This is the author accepted manuscript. It is currently under an indefinite embargo pending publication by NPG. ; Affective disorders are highly heritable but few genetic risk variants have been consistently replicated in molecular genetic association studies. The common method of defining psychiatric phenotypes in molecular genetic research is either a summation of symptom scores or binary threshold score representing risk of diagnosis. Psychometric latent variable methods can improve the precision of psychiatric phenotypes, especially when the data structure is not straightforward. Using data from the British 1946 birth cohort, we compared summary scores with psychometric modelling based on the General Health Questionnaire (GHQ-28) scale for affective symptoms in an association analysis of 27 candidate genes (249 SNPs). The psychometric method utilized a bi-factor model that partitioned the phenotype variances into five orthogonal latent variable factors, in accordance with the multidimensional data structure of the GHQ-28 involving somatic, social, anxiety and depression domains. Results showed that, compared with the summation approach, the affective symptoms defined by the bi-factor psychometric model had a higher number of associated SNPs of larger effect sizes. These results suggest that psychometrically-defined mental health phenotypes can reflect the dimensions of complex phenotypes better than summation scores, and therefore offer a useful approach in genetic association investigations. ; This work was supported by the Wellcome Trust [088869/Z/09/Z to M.R., P.B.J., D.G, and T. J. C,]; Medical Research Council [MC_UU_12019/1 and MC_UU_12019/3 to A.W, D.G., M.R]. Dr. Barnett is an employee of Cambridge Cognition, Ltd. This work forms part of the NIHR CLAHRC EoE that PBJ directs and the NIHR Cambridge Biomedical Research Centre.