 Division of Rheumatology, Department of Internal Medicine, Hanyang University Medical College, Seoul 133-792, Korea

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BMC Proceedings 2007, 1(Suppl 1):S8  doi:

Published: 18 December 2007


Genotype-expression association analysis using linear regression may produce different test results depending on whether founders only or all pedigreed members are used. This difference is not due to the correlation of samples within a pedigree, because linear mixed models have been applied to account for that correlation. We investigated the possibility that the difference is due to a dependence of expression levels on, among other things, the generation number in the pedigree. Indeed, of the 30 or so studied expression quantitative traits, several of them show significant dependence on the generation number. We propose to use all pedigree members in genotype-expression association analyses whenever the complete genotyping information is available.