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Wang, S.R.* ; Agarwala, V.* ; Flannick, J.* ; Chiang, C.W.* ; Altshuler, D.* ; GoT2D Consortium (Gieger, C. ; Grallert, H. ; Hrabě de Angelis, M. ; Huth, C. ; Kriebel, J. ; Meisinger, C. ; Meitinger, T. ; Müller-Nurasyid, M. ; Ried, J.S. ; Peters, A. ; Rathmann, W. ; Strauch, K. ; Strom, T.M.) ; Hirschhorn, J.N.*

Simulation of finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland.

Am. J. Hum. Genet. 94, 710-720 (2014)
DOI PMC
Open Access Green as soon as Postprint is submitted to ZB.
Finnish samples have been extensively utilized in studying single-gene disorders, where the founder effect has clearly aided in discovery, and more recently in genome-wide association studies of complex traits, where the founder effect has had less obvious impacts. As the field starts to explore rare variants' contribution to polygenic traits, it is of great importance to characterize and confirm the Finnish founder effect in sequencing data and to assess its implications for rare-variant association studies. Here, we employ forward simulation, guided by empirical deep resequencing data, to model the genetic architecture of quantitative polygenic traits in both the general European and the Finnish populations simultaneously. We demonstrate that power of rare-variant association tests is higher in the Finnish population, especially when variants' phenotypic effects are tightly coupled with fitness effects and therefore reflect a greater contribution of rarer variants. SKAT-O, variable-threshold tests, and single-variant tests are more powerful than other rare-variant methods in the Finnish population across a range of genetic models. We also compare the relative power and efficiency of exome array genotyping to those of high-coverage exome sequencing. At a fixed cost, less expensive genotyping strategies have far greater power than sequencing; in a fixed number of samples, however, genotyping arrays miss a substantial portion of genetic signals detected in sequencing, even in the Finnish founder population. As genetic studies probe sequence variation at greater depth in more diverse populations, our simulation approach provides a framework for evaluating various study designs for gene discovery.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
ISSN (print) / ISBN 0002-9297
e-ISSN 1537-6605
Journal American Journal of Human Genetics, The
Quellenangaben Volume: 94, Issue: 5, Pages: 710-720 Article Number: , Supplement: ,
Publisher Elsevier
Publishing Place New York, NY
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Experimental Genetics (IEG)
Institute of Genetic Epidemiology (IGE)
Lung Health and Immunity (LHI)
Institute of Epidemiology II (EPI2)
Institute of Human Genetics (IHG)
German Center for Diabetes Reseach (DZD)