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A weighted burden test using logistic regression for integrated analysis of sequence variants, copy number variants and polygenic risk score

Curtis, D; (2018) A weighted burden test using logistic regression for integrated analysis of sequence variants, copy number variants and polygenic risk score. European Journal of Human Genetics , 27 (1) pp. 114-124. 10.1038/s41431-018-0272-6. Green open access

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Abstract

Previously described methods of analysis allow variants in a gene to be weighted more highly according to rarity and/or predicted function and then for the variant contributions to be summed into a gene-wise risk score, which can be compared between cases and controls using a t-test. However, this does not allow incorporating covariates into the analysis. Schizophrenia is an example of an illness where there is evidence that different kinds of genetic variation can contribute to risk, including common variants contributing to a polygenic risk score (PRS), very rare copy number variants (CNVs) and sequence variants. A logistic regression approach has been implemented to compare the gene-wise risk scores between cases and controls, while incorporating as covariates population principal components, the PRS and the presence of pathogenic CNVs and sequence variants. A likelihood ratio test is performed, comparing the likelihoods of logistic regression models with and without this score. The method was applied to an ethnically heterogeneous exome-sequenced sample of 6000 controls and 5000 schizophrenia cases. In the raw analysis, the test statistic is inflated but inclusion of principal components satisfactorily controls for this. In this dataset, the inclusion of the PRS and effect from CNVs and sequence variants had only small effects. The set of genes which are FMRP targets showed some evidence for enrichment of rare, functional variants among cases (p = 0.0005). This approach can be applied to any disease in which different kinds of genetic and non-genetic risk factors make contributions to risk.

Type: Article
Title: A weighted burden test using logistic regression for integrated analysis of sequence variants, copy number variants and polygenic risk score
Location: England
Open access status: An open access version is available from UCL Discovery
DOI: 10.1038/s41431-018-0272-6
Publisher version: https://doi.org/10.1038/s41431-018-0272-6
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10064653
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