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dc.date.accessioned2016-01-29T14:50:54Z
dc.date.available2016-01-29T14:50:54Z
dc.date.created2015-11-19T10:14:48Z
dc.date.issued2015
dc.identifier.citationPage, Christian Baranzini, Sergio E. Mevik, Bjørn-Helge Bos, Steffan Daniel Harbo, Hanne Flinstad Kulle, Bettina . Assessing the Power of Exome Chips. PLoS ONE. 2015, 10(10)
dc.identifier.urihttp://hdl.handle.net/10852/48806
dc.description.abstractGenotyping chips for rare and low-frequent variants have recently gained popularity with the introduction of exome chips, but the utility of these chips remains unclear. These chips were designed using exome sequencing data from mainly American-European individuals, enriched for a narrow set of common diseases. In addition, it is well-known that the statistical power of detecting associations with rare and low-frequent variants is much lower compared to studies exclusively involving common variants. We developed a simulation program adaptable to any exome chip design to empirically evaluate the power of the exome chips. We implemented the main properties of the Illumina HumanExome BeadChip array. The simulated data sets were used to assess the power of exome chip based studies for varying effect sizes and causal variant scenarios. We applied two widely-used statistical approaches for rare and low-frequency variants, which collapse the variants into genetic regions or genes. Under optimal conditions, we found that a sample size between 20,000 to 30,000 individuals were needed in order to detect modest effect sizes (0.5% < PAR > 1%) with 80% power. For small effect sizes (PAR <0.5%), 60,000–100,000 individuals were needed in the presence of non-causal variants. In conclusion, we found that at least tens of thousands of individuals are necessary to detect modest effects under optimal conditions. In addition, when using rare variant chips on cohorts or diseases they were not originally designed for, the identification of associated variants or genes will be even more challenging.en_US
dc.languageEN
dc.language.isoenen_US
dc.publisherPublic Library of Science (PLoS)
dc.relation.ispartofChristian Page (2016) DNA Methylation and Exome Chip Analysis in Complex Disease. Doctoral thesis. http://urn.nb.no/URN:NBN:no-56454
dc.relation.urihttp://urn.nb.no/URN:NBN:no-56454
dc.rightsPublic Domain Dedication
dc.rights.urihttps://creativecommons.org/publicdomain/zero/1.0/
dc.titleAssessing the Power of Exome Chipsen_US
dc.typeJournal articleen_US
dc.creator.authorPage, Christian
dc.creator.authorBaranzini, Sergio E.
dc.creator.authorMevik, Bjørn-Helge
dc.creator.authorBos, Steffan Daniel
dc.creator.authorHarbo, Hanne Flinstad
dc.creator.authorKulle, Bettina
cristin.unitcode185,53,12,0
cristin.unitnameKlinikk for kirurgi og nevrofag
cristin.ispublishedtrue
cristin.fulltextoriginal
cristin.qualitycode1
dc.identifier.cristin1290726
dc.identifier.bibliographiccitationinfo:ofi/fmt:kev:mtx:ctx&ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=PLoS ONE&rft.volume=10&rft.spage=&rft.date=2015
dc.identifier.jtitlePLoS ONE
dc.identifier.volume10
dc.identifier.issue10
dc.identifier.doihttp://dx.doi.org/10.1371/journal.pone.0139642
dc.identifier.urnURN:NBN:no-52655
dc.type.documentTidsskriftartikkelen_US
dc.type.peerreviewedPeer reviewed
dc.source.issn1932-6203
dc.identifier.fulltextFulltext https://www.duo.uio.no/bitstream/handle/10852/48806/1/journal-pone-0139642.pdf
dc.type.versionPublishedVersion
cristin.articleide0139642


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