Schizophrenia Research Forum - A Catalyst for Creative Thinking

Need AC, Ge D, Weale ME, Maia J, Feng S, Heinzen EL, Shianna KV, Yoon W, Kasperaviciute D, Gennarelli M, Strittmatter WJ, Bonvicini C, Rossi G, Jayathilake K, Cola PA, McEvoy JP, Keefe RS, Fisher EM, St Jean PL, Giegling I, Hartmann AM, Möller HJ, Ruppert A, Fraser G, Crombie C, Middleton LT, St Clair D, Roses AD, Muglia P, Francks C, Rujescu D, Meltzer HY, Goldstein DB. A genome-wide investigation of SNPs and CNVs in schizophrenia. PLoS Genet. 2009 Feb 1 ; 5(2):e1000373. Pubmed Abstract

Comments on News and Primary Papers
Comment by:  David J. Porteous, SRF Advisor
Submitted 11 February 2009
Posted 12 February 2009

The answer is unequivocally, “yes”
In co-highlighting the papers from Need et al., 2009, and Tomppo et al., 2009, you pose the question “CNV’s, interacting loci or both?” to which my immediate answer is an unequivocal “yes,” but it actually goes further than that. These two studies, interesting in their own rights, add just two more pieces of evidence now accumulated from case only, case-control, and family-based linkage on the genetic architecture of schizophrenia. Thus, we can reject with confidence a single evolutionary and genetic origin for schizophrenia. If it were so, it would have been found already by the plethora of genomewide studies now completed, studies specifically designed to detect causal variants, should they exist, which are both common to most if not all subjects and ancient in origin—the Common Disease, Common Variant (CDCV) hypothesis.

Moreover, for DISC1, NRG1, NRXN1, and a few others, the criteria for causality are met in some subjects, but none of these is the sole cause of schizophrenia. Their net contributions to individual and population risk remain uncertain and await large scale resequencing as well as SNP and CNV studies to capture the totality of genetic variation and how that contributes to the incidence of major mental illness. Meanwhile, nosological and epidemiological evidence has also forced a re-evaluation of the categorical distinction between schizophrenia and bipolar disorder, let alone schizoaffective disorder (Lichtenstein et al., 2009).

In this regard, DISC1 serves again as an instructive paradigm, with good evidence for genetic association to schizophrenia, BP, schizoaffective disorder, and beyond (Chubb et al., 2008). The study by Hennah et al. (2008) added a further nuance to the DISC1 story by demonstrating intra-allelic interaction. Tomppo et al. (2009) now build upon their earlier evidence to show that DISC1 variants affect subcomponents of the psychiatric phenotype, treated now as a quantitative than a dichotomous trait. In much the same way and just as would be predicted, DISC1 variation also contributes to normal variation in human brain development and behavior (e.g., Callicott et al., 2005). Self-evidently, different classes of genetic variants (SNP or CNV, regulatory or coding) will have different biological and therefore psychiatric consequences (Porteous, 2008).

That Need et al. (2009) failed to replicate previous genomewide association studies (or find support for DISC1, NRG1, and the rest) is just further proof, if any were needed, that there is extensive genetic heterogeneity and that common variants of ancient origin are not major determinants of individual or population risk (Porteous, 2008). Variable penetrance, expressivity, and gene-gene interaction (epistasis) all need to be considered, but these intrinsic aspects of genetic influence are best addressed by family studies (currently lacking for CNV studies) and poorly addressed by large-scale case-control genomewide association studies. Power to test the CDCV hypothesis may increase with increasing numbers of subjects, but so does the inherent heterogeneity, both genetic and diagnostic.

That said, genetics is without doubt the most incisive tool we have to dissect the etiology of major mental illness. The criteria for success (and certainly for causality, rather than mere correlation) must be less about the number of noughts after the “p” and much more about the connection between candidate gene, gene variant, and the biological consequences for brain development and function. In this regard, both studies have something to say and offer.


Lichtenstein P, Yip BH, Björk C, Pawitan Y, Cannon TD, Sullivan PF, Hultman CM. Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study. 2009 Lancet 373:234-9. Abstract

Chubb JE, Bradshaw NJ, Soares DC, Porteous DJ, Millar JK. Mol Psychiatry. The DISC locus in psychiatric illness. 2008 Jan;13(1):36-64. Epub 2007 Oct 2. Abstract

Callicott JH, Straub RE, Pezawas L, Egan MF, Mattay VS, Hariri AR, Verchinski BA,Meyer-Lindenberg A, Balkissoon R, Kolachana B, Goldberg TE, Weinberger DR. Variation in DISC1 affects hippocampal structure and function and increases risk for schizophrenia. 2005 Proc Natl Acad Sci U S A. 2005 102:8627-32. Abstract

Porteous D. Genetic causality in schizophrenia and bipolar disorder: out with the old and in with the new. 2008 Curr Opin Genet Dev. 18:229-34. Abstract

View all comments by David J. PorteousComment by:  Pamela DeRosseAnil Malhotra (SRF Advisor)
Submitted 19 February 2009
Posted 22 February 2009

The results reported by Tomppo et al. and Need et al. collectively instantiate the complexities of the genetic architecture underlying risk for psychiatric illness. Paradoxically, however, while the results of Need et al. suggest that the answer to the complex question of risk genes for schizophrenia (SZ) may be found by searching a very select population for rare changes in genetic sequence, the results of Tomppo et al. suggest that the answer may be found by searching for common variants in large heterogeneous populations. So which is it? Is SZ the result of rare, novel genetic mutations or an accumulation of common ones? Such a conundrum is not a novel predicament in the process of scientific inquiry and such conundrums are often resolved by the reconciliation of both opposing views. Thus, if we allow history to serve as our guide it seems reasonable that the answer to the current question of what genetic mechanisms are responsible for SZ, is that SZ is caused by both rare and common variants.

Although considerable efforts, by our lab and others, are currently being directed towards seeking the type of rare variants that Need et al. suggest may be responsible for risk for SZ, a less concerted effort is being directed towards parsing the effects of more specific, common genetic variations. To date, there are limited data seeking to elucidate the effects of previously identified risk variants for SZ on phenotypic variation within the diagnostic group. The data that are available, however, suggest that risk variants do influence phenotypic variation. Our work with DISC1, for example, has produced relatively robust, and replicated findings linking variation in the gene to cognitive dysfunction (Burdick et al., 2005) as well as an increased risk for persecutory delusions in SZ (DeRosse et al., 2007). Similarly, our work with DTNBP1 indicates a strong association between variants in the gene and both cognitive dysfunction (Burdick et al., 2006) and negative symptoms in SZ (DeRosse et al., 2006). Moreover, the risk for cognitive dysfunction associated with the DTNBP1 risk genotype was also observed in a sample of healthy individuals. Thus, it seems conceivable that genetic variation associated with phenotypic variation within a diagnostic group may also be associated with similar, sub-syndromal phenotypes in non-clinical samples.

The data reported by Tomppo et al. provide support for the utility of parsing the specific effects of genetic variants on phenotypic variation and extend this approach to populations with sub-syndromal psychiatric symptoms. Such an approach is attractive in that it allows us to study the effects of genotype on phenotype without the confound imposed by psychotropic medications. Although the current data linking genes to specific dimensions of psychiatric illness are provocative, the study groups utilized are comprised of patients undergoing varying degrees of pharmacological intervention. Thus, in these analyses quantitative assessment of psychosis is to some extent confounded by treatment history and response. By measuring lifetime history of symptoms, which for most patients includes substantial periods without effective medication, many studies (including our own) may partially overcome this limitation. Still, assessment of the relation between genetic variation and dimensions of psychosis in study groups not undergoing treatment with pharmacological agents would be a compelling source of confirmation for these preliminary findings.

Perhaps most importantly, the data reported by Tomppo et al. suggest that previously identified risk genes should not be marginalized but rather, should be studied in non-clinical samples to identity phenotypic variation that may be related to the signs and symptoms of psychiatric illness.


Burdick KE, Hodgkinson CA, Szeszko PR, Lencz T, Ekholm JM, Kane JM, Goldman D, Malhotra AK. DISC1 and neurocognitive function in schizophrenia. Neuroreport. 2005; 16(12):1399-402. Abstract

Burdick KE, Lencz T, Funke B, Finn CT, Szeszko PR, Kane JM, Kucherlapati R, Malhotra AK. Genetic variation in DTNBP1 influences general cognitive ability. Hum Mol Genet. 2006; 15(10):1563-8. Abstract

DeRosse P, Hodgkinson CA, Lencz T, Burdick KE, Kane JM, Goldman D, Malhotra AK. Disrupted in schizophrenia 1 genotype and positive symptoms in schizophrenia. Biol Psychiatry. 2007; 61(10):1208-10. Abstract

DeRosse P, Funke B, Burdick KE, Lencz T, Ekholm JM, Kane JM, Kucherlapati R, Malhotra AK. Dysbindin genotype and negative symptoms in schizophrenia. Am J Psychiatry. 2006; 163(3):532-4. Abstract

View all comments by Pamela DeRosse
View all comments by Anil MalhotraComment by:  James L. Kennedy, SRF Advisor (Disclosure)
Submitted 25 February 2009
Posted 25 February 2009

Has anyone considered the possibility that the CNVs found to be elevated in schizophrenia versus controls could be a peripheral effect and perhaps not present in brain tissue? For example, the diet of the typical schizophrenia patient is poor, and it is conceivable that chronic folate deficiency could predispose to problems in DNA structure or repair in lymphocytes. Thus, the CNVs could be an effect of the illness, and not a cause. Someone needs to do the experiment that compares CNVs in blood to those in the brain of the same individual. And then we need studies of the stability of CNVs over the lifetime of an individual.

View all comments by James L. KennedyComment by:  Kevin J. Mitchell
Submitted 2 March 2009
Posted 2 March 2009

The papers by Need et al. and Tomppo et al. seem to present conflicting evidence for the involvement of common or rare variants in the etiology of schizophrenia.

On the one hand, Need et al., in a very large and well-powered sample, find no evidence for involvement of any common SNPs or CNVs. Importantly, they show that while any one SNP with a small effect and modest allelic frequency might be missed by their analysis, the likelihood that all such putative SNPs would be missed is vanishingly small. They come to the reasonable conclusion that common variants are unlikely to play a major role in the etiology of schizophrenia, except under a highly specific and implausible genetic model. Does this sound the death knell for the common variants, polygenic model of schizophrenia? Yes and no. These and other empirical data are consistent with theoretical analyses which show that the currently popular purely polygenic model, without some gene(s) of large effect, cannot explain familial risk patterns (Hemminki et al., 2007; Hemminki et al., 2008; Bodmer and Bonilla, 2008). It has been suggested that epistatic interactions may generate discontinuous risk from a continuous distribution of common alleles; however, while comparisons of risk in monozygotic and dizygotic twins are consistent with some contribution from epistasis, they are not consistent with the massive levels that would be required to rescue a purely polygenic mechanism, whether through a multiplicative or (biologically unrealistic) threshold model.

Thus, it seems most parsimonious to conclude that most cases of schizophrenia will involve a variant of large effect. As such variants are likely to be rapidly selected against, they are also likely to be quite rare. The findings of specific, gene-disrupting CNVs or mutations in individual genes in schizophrenia cases by Need et al. and numerous other groups support this idea. Excitingly, they also have highlighted specific molecules and biological pathways that provide molecular entry points to elucidate pathogenic mechanisms. The possible convergence on genes interacting with DISC1, including PCM1 and NDE1 in the current study, provides further support for the importance of this pathway, though, clearly, there may be many other ways to disrupt neural development or function that could lead to schizophrenia. (Conversely, it is becoming clearer that many of the putative causative mutations identified so far predispose to multiple psychiatric or neurological conditions.)

Despite the likely involvement of rare variants in most cases of schizophrenia, it remains possible that common alleles could have a modifying influence on risk—indeed, one early paper commonly cited as supporting a polygenic model for schizophrenia actually provided strong support for a model of a single gene of large effect and two to three modifiers (Risch, 1990). A rare variants/common modifiers model would be consistent with the body of literature on modifying genes in model organisms, where effects of genetic background on the phenotypic expression of particular mutations are quite common and can sometimes be large (Nadeau, 2001). Whether such genetic background effects would be mediated by common or rare variants is another question—there is certainly good reason to think that rare or even private mutations may make a larger contribution to phenotypic variance than previously suspected (Ng et al., 2008; Ji et al., 2008).

Nevertheless, common variants are also likely to be involved, and these effects might be detectable in large association studies, though they would be expected to be diluted across genotypes. This might explain inconsistent findings of association of common variants with disease state for various genes, including COMT, BDNF, and DISC1, for example. This issue has led some to look for association of variants in these genes with endophenotypes of schizophrenia in the general population—psychological or physiological traits that are heritable and affected by the symptoms of the disease, such as working memory, executive function, or, in the study by Tomppo et al., social interaction.

These approaches have tended to lead to statistically stronger and more consistent associations and are undoubtedly revealing genes and mechanisms contributing to normal variation in many psychological traits. How this relates to their potential involvement in disease etiology is far from clear, however. The implication of the endophenotype model is that the disorder itself emerges due to the combination of minor effects on multiple symptom parameters (Gottesman and Gould, 2003; Meyer-Lindenberg and Weinberger, 2006). An alternative interpretation is that these common variants may modify the phenotypic expression of some other rare variant, either due to their demonstrated effect on the psychological trait in question or through a more fundamental biochemical interaction, but that in the absence of such a variant of large effect, no combination of common alleles would lead to disease.


Hemminki K, Försti A, Bermejo JL. The 'common disease-common variant' hypothesis and familial risks. PLoS ONE. 2008 Jun 18;3(6):e2504. Abstract

Hemminki K, Bermejo JL. Constraints for genetic association studies imposed by attributable fraction and familial risk. Carcinogenesis. 2007 Mar;28(3):648-56. Abstract

Bodmer W, Bonilla C. Common and rare variants in multifactorial susceptibility to common diseases. Nat Genet. 2008 Jun;40(6):695-701. Abstract

Risch N. Linkage strategies for genetically complex traits. I. Multilocus models. Am J Hum Genet. 1990 Feb;46(2):222-8. Abstract

Nadeau JH. Modifier genes in mice and humans. Nat Rev Genet. 2001 Mar;2(3):165-74. Abstract

Ng PC, Levy S, Huang J, Stockwell TB, Walenz BP, Li K, Axelrod N, Busam DA, Strausberg RL, Venter JC. Genetic variation in an individual human exome. PLoS Genet. 2008 Aug 15;4(8):e1000160. Abstract

Ji W, Foo JN, O'Roak BJ, Zhao H, Larson MG, Simon DB, Newton-Cheh C, State MW, Levy D, Lifton RP. Rare independent mutations in renal salt handling genes contribute to blood pressure variation. Nat Genet. 2008 May;40(5):592-9. Abstract

Gottesman II, Gould TD. The endophenotype concept in psychiatry: etymology and strategic intentions. Am J Psychiatry. 2003 Apr;160(4):636-45. Abstract

Meyer-Lindenberg A, Weinberger DR. Intermediate phenotypes and genetic mechanisms of psychiatric disorders. Nat Rev Neurosci. 2006 Oct;7(10):818-27. Abstract

View all comments by Kevin J. Mitchell