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Interpretation of knockout experiments: the congenic footprint

Authors

  • L. C. Schalkwyk,

    Corresponding author
    1. Social, Genetic and Developmental Psychiatry Centre (PO82), Institute of Psychiatry, King’s College London, London, United Kingdom and Department of Physiology, Centre of Molecular and Clinical Medicine, University of Tartu, Tartu, Estonia
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  • , C. Fernandes,

    1. Social, Genetic and Developmental Psychiatry Centre (PO82), Institute of Psychiatry, King’s College London, London, United Kingdom and Department of Physiology, Centre of Molecular and Clinical Medicine, University of Tartu, Tartu, Estonia
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  • M. W. Nash,

    1. Social, Genetic and Developmental Psychiatry Centre (PO82), Institute of Psychiatry, King’s College London, London, United Kingdom and Department of Physiology, Centre of Molecular and Clinical Medicine, University of Tartu, Tartu, Estonia
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  • K. Kurrikoff,

    1. Social, Genetic and Developmental Psychiatry Centre (PO82), Institute of Psychiatry, King’s College London, London, United Kingdom and Department of Physiology, Centre of Molecular and Clinical Medicine, University of Tartu, Tartu, Estonia
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  • E. Vasar,

    1. Social, Genetic and Developmental Psychiatry Centre (PO82), Institute of Psychiatry, King’s College London, London, United Kingdom and Department of Physiology, Centre of Molecular and Clinical Medicine, University of Tartu, Tartu, Estonia
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  • S. Kõks

    1. Social, Genetic and Developmental Psychiatry Centre (PO82), Institute of Psychiatry, King’s College London, London, United Kingdom and Department of Physiology, Centre of Molecular and Clinical Medicine, University of Tartu, Tartu, Estonia
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  • Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.

*L. C. Schalkwyk, Social, Genetic and Developmental Psychiatry Centre (PO82), Institute of Psychiatry, King’s College London, London SE5 8AF, UK. E-mail: l.schalkwyk@iop.kcl.ac.uk

Abstract

In gene targeting experiments, the importance of genetic background is now widely appreciated, and knockout alleles are routinely backcrossed onto a standard inbred background. This produces a congenic strain with a substantial segment of embryonic stem (ES)-cell-derived chromosome still flanking the knockout allele, a phenomenon often neglected in knockout studies. In cholecystokynin 2 (Cckbr) knockout mice backcrossed with C57BL/6, we have found a clear ‘congenic footprint’ of expression differences in at least 10 genes across 40 Mb sequence flanking the Cckbr locus, each of which is potentially responsible for aspects of the ‘knockout’ phenotype. The expression differences are overwhelmingly in the knockout-low direction, which may point to a general phenomenon of background dependence. This finding emphasizes the need for caution in using gene knockouts to attribute phenotypic effects to genes. This is especially the case when the gene is of unknown function or the phenotype is unexpected, and is a particular concern for large-scale knockout and phenotypic screening programmes. However, the impact of genetic background should not be simply viewed as a potential confound, but as a unique opportunity to study the broader responses of a system to a specific (genetic) perturbation.

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