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

2.50
Hdl Handle:
http://hdl.handle.net/11287/618355
Title:
Simulation of Finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland.
Authors:
Wang, S. R. [et al]; Hattersley, Andrew T.; Frayling, T. M.
Abstract:
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.
Citation:
Simulation of Finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland. 2014, 94 (5):710-20 Am. J. Hum. Genet.
Publisher:
Cell Press
Journal:
American Journal of Human Genetics
Issue Date:
1-May-2014
URI:
http://hdl.handle.net/11287/618355
DOI:
10.1016/j.ajhg.2014.03.019
PubMed ID:
24768551
Additional Links:
http://linkinghub.elsevier.com/retrieve/pii/S0002-9297(14)00151-7
Note:
This article is freely available via Open Access. Click on the 'Additional Link' above to access the full text via the publisher's site.
Type:
Journal Article; Research Support, N.I.H., Extramural
Language:
en
Description:
Andrew Hattersley and T Frayling were collaborators on this journal article/project.
ISSN:
1537-6605
Appears in Collections:
2014 RD&E publications; Diabetes/Endocrine Services

Full metadata record

DC FieldValue Language
dc.contributor.authorWang, S. R. [et al]en
dc.contributor.authorHattersley, Andrew T.en
dc.contributor.authorFrayling, T. M.en
dc.date.accessioned2016-08-12T08:45:17Z-
dc.date.available2016-08-12T08:45:17Z-
dc.date.issued2014-05-01-
dc.identifier.citationSimulation of Finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland. 2014, 94 (5):710-20 Am. J. Hum. Genet.en
dc.identifier.issn1537-6605-
dc.identifier.pmid24768551-
dc.identifier.doi10.1016/j.ajhg.2014.03.019-
dc.identifier.urihttp://hdl.handle.net/11287/618355-
dc.descriptionAndrew Hattersley and T Frayling were collaborators on this journal article/project.en
dc.description.abstractFinnish 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.en
dc.language.isoenen
dc.publisherCell Pressen
dc.relation.urlhttp://linkinghub.elsevier.com/retrieve/pii/S0002-9297(14)00151-7en
dc.rightsArchived with thanks to American journal of human geneticsen
dc.subjectWessex Classification Subject Headings::Oncology. Pathology.::Geneticsen
dc.titleSimulation of Finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland.en
dc.typeJournal Articleen
dc.typeResearch Support, N.I.H., Extramuralen
dc.identifier.journalAmerican Journal of Human Geneticsen
dc.description.noteThis article is freely available via Open Access. Click on the 'Additional Link' above to access the full text via the publisher's site.en
dc.type.versionPublisheden

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