Comment by:  Daniel Weinberger (SRF Advisor)
Submitted 3 July 2009
Posted 3 July 2009

The three Nature papers reporting GWAS results in a large sample of cases of schizophrenia and controls from around Western Europe and the U.S. are decidedly disappointing to those expecting this strategy to yield conclusive evidence of common variants predicting risk for schizophrenia. Why has this extensive and very costly effort not produced more impressive results? There are likely to be many explanations for this, involving the usual refrains about clinical and genetic heterogeneity, diagnostic imprecision, and technical limitations in the SNP chips. But the likely, more fundamental problem in psychiatric genetics involves the biologic complexity of the conditions themselves, which renders them especially poorly suited to the standard GWAS strategy. The GWA analytic model assumes fixed, predictable relationships between genetic risk and illness, but simple relationships between genetic risk and complex pathophysiological mechanisms are unlikely. Many biologic functions show non-linear relationships, and depending on the biologic context, more of a potential pathogenic [...continued] factor, can make things worse or it can make them better. Studies of complex phenotypes in model systems illustrate that individual gene effects depend upon non-linear interactions with other genes (Toma et al., 2002; Shaoa et al, 2008). Similar observations are beginning to emerge in human disorders, e.g., in risk for cancer (Lo et al., 2008) and depression (Pezawas et al., 2008).

The GWA approach also assumes that diagnosis represents a unitary biological entity, but most clinical diagnoses are syndromal and biologically heterogeneous, and this is especially true in psychiatric disorders. Type 2 diabetes is the clinical expression of changes in multiple physiologic processes, including in pancreatic function, in adipose cell function, as well as in eating behavior. Likewise, hypertension results from abnormalities in many biologic processes (e.g., vascular reactivity, kidney function, CNS control of blood pressure, metabolic factors, sodium regulation), and even a large effect on any specific process within a subset of individuals will seem small when measured in large unrelated samples (Newton-Cheh et al., 2009). In the case of the cognitive and emotional problems associated with psychiatric disorders, the biologic pathways to clinical manifestations are probably much more heterogeneous. While the results of GWAS in disorders like type 2 diabetes and hypertension have been more informative than in the schizophrenia results so far, they, too, have been disappointing, considering all the fanfare about their expectations. But given the pathophysiologic realities of diabetes, hypertension, or psychiatric disorders, how could the effect of any common genetic variant acting on only one of the diverse pathophysiological mechanisms implicated in these disorders be anything other than small when measured in large pathophysiologically heterogeneous populations? Other approaches, e.g., family studies, studies of smaller but much better characterized samples, and studies of genetic interactions in these samples, will be necessary to understand the variable genetic architectures of such biologically complex and heterogeneous disorders.


Toma DP, White KP, Hirsch J and Greenspan RJ: Identification of genes involved in Drosophila melanogaster geotaxis, a complex behavioral trait. Nature Genetics 2002; 31: 349-353. Abstract

Shaoa H, Burragea LC, Sinasac DS et al : Genetic architecture of complex traits: Large phenotypic effects and pervasive epistasis. PNAS 2008 105: 1991019914. Abstract

Lo S-W, Chernoff H, Cong L, Ding Y, and Zheng T: Discovering interactions among BRCA1 and other candidate genes associated with sporadic breast cancer. PNAS 2008; 105: 1238712392. Abstract

Pezawas L, Meyer-Lindenberg A, Goldman AL, et al.: Biologic epistasis between BDNF and SLC6A4 and implications for depression. Mol Psychiatry 2008;13:709-716. Abstract

Newton-Cheh C, Larson MG, Vasan RS: Association of common variants in NPPA and NPPB with circulating natriuretic peptides and blood pressure. Nat Gen 2009; 41: 348-353. Abstract