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Investigating Genetic Heterogeneity in Major Depression Through Item-level Genetic Analyses of the PHQ-9

By Jackson G Thorp, Andries T. Marees, Jue-Sheng Ong, Jiyuan An, Stuart MacGregor, Eske M. Derks

Posted 23 Jan 2019
bioRxiv DOI: 10.1101/528067 (published DOI: 10.1017/S0033291719002526)

Background: Major Depressive Disorder (MDD) is a clinically heterogeneous disorder. Previous large-scale genetic studies of MDD have explored genetic risk factors of MDD case-control status or aggregated sums of depressive symptoms, ignoring possible clinical or genetic heterogeneity. Aim: In this study, we present the results of symptom-level genetic analyses and compare SNP-based heritability (h2 SNP) and genetic correlations across major depression symptoms. We further investigate genetic correlations with a range of psychiatric disorders and other associated traits. Methods: We have analysed data from the UK biobank and included 148,752 subjects of White British ancestry with genotype data who completed nine items of a self-rated measure of depression: the Patient Health Questionnaire (PHQ-9). Genome-Wide Association analyses were conducted for nine symptoms and two composite measures. LD score regression analysis was used to calculate SNP-based heritability (h2 SNP) and genetic correlations (rg) across symptoms and to investigate genetic correlations with 25 external phenotypes. Confirmatory factor analyses were applied to test whether one, two, or three-factor models best fit the pattern of genetic correlations across the nine symptoms. Results: We identified 9 novel genome-wide significant genomic loci, with no overlap in loci across depression symptoms. h2 SNP ranged from 3% (suicidal ideation) to 11% (fatigue). Genetic correlations range from 0.54 to 0.96 (all p < 1.39e-3) with 30 of 36 correlations being significantly smaller than 1. A 3-factor model provided the best fit to the genetic correlation matrix, with factors representing psychological, neurovegetative, and psychomotor / concentration symptoms. The genetic correlations with external phenotypes showed large variation across the nine symptoms. Discussion: Patterns of h2 SNP and genetic correlations differed across the nine symptoms of depression. Our findings suggest that the large phenotypic heterogeneity observed for MDD is recapitulated at a genetic level. Future studies should investigate how genetic heterogeneity in MDD influences the efficacy of clinical interventions.

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