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

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Two-stage analyses of sequence variants in association with quantitative traits

Jennifer H Barrett* and Jérémie Nsengimana

Author Affiliations

Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, University of Leeds, Cancer Genetics Building, St. James’s University Hospital, Beckett Street, Leeds, LS9 7TF, UK

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BMC Proceedings 2011, 5(Suppl 9):S53  doi:10.1186/1753-6561-5-S9-S53

Published: 29 November 2011


We propose a two-stage design for the analysis of sequence variants in which a proportion of genes that show some evidence of association are identified initially and then followed up in an independent data set. We compare two different approaches. In both approaches the same summary measure (total number of minor alleles) is used for each gene in the initial analysis. In the first (simple) approach the same summary measure is used in the analysis of the independent data set. In the second (alternative) approach a more specific hypothesis is formed for the second stage; the summary measure used is the count of minor alleles in only those variants that in the initial data showed the same direction of association as was seen overall. We applied the methods to the simulated quantitative traits of Genetic Analysis Workshop 17, blind to the simulation model, and then evaluated their performance once the underlying model was known. Performance was similar for most genes, but the simple strategy considerably out-performed the alternative strategy for one gene, where most of the effect was due to very rare variants; this suggests that the alternative approach would not be advisable when the effect is seen in very rare variants. Further simulations are needed to investigate the potential superior power of the alternative method when some variants within a gene have opposing effects. Overall, the power to detect associations was low; this was also true when using a more powerful joint analysis that combined the two stages of the study.