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https://hdl.handle.net/2440/88220
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Type: | Journal article |
Title: | Meta-analysis of gene-level associations for rare variants based on single-variant statistics |
Author: | Hu, Y. Berndt, S. Gustafsson, S. Ganna, A. Genetic Investigation of ANthropometric Traits (GIANT) Consortium, Hirschhorn, J. North, K. Ingelsson, E. Lin, D. |
Citation: | American Journal of Human Genetics, 2013; 93(2):236-248 |
Publisher: | University of Chicago Press |
Issue Date: | 2013 |
ISSN: | 0002-9297 1537-6605 |
Statement of Responsibility: | Yi-Juan Hu, Sonja I. Berndt, Stefan Gustafsson, Andrea Ganna, Genetic Investigation of ANthropometric Traits, GIANT, Consortium, Joel Hirschhorn, Kari E. North, Erik Ingelsson, and Dan-Yu Lin |
Abstract: | Meta-analysis of genome-wide association studies (GWASs) has led to the discoveries of many common variants associated with complex human diseases. There is a growing recognition that identifying "causal" rare variants also requires large-scale meta-analysis. The fact that association tests with rare variants are performed at the gene level rather than at the variant level poses unprecedented challenges in the meta-analysis. First, different studies may adopt different gene-level tests, so the results are not compatible. Second, gene-level tests require multivariate statistics (i.e., components of the test statistic and their covariance matrix), which are difficult to obtain. To overcome these challenges, we propose to perform gene-level tests for rare variants by combining the results of single-variant analysis (i.e., p values of association tests and effect estimates) from participating studies. This simple strategy is possible because of an insight that multivariate statistics can be recovered from single-variant statistics, together with the correlation matrix of the single-variant test statistics, which can be estimated from one of the participating studies or from a publicly available database. We show both theoretically and numerically that the proposed meta-analysis approach provides accurate control of the type I error and is as powerful as joint analysis of individual participant data. This approach accommodates any disease phenotype and any study design and produces all commonly used gene-level tests. An application to the GWAS summary results of the Genetic Investigation of ANthropometric Traits (GIANT) consortium reveals rare and low-frequency variants associated with human height. The relevant software is freely available. |
Keywords: | No keywords specified |
Description: | Lyle J. Plamer is a member of the GIANT Consortium |
Rights: | © 2013 by The American Society of Human Genetics. All rights reserved |
DOI: | 10.1016/j.ajhg.2013.06.011 |
Published version: | http://dx.doi.org/10.1016/j.ajhg.2013.06.011 |
Appears in Collections: | Aurora harvest 7 Translational Health Science publications |
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