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Minimal phenotyping yields GWAS hits of low specificity for major depression
Joana A. Revez,
Mark James Adams,
Enda M. Byrne,
Hans J J Grabe,
Steven P Hamilton,
Douglas F. Levinson,
Cathryn M Lewis,
Nicholas G Martin,
Brenda W.J.H. Penninx,
Roy H Perlis,
James B. Potash,
Sandra Van der Auwera,
Myrna M. Weissman,
MDD Working Group of the Psychiatric Genomics Consortium,
Kenneth S. Kendler,
Posted 11 Oct 2018
bioRxiv DOI: 10.1101/440735
Posted 11 Oct 2018
Minimal phenotyping refers to the reliance on self-reported responses to one or two questions for disease case identification. This strategy has been applied to genome-wide association studies (GWAS) of major depressive disorder (MDD). Here we report that the genotype derived heritability (h2SNP) of depression defined by minimal phenotyping (14%, SE = 0.8%) is lower than strictly defined MDD (26%, SE = 2.2%), and that it shares as much genetic liability with strictly defined MDD (0.81, SE = 0.03) as it does with neuroticism (0.84, SE = 0.05), a trait not defined by the cardinal symptoms of depression. While they both show similar shared genetic liability with the personality trait neuroticism, a greater proportion of the genome contribute to the minimal phenotyping definitions of depression (80.2%, SE = 0.6%) than to strictly defined MDD (65.8%, SE = 0.6%). We find that GWAS loci identified in minimal phenotyping definitions of depression are not specific to MDD: they also predispose to other psychiatric conditions. Finally, genetic predictors based on minimal phenotyping definitions are not predictive of strictly defined MDD in independent cohorts. Our results reveal that genetic analysis of minimal phenotyping definitions of depression identifies non-specific genetic factors shared between MDD and other psychiatric conditions. Reliance on results from minimal phenotyping for MDD may thus bias views of the genetic architecture of MDD and impedes ability to identify pathways specific to MDD.
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