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The rate of false polymorphisms introduced when imputing genotypes from global imputation panels

Ida Surakka, Antti-Pekka Sarin, Sanni E Ruotsalainen, Richard Durbin, Veikko Salomaa, Mark J Daly, Aarno Palotie, Samuli Ripatti, SISu project group
doi: https://doi.org/10.1101/080770
Ida Surakka
1Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
2Department of Health, National Institute for Health and Welfare, Helsinki, Finland
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Antti-Pekka Sarin
1Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
2Department of Health, National Institute for Health and Welfare, Helsinki, Finland
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Sanni E Ruotsalainen
1Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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Richard Durbin
3Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
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Veikko Salomaa
2Department of Health, National Institute for Health and Welfare, Helsinki, Finland
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Mark J Daly
1Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
4Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
5Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
6Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Aarno Palotie
1Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
4Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, USA
6Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
7Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts, USA
8Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
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Samuli Ripatti
1Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
3Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
9Department of Public Health, University of Helsinki, Helsinki, Finland
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Abstract

Previous studies1,2 have shown that large multi-population imputation reference panels increases the number of well-imputed variants. However, to our knowledge, no previous studies have evaluated the rate of introduced variation in monomorphic sites of the study population when using imputation panels with admixed populations. In this study we evaluate the rate of false positive variants introduced by the imputation of Finnish genotype data using global reference panels (Haplotype Reference Consortium1; HRC, and the 1000Genomes project Phase I3; 1000G) and compare the results to a Finnish population-specific reference panel combining whole genome and exome sequenced samples. In sites that were monomorphic in our test set, we observed high false positive rates for the global reference panels (4.0% for 1000G and 2.6% for HRC) compared to the Finnish panel (0.26%). This rate was even higher (7.4%) when using a combination panel of 1000G and Finnish whole genome sequences with cross-panel imputation.

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Posted October 13, 2016.
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The rate of false polymorphisms introduced when imputing genotypes from global imputation panels
Ida Surakka, Antti-Pekka Sarin, Sanni E Ruotsalainen, Richard Durbin, Veikko Salomaa, Mark J Daly, Aarno Palotie, Samuli Ripatti, SISu project group
bioRxiv 080770; doi: https://doi.org/10.1101/080770
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The rate of false polymorphisms introduced when imputing genotypes from global imputation panels
Ida Surakka, Antti-Pekka Sarin, Sanni E Ruotsalainen, Richard Durbin, Veikko Salomaa, Mark J Daly, Aarno Palotie, Samuli Ripatti, SISu project group
bioRxiv 080770; doi: https://doi.org/10.1101/080770

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