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Polygenic risk score for schizophrenia is not strongly associated with the expression of specific genes or gene sets

Curtis, Davida,b

doi: 10.1097/YPG.0000000000000197
Original Article

Background The polygenic risk score (PRS) is derived from single nucleotide polymorphisms (SNPs) including those that are genome-wide significant and also including a large number of others more weakly associated with schizophrenia. Such variants are widely dispersed, though concentrated near genes expressed in the brain, and it has been proposed that these SNP associations result from impacts on cell regulatory networks that ultimately affect the expression or function of a modest number of ‘core’ genes. A previous study showed association of some genome-wide association study-significant variants with expression of a number of genes, by examining pairwise correlations of gene expression with SNP genotypes.

Methods The present study used data downloaded from the CommonMind Consortium site, consisting of SNP genotypes and RNAseq expression data from the dorsolateral prefrontal cortex, to examine whether the expression of individual genes or sets of genes correlated with PRS in 207 controls and 209 schizophrenia cases.

Results Although the PRS was significantly associated with phenotype, the correlations with genes and gene sets followed distributions expected by chance. Thus, this analysis failed to show that the PRS captures a cumulative effect of multiple variants impacting the expression of a small number of genes and it failed to focus attention on a small number of genes of biological relevance.

Conclusion The multiple SNP associations observed in schizophrenia may result from other mechanisms, including effects mediated indirectly through environmental risk factors.

aUCL Genetics Institute, University College London

bCentre for Psychiatry, Barts and the London School of Medicine and Dentistry, London, UK

Correspondence to David Curtis, MA, MD, PhD, FRCPsych, UCL Genetics Institute, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK Tel: +44 797 390 6143; e-mail: d.curtis@ucl.ac.uk

Received December 28, 2017

Accepted March 26, 2018

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