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Polygenic risk score for schizophrenia is more strongly associated with ancestry than with schizophrenia

David Curtis
doi: https://doi.org/10.1101/287136
David Curtis
1UCL Genetics Institute, UCL, Darwin Building, Gower Street, London WC1E 6BT
2Centre for Psychiatry, Barts and the London School of Medicine and Dentistry, Charterhouse Square, London EC1M 6BQ
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  • For correspondence: d.curtis@ucl.ac.uk
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Abstract

Background The polygenic risk score (PRS) for schizophrenia, derived from very large numbers of weakly associated genetic markers, has been repeatedly shown to be robustly associated with schizophrenia in independent samples and also with other diseases and traits.

Aims To explore the distribution of the schizophrenia PRS in subjects of different ancestry.

Method The schizophrenia PRS derived from the large genome-wide association study carried out by the Psychiatric Genetics Consortium was calculated using the downloaded genotypes of HapMap subjects from eleven different ancestral groups. It was also calculated using downloaded genotypes of European schizophrenia cases and controls from the CommonMind Consortium.

Results The PRS for schizophrenia varied significantly between ancestral groups (p < 2*10−16) and was much higher in African than European HapMap subjects. The mean difference between these groups was ten times as high as the mean difference between European schizophrenia cases and controls. The distributions of scores for African and European subjects hardly overlapped.

Conclusions The PRS cannot be regarded as simply a measure of the polygenic contribution to risk of schizophrenia and clearly contains a strong ancestry component. It is possible that this could be controlled for to some extent by incorporating principal components as covariates but doubts remain as to how it should be interpreted. The PRS derived from European subjects cannot be applied to non-Europeans, limiting its potential usefulness and raising issues of inequity. Previous studies which have used the PRS should be re-examined in the light of these findings.

Declaration of interest The author declares he has no conflict of interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted March 23, 2018.
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Polygenic risk score for schizophrenia is more strongly associated with ancestry than with schizophrenia
David Curtis
bioRxiv 287136; doi: https://doi.org/10.1101/287136
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Polygenic risk score for schizophrenia is more strongly associated with ancestry than with schizophrenia
David Curtis
bioRxiv 287136; doi: https://doi.org/10.1101/287136

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