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This article is part of the supplement: Genetic Analysis Workshop 17: Unraveling Human Exome Data

Open Access Proceedings

Pathway-based joint effects analysis of rare genetic variants using Genetic Analysis Workshop 17 exon sequence data

Pingzhao Hu1, Wei Xu23, Lu Cheng3, Xiang Xing4 and Andrew D Paterson12*

Author Affiliations

1 The Centre for Applied Genomics (TCAG) and Program in Genetics and Genome Biology, The Hospital for Sick Children, 101 College Street, Toronto, ON M5G 1L7, Canada

2 Dalla Lana School of Public Health, University of Toronto, Health Sciences Building, 155 College Street, Toronto, ON M5T 3M7, Canada

3 Department of Biostatistics, Princess Margaret Hospital, 610 University Avenue, Toronto, ON M5G 2M9, Canada

4 Department of Computer Science and Statistics Department, University of Toronto, 40 St. George Street, Toronto, ON M5S 2E4, Canada

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BMC Proceedings 2011, 5(Suppl 9):S45  doi:10.1186/1753-6561-5-S9-S45

Published: 29 November 2011


Pathway-based analysis has been recently used in joint tests of association between disease and a group of common genetic variants. Here we explore this idea for the joint effects analysis of rare genetic variants and their association with quantitative traits and disease. We accumulate multiple rare minor alleles in a genetic risk score for each individual in a given pathway; this score is then used to assess association with quantitative phenotypes and disease. We demonstrate that this approach may be better than studying single rare variants or a gene risk score for identifying individuals with significantly greater risk.