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

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Association screening for genes with multiple potentially rare variants: an inverse-probability weighted clustering approach

Ying Liu1, Chien Hsun Huang1, Inchi Hu2, Shaw-Hwa Lo1 and Tian Zheng1*

Author Affiliations

1 Department of Statistics, Columbia University, New York, NY 10027, USA

2 Department of Information Systems, Business Statistics, and Operations Management (ISOM), Hong Kong University of Science and Technology, Kowloon, Hong Kong

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BMC Proceedings 2011, 5(Suppl 9):S106  doi:10.1186/1753-6561-5-S9-S106

Published: 29 November 2011


Both common variants and rare variants are involved in the etiology of most complex diseases in humans. Developments in sequencing technology have led to the identification of a high density of rare variant single-nucleotide polymorphisms (SNPs) on the genome, each of which affects only at most 1% of the population. Genotypes derived from these SNPs allow one to study the involvement of rare variants in common human disorders. Here, we propose an association screening approach that treats genes as units of analysis. SNPs within a gene are used to create partitions of individuals, and inverse-probability weighting is used to overweight genotypic differences observed on rare variants. Association between a phenotype trait and the constructed partition is then evaluated. We consider three association tests (one-way ANOVA, chi-square test, and the partition retention method) and compare these strategies using the simulated data from the Genetic Analysis Workshop 17. Several genes that contain causal SNPs were identified by the proposed method as top genes.