Unlike approaches that assume homogeneity of effects across SNPs,11 Genomic SEM includes diagnostic indices for its key assumptions, including a test for heterogeneity, QSNP, that can be applied at the level of the individual SNPs. This offers the unique ability to identify SNPs that confer specific risk to individual phenotypes. This question may be of particular interest as the large degrees of genetic overlap identified across phenotypes (e.g., bipolar disorder and schizophrenia) beg the question: what are the genetic causes of phenotypic divergence? Whereas previous GWASs have combined items tapping genetically-related phenotypes into a single score, or even combined cases with different diagnoses to obtain a shared genetic effect, Genomic SEM allows researchers to interrogate shared genetic effects between diagnoses or indicators, while concurrently testing for causes of divergence (i.e., loci that are related only to a specific phenotype, or subset of phenotypes, but not the more general liability). In the context of neuroticism, for example, we identified 69 loci that were significantly involved in one manifestation of neuroticism but whose effects were not shared through a common factor, offering
