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More Evidence for CNVs in Schizophrenia Etiology—Jury Still Out on Practical Implications

31 July 2008. Three large, independent studies aimed at understanding the genetic causes of schizophrenia were published online in Nature journals on July 30—two studies looking at rare genetic deletions or duplications implicate the same two novel chromosomal locations in the disease, while a third study parsing the contribution of common genetic variants comes up with one new candidate risk gene. The studies, which together involve thousands of people with and without schizophrenia, are likely to stimulate much news coverage in the media, and debate within the research community about just what the results mean, and where to go from here.

The two studies of rare copy number variations (CNVs) appear back to back in Nature, where one reports that the number of rare deletions or duplications leading to aberrant gene copy number is increased modestly in patients with schizophrenia. Both studies identify the same two chromosomal regions (1q21.1, 15q13.3) where copy number variation is associated with the risk of schizophrenia. The third study, based on a genome-wide association study, finds that variants in a putative gene regulator may play a role in schizophrenia and bipolar disorder.

The additions and subtractions multiply
The risk for schizophrenia is widely believed to have a large genetic component, and the prevailing theory of genetic causation is that common variants of multiple susceptibility genes each have small effects that couple with environmental influences to cause the disease. However, that view is being challenged by researchers who are studying small deletions or amplifications of parts of chromosomes that cause changes in gene copy number. CNVs were recently recognized as a major source of genetic variation among people (see SRF related news story), and have been linked to autism (see SRF related news story). Recent studies suggest a link between CNVs and schizophrenia: people with schizophrenia are reported to have elevated incidence of CNVs (see SRF related news story), including CNVs that are not inherited but have originated in the individuals (de novo CNVs; see SRF related news story).

While previous studies looked at relatively few subjects, the two studies published today use much larger sample sizes to identify rare CNVs and then to measure their impact on the risk of schizophrenia. One study, from the International Schizophrenia Consortium (ISC), looked at the genome-wide occurrence of rare CNVs in 3,391 patients and 3,181 controls, and the association of specific CNVs with disease. The researchers, a large group from Europe, North America, and Australia, were managed by corresponding author Pamela Sklar and colleagues at the Broad Institute of Harvard and MIT in Cambridge, Massachusetts. The investigators report first of all that people with schizophrenia had more rare deletions and insertions (defined as present in less than 1 percent of people and more than 100 kilobases long) than the control population, and that the CNVs involved more genes. Control subjects had an average of 0.99 CNV per person. In people with schizophrenia, the number of CNVs was increased 15 percent, a difference that was “subtle but highly statistically significant,” according to the authors. The number of affected genes was 1.41 times higher in the disease group than in healthy controls. When the researchers looked only at CNVs that were seen only once in the sample, or were larger than 100 kilobases, or disrupted at least one known gene, all of those categories showed even stronger evidence of increased occurrence in schizophrenia. These data would appear to support and extend the recent findings of Walsh et al., 2008 and SRF related news story cited above) in a far larger sample. The authors write, “The etiology of schizophrenia has been vigorously debated. We now have strong and replicated evidence that individuals with schizophrenia have a greater burden of structural variation across their genomes.”

Because of the sample size, the investigators were able to test specific CNV regions for association with the disease. As expected, they found deletions at 22q11.2 (the region involved in velo-cardio-facial syndrome and previously associated with schizophrenia) in 13 cases but no controls. There were two additional regions where patients showed significantly more CNVs than controls. Chromosome 15q13.3 showed up in nine cases and no controls, while 1q21.1 was seen in 10 cases and one control. The 1q21.1 region, which contains 27 known genes, has been previously linked to schizophrenia (Brzustowics et al., 2000; Gurling et al., 2001), while 15q13.3 has not. That region, however, recently turned up in relation to a syndrome of mental retardation with seizures (Sharp et al., 2008). A schizophrenia candidate gene also lies in this region. CHRNA7 encodes the a7 subunit of the nicotinic acetylcholine receptor, and has been linked to the schizophrenia-associated phenotype of auditory evoked potential deficits (Freedman et al., 1997; Xu et al., 2001).

There are other CNVs that were found only in the schizophrenia subjects, and of these the authors write, “At least some of these rare CNVs seen in cases but not in controls are probably risk factors for schizophrenia, although like Walsh et al., we are unable to identify which.” An important future direction will be to characterize clinically and phenotypically deletion carriers with an eye to establishing a biologically plausible link to the affected genes.

The second study, another worldwide collaborative effort, by the SGENE consortium, was led by senior author Kari Stefansson of deCODE Genetics, Reykjavik, Iceland. The trio of first authors were Hreinn Stefansson, also of deCODE, Dan Rujescu of Ludwig-Maximilians-University, Munich, Germany, and Sven Cichon of University of Bonn, also in Germany. Their working hypothesis was that the reduced reproductive success associated with severe mental disorders puts negative selective pressure on risk alleles, so that genes conferring considerable risk will be quite rare. By this reasoning, rare variants may contribute a larger percentage of risk for schizophrenia than assumed, but are accordingly harder to find. As the researchers themselves allow, it is very difficult to screen for rare nucleotide changes, but somewhat easier to look for CNVs. To look for rare large and recurrent CNVs that seemed to be under negative selective pressure, the group carried out a genome-wide search for de novo CNVs in a group of unaffected people made up of 2,160 trios of two parents and one child, plus 5,558 parent-child pairs. They identified 66 de novo CNVs, which they then examined in nearly 5,000 people with schizophrenia.

For eight of the 66 CNVs tested, at least one schizophrenia patient carried the CNV, and for three large deletions, nominal association with schizophrenia and related psychoses was detected. The three deletions nominally associating with schizophrenia in the first sample were followed up in up to six samples comprising a total of 3,285 cases and 7,951 controls. All three deletions, at 1q21.1, 15q11.2, and 15q13.3, significantly associate with schizophrenia and psychosis in the combined sample with high odds ratio (OR) (OR = 14.83, OR = 2.73, and OR = 11.54, respectively).

The results implicated the same two regions as the ISC study, with deletions at 1q21.1 detected in 11 out of 4,718 cases (0.23 percent) compared to eight of 4,119 controls (0.02 percent). Chromosome 15q13.3 was also significantly associated with schizophrenia and related psychoses in both studies. Only the SGENE study found an association with the 15q11.2 region. This part of the chromosome contains the CYFIP1 gene, which is interesting in that its deletion has been associated with Prader-Willi syndrome, which may present with perseverative behavior (lack of cognitive flexibility, also a feature of schizophrenia) and Angelman syndrome, which may present with autistic features.

The authors conclude, “The identification of these rare, recurrent risk variants, having occurred independently in multiple founders and being subject to negative selection, is important in itself. CNV analysis may also point the way to identification of additional and more prevalent risk variants in genes and pathways involved in schizophrenia.”

Don’t forget SNP associations
The new studies might indicate to some that the search for common variations with modest risk profiles has given way to the hunt for rare but catastrophic genetic changes. However, a third report, published today’s in Nature Genetics, suggests it is too early to give up the search for common genetic variants that contribute to schizophrenia. In that work, Michael O’Donovan and Michael Owen at Cardiff University, United Kingdom, and collaborators argue that studies on genome-wide associations of using single nucleotide polymorphism data (SNPs) have successfully identified genes with very small effects on other diseases, similar to what is expected for schizophrenia. They described a genome-wide association study using a multi-step approach and a total of more than 6,286 cases and 12,993 controls. Their initial analysis included 479 cases compared to 2,937 controls, genotyped at 362,532 single nucleotide polymorphisms (SNPs). They chose 12 SNPs with moderately strong evidence for association for follow-up in another set of 1,664 cases and 3,541 controls, which replicated six of the 12 SNPs. A second replication set of 4,143 cases and 6,515 controls supported the significance of the ZNF804A gene in 2q32.1 as a schizophrenia susceptibility variant, and also pinpointed two intergenic regions at 11p14.1 and 16p13.12.

In a secondary analysis, they added additional samples from people with bipolar disorder, and found the ZNF804A association was strengthened, suggesting that variants of the gene could be linked to a broader psychosis phenotype (see SRF live discussion). The protein encoded by the gene is uncharacterized, and while its function is unknown, it bears some resemblance to a possible transcription factor.

“Our study demonstrates that despite the lack of biological validating criteria for diagnosis, schizophrenia is amenable to the same genetic approaches as other common disorders, and like most other disorders, the effect sizes are small,” the authors conclude. “Our findings strongly suggest that further GWA analysis of larger samples will identify many additional specific genetic risk factors with the potential to shed light into the pathophysiology of one of the most enigmatic major causes of human morbidity. Collection and analysis of large enough samples to provide convincing association signals should now be a priority,” they write.—Pat McCaffrey.

References:
The International Schizophrenia Consortium. Rare chromosomal deletions and duplications increase risk of schizophrenia. Nature. 2008 July 30, Advance online publication. Abstract

Stefansson H., Rujescu D., Cichon S. et al. Large recurrent microdeletions associated with schizophrenia. Nature. 2008 July 30, Advance online publication. Abstract

O’Donovan MC. et al. Identification of loci associated with schizophrenia by genome-wide association and follow-up. Nature Genet. 2008 July 30, Advance online publication. Abstract

Comments on News and Primary Papers
Comment by:  Christopher RossRussell L. Margolis
Submitted 1 August 2008
Posted 1 August 2008

The two recent papers in Nature, from the Icelandic group (Stefansson et al., 2008), and the International Schizophrenia Consortium (2008) led by Pamela Sklar, represent a landmark in psychiatric genetics. For the first time two large studies have yielded highly significant consistent results using multiple population samples. Furthermore, they arrived at these results using quite different methods. The Icelandic group used transmission screening and focused on de novo events, using the Illumina platform in both a discovery population and a replication population. By contrast, the ISC study was a large population-based case-control study using the Affymetrix platform, which did not specifically search for de novo events.

Both identified the same two regions on chromosome 1 and chromosome 15, as well as replicating the previously well studied VCFS region on chromosome 22. Thus, we now have three copy number variants which are replicated and consistent across studies. This provides data on rare highly penetrant variants complementary to the family based study of DISC1 (Porteous et al., 2006), in which the chromosomal translocation clearly segregates with disease, but in only one family. In addition, they are in general congruent with three other studies (Walsh et al., 2008; Kirov et al., 2008; Xu et al., 2008) which also demonstrate a role for copy number variation in schizophrenia. These studies together should put to rest many of the arguments about the value of genetics in psychiatry, so that future studies can now begin from a firmer base.

However, these studies also raise at least as many questions as they answer. One is the role of copy number variation in schizophrenia in the general population. The number of cases accounted for by the deletions on chromosome 1 and 15 in the ISC and Icelandic studies is extremely small--on the order of 1% or less. The extent to which copy number variation, including very rare or even private de novo variants, will account for the genetic risk for schizophrenia in the general population is still unknown. The ISC study indicated that there is a higher overall load of copy number variations in schizophrenia, broadly consistent with Walsh et al and Xu et al but backed up by a much larger sample size, allowing the results to achieve high statistical significance. The implications of these findings are still undeveloped,

Another issue is the relationship to the phenotype of schizophrenia in the general population. Many more genotype-phenotype studies will need to be done. It will be important to determine whether there is a higher rate of mental retardation in the schizophrenia in these studies than in other populations.

Another question is the relationship between these copy number variations (and other rare events) and the more common variants accounting for smaller increases in risk, as in the recent O’Donovan et al. (2008) association study in Nature Genetics. It is far too early to know, but there may well be some combination of rare mutations plus risk alleles that account for cases in the general population. This would then be highly reminiscent of Alzheimer’s disease, Parkinson’s disease, and other diseases which have been studied for a longer period of time.

For instance, in Alzheimer’s disease there are rare mutations in APP and presenilin, as well as copy number variation in APP, with duplications causing the accelerated Alzheimer’s disease seen in Down syndrome. These appear to interact with the risk allele in APOE, and possibly other risk alleles, and are part of a pathogenic pathway (Tanzi and Bertram, 2005). Similarly in Parkinson’s disease, rare mutations in α-synuclein, LRRK2 and other genes can be causative of PD, though notably the G2019S mutation in LRRK2 has incomplete penetrance. In addition, duplications or triplications of α-synuclein can cause familial PD, and altered expression due to promoter variants may contribute to risk. By contrast, deletions in Parkin cause an early onset Parkinsonian syndrome (Hardy et al., 2006). Finally, much of PD may be due to genetic risk factors or environmental causes that have not yet been identified. Further studies will likely lead to the elucidation of pathogenic pathways. These diseases can provide a paradigm for the study of schizophrenia and other psychiatric diseases. One difference is that the copy number variations in the neurodegenerative diseases are often increases in copies (as in APP and α-synuclein), consistent with gain of function mechanisms, while the schizophrenia associations were predominantly with deletions, suggesting loss of function mechanisms. The hope is that as genes are identified, they can be linked together in pathways, leading to understanding of the neurobiology of schizophrenia (Ross et al., 2006).

The key unanswered questions, of course, are what genes or other functional domains are deleted at the chromosome 1, 15, and 22 loci, whether the deletions at these loci are sufficient in themselves to cause schizophrenia, and, if sufficient, the extent to which the deletions are penetrant. Both of the current studies identified deletions large enough to include several genes. The hope is that at least a subset of copy number variations (unlike SNP associations identified in schizophrenia to date) may be causative, making the identification of the relevant genes or other functional domains—at least in principle—more feasible.

Another tantalizing observation is that the copy number variations associated with schizophrenia were defined by flanking repeat regions. This raises the question of the extent to which undetected smaller insertions, deletions or other copy number variations related to other repetitive motifs, such as long tandem repeats, may also be associated with schizophrenia. Identification and testing of these loci may prove a fruitful approach to finding additional genetic risk factors for schizophrenia.

References:

Hardy J, Cai H, Cookson MR, Gwinn-Hardy K, Singleton A. Genetics of Parkinson's disease and parkinsonism. Ann Neurol. 2006 Oct;60(4):389-98. Abstract

Kirov G, Gumus D, Chen W, Norton N, Georgieva L, Sari M, O'Donovan MC, Erdogan F, Owen MJ, Ropers HH, Ullmann R. Comparative genome hybridization suggests a role for NRXN1 and APBA2 in schizophrenia. Hum Mol Genet . 2008 Feb 1 ; 17(3):458-65. Abstract

Porteous DJ, Thomson P, Brandon NJ, Millar JK. The genetics and biology of DISC1—an emerging role in psychosis and cognition. Biol Psychiatry. 2006 Jul 15;60(2):123-31. Abstract

Ross CA, Margolis RL, Reading SA, Pletnikov M, Coyle JT. Neurobiology of schizophrenia. Neuron. 2006 Oct 5;52(1):139-53. Abstract

Singleton A, Myers A, Hardy J. The law of mass action applied to neurodegenerative disease: a hypothesis concerning the etiology and pathogenesis of complex diseases. Hum Mol Genet. 2004 Apr 1;13 Spec No 1:R123-6. Abstract

Tanzi RE, Bertram L. Twenty years of the Alzheimer's disease amyloid hypothesis: a genetic perspective. Cell. 2005 Feb 25;120(4):545-55. Abstract

Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, Cooper GM, Nord AS, Kusenda M, Malhotra D, Bhandari A, Stray SM, Rippey CF, Roccanova P, Makarov V, Lakshmi B, Findling RL, Sikich L, Stromberg T, Merriman B, Gogtay N, Butler P, Eckstrand K, Noory L, Gochman P, Long R, Chen Z, Davis S, Baker C, Eichler EE, Meltzer PS, Nelson SF, Singleton AB, Lee MK, Rapoport JL, King MC, Sebat J. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science. 2008 Apr 25;320(5875):539-43. Abstract

Xu B, Roos JL, Levy S, van Rensburg EJ, Gogos JA, Karayiorgou M. Strong association of de novo copy number mutations with sporadic schizophrenia. Nat Genet. 2008 Jul;40(7):880-5. Abstract

View all comments by Christopher Ross
View all comments by Russell L. MargolisComment by:  Daniel Weinberger, SRF Advisor
Submitted 3 August 2008
Posted 3 August 2008

Several recent reports have suggested that rare CNVs may be highly penetrant genetic factors in the pathogenesis of schizophrenia, perhaps even singular etiologic events in those cases of schizophrenia who have them. This is potentially of enormous importance, as the definitive identification of such a “causative” factor may be a major step in unraveling the biologic mystery of the condition. I would stress several issues that need to be considered in putting these recent findings into a broader perspective.

It is very difficult to attribute illness to a private CNV, i.e., one found only in a single individual. This point has been potently illustrated by a study of clinically discordant MZ twins who share CNVs (Bruder et al., AJHG, 2008). Inherited CNVs, such as those that made up almost all of the CNVs described in the childhood onset cases of the study by Walsh et al. (Science, 2008), are by definition not highly penetrant (since they are inherited from unaffected parents). The finding by Xu et al. (Nat Gen, 2008) that de novo (i.e., non-inherited) CNVs are much more likely to be associated with cases lacking a family history is provocative but difficult to interpret as no data are given about the size of the families having a family history and those not having such a history. Unless these family samples are of comparable size and obtained by a comparable ascertainment strategy, it is hard to know how conclusive the finding is. Indeed, in the study of Walsh et al., rare CNVs were just as likely to be found in patients with a positive family history. Finally, in contrast to private CNVs, recurrent (but still rare) CNVs, such as those identified on 1q and 15q in the studies of the International Schizophrenia Consortium (Nature, 2008) and Stefansson et al. (Nature, 2008), are strongly implicated as being associated with the diagnosis of schizophrenia and therefore likely involved in the causation of the illnesses in the cases having these CNVs. In all, these new CNV regions, combined with the VCFS region on 22q, suggest that approximately five to 10 patients out of 1,000 who carry the diagnosis of schizophrenia may have a well-defined genetic lesion (i.e., a substantial deletion or duplication).

The overarching question now is how relevant these findings are to the other 99 percent of individuals with this diagnosis who do not have these recurrent CNVs. Before we had the capability to perform high-density DNA hybridization and SNP array analyses, chromosomal anomalies associated with the diagnosis of schizophrenia were identified using cytogenetic techniques. Indeed, VCFS, XXX, XXY (Kleinfelter’s syndrome), and XO (Turner syndrome) have been found with similarly increased frequency in cases with this diagnosis in a number of studies. Now that we have greater resolution to identify smaller structural anomalies, the list of congenital syndromes that increase the possibility that people will manifest symptoms that earn them this diagnosis appears to be growing rapidly. Are we finding causes for the form of schizophrenia that most psychiatrists see in their offices, or are we instead carving out a new set of rare congenital syndromes that share some clinical characteristics, as syphilis was carved out from the diagnosis of schizophrenia at the turn of the twentieth century? Is schizophrenia a primary expression of these anomalies or a secondary manifestation? VCFS is associated with schizophrenia-like phenomena but even more often with mild mental retardation, autism spectrum, and other psychiatric manifestations. The same is true of the aneuploidies that increase the probability of manifesting schizophrenia symptoms. The two new papers in Nature allude to the possibility that epilepsy and intellectual limitations may also be associated with these CNVs. The diagnostic potential of any of these new findings cannot be determined until the full spectrum of their clinical manifestations is clarified.

One of the important insights that might emerge from identification of these new CNV syndromes is the identification of candidate genes that may show association with schizophrenia based on SNPs in these regions. VCFS has been an important source of promising candidate genes with broader clinical relevance (e.g., PRODH, COMT). Stefansson et al. report, however, that none of the 319 SNPs in the CNV regions showed significant association with schizophrenia in quite a large sample of individuals not having deletions in these regions. The Consortium report also presumably has the results of SNP association testing in these regions in their large sample but did not report them. It is very important to explore in greater genetic detail these regions of the genome showing association with the diagnosis of schizophrenia in samples lacking these lesions and to fully characterize the clinical picture of individuals who have them. It is hoped that insights into the pathogenesis of symptoms related to this diagnosis will emerge from these additional studies.

Anyone who has worked in a public state hospital or chronic schizophrenia care facility (where I spent over 20 years) is not surprised to find an occasional patient with a rare congenital or acquired syndrome who expresses symptoms similar to those individuals also diagnosed with schizophrenia who do not have such rare syndromes. Our diagnostic procedures are not precise, and the symptoms that earn someone this diagnosis are not specific. Schizophrenia is not something someone has; it is a diagnosis someone is given. In an earlier comment for SRF on structural variations in the genome related to autism, I suggested that, “From a genetic point of view, autism is a syndrome that can be reached from many directions, along many paths. It is not likely that autism is any more of a discrete disease entity than say, blindness or mental retardation.” These new CNV syndromes manifesting schizophrenia phenomena are probably a reminder that the same is true of what we call schizophrenia.

View all comments by Daniel Weinberger

Primary Papers: Identification of loci associated with schizophrenia by genome-wide association and follow-up.

Comment by:  Timothy Crow
Submitted 18 December 2008
Posted 18 December 2008

O’Donovan and colleagues have conducted an intensive genomewide association study designed to isolate genes predisposing to schizophrenia. They conclude that of 12 loci with P <10(-5) deviations from expectation, three had strong independent support (P <5 x 10[-4]) in two replication studies. They argue that the relevance of this pattern of genes was emphasized by a meta-analysis, including bipolar disorder with a P equal to 9.96 x 10(-9).

While a very considerable amount of work and analysis has gone into this whole-genome survey, and this is to be welcomed, other interpretations and findings deserve consideration:

1. Although this group refer to a previous summary of the literature (Craddock et al., 2005) in which they concluded that a basket of genes (neuregulin, dysbindin, DISC1, G72, DAO, and others) were established as relevant to schizophrenia, no support for these genes was forthcoming from this study. This negative finding deserves note.

2. The strategy that O’Donovan et al. have adopted requires that genes identified in Phase 1 be re-examined in the replication phases, and in this way those that are genuinely associated with disease are separated from those that are merely chance findings. Thus, the three genes that O’Donovan et al. select out should be distinct from those that they identify as chance findings.Table 1 (extracted from Table 2 of O’Donovan et al.) illustrates the problem.

Inspection of this table reveals that the odds ratios in the replication study are reduced relative to the initial study, and the P values, although they vary, are not obviously lower than in the original study. Therefore, it is unclear that an increase in sample size by a factor of 10 has led to any change in the P values observed. Importantly, there is not a clear discontinuity or distinction among the odds ratios for the three loci that O’Donovan et al. emphasize (the first three in Table 1) and those that they regard as probably chance findings. Both show a scatter of P values not obviously decreased, and regression to the mean of the odds ratio.

3. Findings with respect to these gene loci were not replicated in another genomewide association study of schizophrenia (Lencz et al., 2007). Although the authors emphasize a relationship to bipolar disorder, these loci were not shown to be associated in the recent study of Sklar et al. (2008).

These considerations emphasize the fragility of whole-genome analysis as an approach to genes predisposing to psychosis, and the salient absence of replicated findings in the field.

References:

Craddock N, O’Donovan MC, Owen MJ. The genetics of schizophrenia and bipolar disorder: dissecting psychosis. J Med Genet. 2005;42:193-204. Abstract

Lencz T, Morgan T, Athanasiou M, Dain B, Reeds CR, Kane JM, Kucherlapati R, Malhotra AK. Converging evidence for a Pseudoautosomal cytokine receptor gene locus in schizophrenia. Mol Psychiatry. 2007;12:572-80. Abstract

Sklar P, Smoller JW, Fan J, Ferreira MAR, Perlis RH, Chambert K, Nimgaonkar VL, McQueen MB, Farone SV, Kirby A, de Bakker PIW, Ogdie MN, Thase ME, Sachs GS, Todd-Brown K, Gabriel SB, Sougnez C, Gates C, Blumenstiel B, Defelice M, Ardlie KG, Franklin J, Muir WJ, McGhee KA, MacIntyre DJ, McLean A, VanBeck M, McQuillin A, Bass NJ, Robinson M, Lawrence J, Anjorin A, Curtis D, Scolnick EM, Daly MJ, Blackwood DH, Gurling HM, Purcell SM. Whole-genome association study of bipolar disorder. Mol Psychiatry. 2008;13:558-69. Abstract

View all comments by Timothy Crow

Primary Papers: Identification of loci associated with schizophrenia by genome-wide association and follow-up.

Comment by:  Michael O'Donovan, SRF AdvisorNick CraddockMichael Owen (SRF Advisor)
Submitted 6 January 2009
Posted 7 January 2009

Response to Comment by Tim Crow
Dr. Crow makes a few points concerning our recent genomewide association study (GWAS) of schizophrenia that he believes merit consideration. He draws attention to a reduction in the effect sizes we observed in the replication samples we used in our study in comparison to those we observed in our GWAS. As a related issue he notes that the P values are not obviously lower in the replication study than in the original study despite an increased sample size. This is factually correct. It is also expected when dealing with small effect sizes. It is well known that for true findings, initial studies will generally overestimate the effect sizes and that these will therefore subsequently drop in replication studies. This phenomenon is widely known as the winner's curse (see, e.g., Zollner and Pritchard, 2007). The reasons for the winner’s curse have been outlined elsewhere by many including ourselves (Craddock et al., 2008). Of course, it is also true that effect sizes will also drop for false positives taken forward, so it is reasonable to require significant replication before a finding can be accepted as true. In our paper, for a number of loci, we obtained strong replication evidence that would easily survive correction for multiple testing, but for no single locus did we consider the evidence to be sufficient to allow us to say the evidence was unequivocal. We did find, however, that the distribution of independent replication signals we obtained in our follow-up sample was extremely unlikely (p = 9x10-8) to have occurred with a random set of SNPs. So improbable is that finding under the null hypothesis that this seems to us compelling evidence that one or more of the loci we highlight represents a true susceptibility locus. If Dr. Crow has a more credible alternative explanation, we would be very keen to hear it.

In addition to the above, Dr. Crow makes familiar points relating to cross-study replication. Replication is, of course, the gold standard; that is why we sought (and obtained) it using much larger and more powerful samples than have been used to date in schizophrenia genetics. When assessing failures to replicate, Dr. Crow entirely ignores power issues, which are so vital when trying to infer evidence for an absence of effect from absence of evidence for an effect. For example, in the earlier GWAS study of Lencz and colleagues (Lencz et al., 2007), that study had power of less than 10 percent to detect an association to the strongest finding we reported (ZNF804A) at p = 0.05, and power of less than one-thousandth of 1 percent to detect the ZNF804A finding at a threshold similar to that which we obtained in our GWAS.

While we certainly accept that our GWAS study does not provide definitive evidence for (or, for power reasons, against) any specific gene, our study is properly interpreted as providing compelling evidence for the existence of some common risk alleles of small effect in schizophrenia and that some of the loci we have highlighted represent true susceptibility alleles. We also consider that our promising findings point to the likely success of the GWAS approach as datasets expand in power in the coming years. In saying so, we certainly do not think GWAS studies are a panacea, nor do we think they will uncover the entirety of the genetic architecture of schizophrenia, which may include effects too small and/or too rare to be detectable by GWAS in realistic samples. We are not entirely sure what Dr. Crow means by ”the fragility of whole-genome analysis as an approach to genes predisposing to psychosis,” but if he has any novel ideas about methods which come with a guarantee for identifying common risk alleles with small effects, we and the whole field of human genetics would no doubt be delighted to hear them.

References:

Zollner S, Pritchard JK. Overcoming the winner's curse: estimating penetrance parameters from case-control data. Am J Hum Genet. 2007 Apr 1;80(4):605-15. Abstract

Craddock N, O'Donovan MC, Owen MJ. Genome-wide association studies in psychiatry: lessons from early studies of non-psychiatric and psychiatric phenotypes. Mol Psychiatry. 2008 Jul 1;13(7):649-53. Abstract

Lencz T, Morgan TV, Athanasiou M, Dain B, Reed CR, Kane JM, Kucherlapati R, Malhotra AK. Converging evidence for a pseudoautosomal cytokine receptor gene locus in schizophrenia. Mol Psychiatry. 2007 Jun 1;12(6):572-80. Abstract

View all comments by Michael O'Donovan
View all comments by Nick Craddock
View all comments by Michael Owen

Primary Papers: Identification of loci associated with schizophrenia by genome-wide association and follow-up.

Comment by:  Timothy Crow
Submitted 27 January 2009
Posted 27 January 2009

I am grateful to Craddock et al. for a measured and thoughtful response to my comments and to SRF for providing a platform for discussion.

Craddock et al. concede that an increase in sample size by a factor of 10 did not lead to an increase in significance of the main finding of their whole-genome association study (O'Donovan et al., 2008). They invoke the “winner’s curse” (the scenario in which a genuine positive finding is followed by weaker or negative findings in attempts at replication) as the explanation. This seems to me risky logic. Science depends upon replication: if it’s not there, it’s not there.

These authors scrutinize their P values and pronounce that they have “strong replication evidence that would easily survive correction for multiple testing”…. I look at their table 2 and conclude they have identified the positive tail of the distribution of variation within the whole genome and are seeing its disappearance as the sample size is increased. My argument is that the gene they identify as related to schizophrenia is not distinguished from the set of other genes selected by statistical association in the replication procedure. I agree it is interesting that the P value decreases when a bipolar sample is added, but this was not the primary analysis, and the fact is that the independent study of Sklar et al. (2008) of bipolar disorder did not identify anything at this locus. In this multivariate literature we can all recollect alluring P values that subsequently melted away!

Craddock et al. are right to point out that their core study was larger than that of Lencz et al. (2007) by a factor of 1.37 for schizophrenia probands and 20 for the control population. Statistical power indeed is important. The point has force in the reverse comparison, i.e., of Lencz et al. with the Wellcome sample. The single positive finding (in the pseudo-autosomal region) in Lencz et al. was not confirmed in the Wellcome sample, and therefore cannot be regarded as replicated.

Craddock et al. question my phrase “the fragility of whole-genome analysis as an approach.” What I should have said was “fragility of the findings of whole-genome analysis....” With civility they then ask if I have “any novel ideas about methods which come with a guarantee for identifying…” what they describe as common “risk alleles with small effects...” for which I substitute...“the genetic predisposition to psychosis.” My response to their invitation is that the possibility should not be excluded that the variation we all seek lies not in the sequence, but in a modification of the histone structure with which the sequence is associated in the chromosome. These authors will be bored to hear me repeat that the transition from a prior species to modern Homo sapiens and its associated variation is the critical genetic event we have to identify, but the case is on record (Crow, 2008; Williams et al., 2006).

This brings me to the point in my commentary that Craddock et al. have overlooked, and of which I would very much like to hear their opinion—that the findings in the Wellcome Trust samples that they report have a bearing on the set of “candidate genes” that are so prominent in the current literature. Is it not the case that if there is really significant sequence variation associating schizophrenia with dysbindin, neuregulin, DISC1, etc., and such variation is transmitted through generations, it should have been detected in the study they report? Is not the fact that it is not seen significant? Why was it not seen either in their study or in other association studies (Sanders et al., 2008)? These studies are sufficiently powered to detect variation of the size implicated by the original positive linkage studies (though the linkage findings were generally not supported by systematic sibling pair studies—Crow [2007]). Do we not have here a critical test of the type that Medawar (1969) and other philosophers of science would urge us to seek, and a decisive refutation of the basket of hypotheses associated with candidate genes?

If so, then a robust statement to this effect from the Cardiff group (who have been sanguine about the candidate genes in their reviews) would have a salutary effect on the field. It would signal the elimination of hypotheses that have been widely discussed, and therefore would indicate progress. It would recognize the possibility that unearthing the genetic predisposition to psychosis is a more difficult task than any of us have thought.

References:

Crow TJ. How and why genetic linkage has not solved the problem of psychosis: review and hypothesis. Am J Psychiatry. 2007 Jan 1;164(1):13-21. Abstract

Crow TJ. The 'big bang' theory of the origin of psychosis and the faculty of language. Schizophr Res. 2008 Jul 1;102(1-3):31-52. Abstract

Lencz T, Morgan TV, Athanasiou M, Dain B, Reed CR, Kane JM, Kucherlapati R, Malhotra AK. Converging evidence for a pseudoautosomal cytokine receptor gene locus in schizophrenia. Mol Psychiatry. 2007 Jun 1;12(6):572-80. Abstract

Medawar, P.B. (1969), Induction and Intuition in Scientific Thought Methuen, London.

O'Donovan MC, Craddock N, Norton N, Williams H, Peirce T, Moskvina V, Nikolov I, Hamshere M, Carroll L, Georgieva L, Dwyer S, Holmans P, Marchini JL, Spencer CC, Howie B, Leung HT, Hartmann AM, Möller HJ, Morris DW, Shi Y, Feng G, Hoffmann P, Propping P, Vasilescu C, Maier W, Rietschel M, Zammit S, Schumacher J, Quinn EM, Schulze TG, Williams NM, Giegling I, Iwata N, Ikeda M, Darvasi A, Shifman S, He L, Duan J, Sanders AR, Levinson DF, Gejman PV, Cichon S, Nöthen MM, Gill M, Corvin A, Rujescu D, Kirov G, Owen MJ, Buccola NG, Mowry BJ, Freedman R, Amin F, Black DW, Silverman JM, Byerley WF, Cloninger CR, . Identification of loci associated with schizophrenia by genome-wide association and follow-up. Nat Genet. 2008 Sep 1;40(9):1053-5. Abstract

Sanders AR, Duan J, Levinson DF, Shi J, He D, Hou C, Burrell GJ, Rice JP, Nertney DA, Olincy A, Rozic P, Vinogradov S, Buccola NG, Mowry BJ, Freedman R, Amin F, Black DW, Silverman JM, Byerley WF, Crowe RR, Cloninger CR, Martinez M, Gejman PV. No significant association of 14 candidate genes with schizophrenia in a large European ancestry sample: implications for psychiatric genetics. Am J Psychiatry. 2008 Apr 1;165(4):497-506. Abstract

Sklar P, Smoller JW, Fan J, Ferreira MA, Perlis RH, Chambert K, Nimgaonkar VL, McQueen MB, Faraone SV, Kirby A, de Bakker PI, Ogdie MN, Thase ME, Sachs GS, Todd-Brown K, Gabriel SB, Sougnez C, Gates C, Blumenstiel B, Defelice M, Ardlie KG, Franklin J, Muir WJ, McGhee KA, MacIntyre DJ, McLean A, VanBeck M, McQuillin A, Bass NJ, Robinson M, Lawrence J, Anjorin A, Curtis D, Scolnick EM, Daly MJ, Blackwood DH, Gurling HM, Purcell SM. Whole-genome association study of bipolar disorder. Mol Psychiatry. 2008 Jun 1;13(6):558-69. Abstract

Williams NA, Close JP, Giouzeli M, Crow TJ. Accelerated evolution of Protocadherin11X/Y: a candidate gene-pair for cerebral asymmetry and language. Am J Med Genet B Neuropsychiatr Genet. 2006 Sep 5;141B(6):623-33. Abstract

View all comments by Timothy Crow

Comments on Related News


Related News: New Human Genome Map Shows Extensive Copy Number Variation

Comment by:  Jonathan Sebat
Submitted 27 November 2006
Posted 27 November 2006

This study is the first to systematically map large-scale copy number variation (CNV) across a large sample representing different populations. The investigators have significantly enhanced our knowledge of genomic diversity by identifying approximately 1,000 CNVs that had not been previously reported in the literature, thereby almost doubling the catalogue of published structural variants in healthy individuals. This data set will serve as the framework for a genomic resource on structural variation. It will continue to be refined through continued efforts of many groups and may soon be a very comprehensive map. It is currently just the tip of the iceberg.

View all comments by Jonathan Sebat

Related News: Autism Genes: A Handful, or More?

Comment by:  Daniel Weinberger, SRF Advisor
Submitted 19 March 2007
Posted 19 March 2007

Sense and Nonsense: General Lessons from Genetic Studies of Autism
The capability to characterize genetic variation across the entire genome in one fell swoop has generated considerable enthusiasm and expectation that the important genes for mental illness will “finally” be found. Whole genome association (WGA) is being touted as the path to genetic success in psychiatry. Is this sensible? Before considering the likely successes and limitations of this new capability, it is worth reminding ourselves of how we got here.

With respect to schizophrenia, over 50 years of studies of twin samples and of infants adopted away at birth have demonstrated that the lion’s share of risk for schizophrenia is determined by genes, to the tune of over 70 percent of the variance in liability (“heritability”). Family segregation studies have shown that the pattern of relative risk across relationships is most consistent with at minimum oligogenic inheritance, and more likely polygenic inheritance (Gottesman, I. I., Schizophrenia Genesis: The Origin of Madness, New York: W.H. Freeman.1991). After over a decade of linkage studies, it is clear that across diverse family samples, schizophrenia is not related to a common genetic locus, and no locus accounts for more than a fraction of risk for illness. Because we know that schizophrenia is highly heritable, the failure of linkage to reveal a chromosomal locus providing a highly significant LOD score in most samples is not because there are no genetic variations accounting for the heritability, but because, among other reasons, there is just too much locus heterogeneity across samples.

If we accept that schizophrenia is polygenic and genetically heterogeneous, meaning that in any sample under study, some cases will be ill because they have risk genes W, X, Y, and Z, while other cases will be ill because they have risk genes C, D, E, and F, then any common linkage signals will be diluted by this genetic heterogeneity if these genes are spread throughout the genome. In light of this situation, why, then, have some recent linkage studies of schizophrenia revealed significant and replicable linkage regions? Notwithstanding improvement in ascertainment methods and the informativeness of DNA marker sets, it is likely that linkage has worked in some regions of the genome because some of the genetic heterogeneity is concentrated in these areas, meaning that heterogeneity across families does not necessarily dilute the linkage signal at these loci. For example, in the 8p linkage peak, there are at least five genes that have been found to show association with schizophrenia in various samples: NRG1, PCM1, PPP3CC, DRP2, and FZD3, so if 10 percent of the families have risk alleles in NRG1 that contribute to their risk profile, and even if 10 percent have no NRG1 risk alleles but PCM1 alleles, and the same for PPP3CC and so on, this genetic heterogeneity will not dilute the linkage signal and the 8p locus containing these five genes will be positive in these families. Of course, in a subsequent association study, samples will be positive or negative for any one of these individual genes depending on which alleles happen to be enriched in that sample. This is how heterogeneity affects the prospects for positive linkage and association. Many observers of psychiatric genetics who argue against the validity of linkage and association in psychiatry like to talk about multifactorial medical illnesses such as heart disease and schizophrenia being genetically heterogeneous, but they do not like the walk when it comes to acknowledging the implications for finding association, positive or negative.

Heterogeneity has obvious implications for studies that attempt to survey variation in the entire genome and compare allele frequencies across ill and well samples. Heterogeneity in such studies dilutes the statistical effect of any single DNA polymorphism in the entire sample. Because literally hundreds of thousands of variations may be typed at one time, many of which have no prior probability of being related to the phenotype of interest, it is critical to employ some approach to statistical correction for the possibility of random positive associations. If one were to correct for 500,000 tests, the likelihood that any SNP related to a condition like schizophrenia will survive this level of correction, at least to the extent that the illness is polygenic and heterogeneous, is very small. Based on the strength of the existing data, none of the well-supported candidate susceptibility genes for schizophrenia that have been identified to date (e.g., DTNPB1, NRG1, DISC1, etc.) would survive such correction. It has been argued that the solution to this conundrum is the collection of very large datasets. This may increase power and generate impressive p values for a few genes, but the effect size of the association does not change with sample size, only the p value. It is also important to remember that the larger the sample size, the greater the potential for heterogeneity, because the collection of very large samples often requires multiple collection centers, each with their own ascertainment quirks. Thus, this approach runs the risk of a paradoxical reduction in the strength of linkage and association (see Brzustowicz, 2007).

These considerations have implications for studies of the genetic origins of other neuropsychiatric disorders, such as depression, bipolar disorder, anxiety disorders, and autism. Two recent important papers related to autism illustrate each of these points and offer important lessons for WGA studies that will be emerging soon related to schizophrenia and other psychiatric disorders.

The paper by the Autism Genome Project Consortium (AGPC) reports the largest linkage study of families (over 1,490 families) with children having the autism spectrum syndrome and the most informative set of linkage markers yet reported. This study illustrates in dramatic detail the complications alluded to above. Many areas of the genome show evidence of linkage, i.e., locus heterogeneity, but the individual signals are statistically weak. Indeed, using strict criteria for statistical analysis, no region would have been considered positive, and the region that was closest (11p12-13) was not identified as a promising region in earlier linkage studies.

In a series of exploratory post-hoc reanalyses of the data, trying to create more theoretically homogeneous clinical samples (e.g., gender specific, narrower diagnosis), several linkage signals became slightly more positive, but also involving regions of the genome not highlighted in earlier linkage studies. Does this failure to find an impressive statistical result in such an impressively large sample mean that this study is negative? Not if we expect autism to be genetically complex in the ways enumerated above. The results are exactly what would be predicted. Indeed, similar results have been reported before (Risch et al., 1999). The AGPC study also discovered regions where evidence of genomic structural changes, so-called sequence copy number variations (CNVs), might be associated with clinical diagnosis. Their data suggest that as many as 253 CNVs were discovered in 196 cases. The CNVs were found in many chromosomal regions (i.e., locus heterogeneity); involved duplications more often than deletions; varied considerably from one family to another; were spontaneous in most cases but inherited in some; and were most often found only in one individual, though recurrences occurred across ill subjects in some instances. It is very difficult to determine from these data how much of the genetic contribution to autism in this sample is explained by these copy number variations. In a few families, where multiple affected individuals had the same deletion, the data look convincing. However, it appears that CNVs were just as frequent, just as large (average 3.4 Mb) and just as likely to be duplications or deletions in the unaffected siblings of the children with autism.

The paper by Sebat and colleagues surveys the genome exclusively for evidence of structural changes related to variable copy numbers of DNA sequences and uses a putatively more sensitive method. They discovered submicroscopic deletions of 17 chromosomal regions in 14 children with autism spectrum disorder (7 percent of their ill sample). By design, all of the deletions described in this report were de novo, or spontaneous, meaning they were not found in the parents of the affected offspring and were thus not inherited. In other words, these deletions do not explain the very substantial heritability of autism, nor did they map to the regions of the genome that have shown up in linkage studies, which look specifically for loci that contribute to heritable risk (including the regions in the AGPC), nor did they highlight genes that have emerged from linkage studies as likely candidates accounting for the heritability of autism. Moreover, with one exception, all of the deletions were private, meaning they occurred in only one individual. As Sebat and colleagues point out, however, the infrequency of these copy number variations does not preclude them from pointing to more generalizable insights about genetic risk factors that operate in other cases. The genes affected by these infrequent structural variations may in other cases show common variations (e.g., SNPs) that contribute more widely to genetic liability. It is not clear how much overlap there is between the findings of these two studies, but clearly there are major differences.

The bottom line here is that genetic heterogeneity appears to be the rule in autism. While most cases are related to a complex set of inherited risk factors, some may be related to spontaneous genetic lesions, with many different lesions producing a similar clinical phenotype. None of this should surprise us, as diverse congenital encephalopathies can manifest the autism syndrome, e.g., fragile X syndrome, Rett syndrome, tuberous sclerosis. From a genetic point of view, autism is a syndrome that can be reached from many directions, along many paths. It is not likely that autism is any more of a discrete disease entity than, say, blindness or mental retardation.

So where does this leave us with respect to the goal of fully defining the genetic origins of mental disorders such as schizophrenia? The current list of promising candidate genes for schizophrenia is growing rapidly, and some already are leading to insights about potential pathophysiologic mechanisms and potential treatment targets (Straub and Weinberger, 2006). Genome variation scans will hopefully uncover many more novel genes that contribute to the risk for schizophrenia, and regardless of their outcome, these types of studies will be very important. It is likely that within the next 5 years we will have a good sense of all the common genetic variants that contribute to schizophrenia across many world samples. It is also likely that some cases will be related to structural variations (e.g., the 22q11 deletion associated with the velocardiofacial syndrome [VCFS]), both spontaneous and inherited. But, a phoenix rising from this newest chapter of investigation is not likely. Rather, as the recent autism studies illustrate, many genetic loci and many genes, again each accounting for only a relatively small percentage of ill subjects, will likely be the legacy of these studies. It is the legacy of all the work up to this point, and it is not likely to be different now that we can do many more of the same SNP assays all at one time. I doubt that genes that are discovered via WGA or related approaches will show greater effect sizes than the current top candidates, but there certainly will be more of them. Schizophrenia, like autism, is almost certainly a disorder that can be reached from many directions, along many paths. This being said, is it likely that a few genes with “highly significant” p values will be observed in a few of the multitude of WGA studies that will hit the press over the next year or two? Of course it is. Will these be the most important genes? Not necessarily. The challenge for our using these new data will be to make strategic choices about which of the various signals to pursue further and how to pursue them. The most important genes will be the ones that can be translated into meaningful information about disease mechanisms, therapeutic target identification, and clinical prediction.

View all comments by Daniel Weinberger

Related News: Autism Genes: A Handful, or More?

Comment by:  Paul Patterson
Submitted 21 March 2007
Posted 22 March 2007

Regarding the very high "heritability" of schizophrenia and autism: these values are usually based on twin studies, and there is good reason to be skeptical about these numbers.

For instance, the frequency of schizophrenia in dizygotic twins is twice as high as for siblings, suggesting a role for the fetal environment. Second, the concordance for monozygotic twins is 60 percent if they share a placenta, but only 11 percent if they have separate placentas, again highlighting the importance of the fetal environment. (Two-thirds of monozygotic twins share a placenta.) It is also relevant that roughly two-thirds of schizophrenia subjects do not have a primary or secondary relative with the disorder.

No one questions that genes play a role in the risk for schizophrenia and autism, but twins share a fetal environment as well as genes. The importance of the fetal environment is very well illustrated by the work of Brown and colleagues in their studies of the risk factor, maternal respiratory infection.

References:

Phelps J, Davis J, Schartz K. Nature, Nurture, and Twin Research Strategies. Curr. Directions in Pyschol. Sci. 1997;6:117-120.

Brown AS. Prenatal infection as a risk factor for schizophrenia. Schizophr Bull. 2006 Apr;32(2):200-2. Epub 2006 Feb 9. Abstract

Brown AS, Susser ES. In utero infection and adult schizophrenia. Ment Retard Dev Disabil Res Rev. 2002;8(1):51-7. Review.

Ryan B, Vandenbergh J. Intrauterine position effects. Neuroscience and Biobehavioral Reviews. 2002;26:665–678. Abstract

View all comments by Paul Patterson

Related News: Autism Genes: A Handful, or More?

Comment by:  Ben Pickard
Submitted 24 March 2007
Posted 24 March 2007

The Curious Incident of the Gap in the Chromosome
Our bodies are accustomed to a double dose of genes. The cellular ecosystem has been evolutionarily fine-tuned to this baseline of gene expression. Even the exceptions to the rule such as the sex-specific imbalance of X/Y chromosomes or the set of imprinted genes serve to highlight the compensatory mechanisms that have allowed the cell to adapt. Therefore, it is not surprising that chromosomal dosage changes are associated with disease states.

An ever-increasing appreciation of the link between disease and gene copy number has followed closely behind advances in techniques that have enabled the measurement of copy number variation at ever-greater resolution and sensitivity. Starting with Giemsa-stained chromosomes in classical cytogenetics, which identified visible aneuploidies such as trisomy 21, the field has progressed through fluorescence in situ hybridization (FISH) studies which pinpointed finer abnormalities, including those discovered through comparative genomic hybridization and sub-telomeric analysis, to today’s chip-based approaches, which can survey the whole genome at once. (In fact, as an aside, the sensitivity of the current state-of-the-art techniques is only likely to be truly improved upon with the advent of whole-genome sequencing—realistically, that is not likely for a decade or so.)

Despite this progress, the one-off nature and scarcity of many chromosome abnormalities have often led to their dismissal as genetic quirks and not relevant to disease biology at the population level. Perhaps the tide is now turning in their favor as recent studies of sub-microscopic gene copy number changes have yielded intriguing and provocative discoveries. The two papers summarized on this site asked whether a proportion of autism spectrum disorders are caused by CNVs. The same question could, and doubtless will, be asked of schizophrenia, bipolar disorder, and other psychiatric conditions and so is worthy of discussion in this forum. The answer for autism seems to be a resounding “yes,” and this is likely to precipitate a sea change in autism research, both at the genetic and biological levels. Sebat et al. (Science, 15 March, 2007) and The Autism Genome Project Consortium (“AGPC,” Nature Genetics, 18 February, 2007) used slightly different variations on the chip theme in their studies: the former had the advantage of a more discrete output for copy number compared to the continuous distribution from the latter approach. This had consequences for the setting of statistical detection thresholds, but both groups were quite thorough in the confirmation of many of their findings using secondary detection approaches.

Understanding the Consequences of Experimental Design: Choice of Samples and Assessment
The samples chosen for analysis by both research groups focused on nominally family-based collections rather than sporadic cases. Thus, the mutations represented are highly likely to be of higher penetrance and relatively rare. In my opinion, the high level of locus heterogeneity that accompanies such a sample set makes the multiple-family linkage approach unlikely to yield practical dividends—indeed, the linkage component from the AGPC group is the least impressive aspect of their paper. The main linkage peak at 11p12-p13 was not a replication of the typical autism linkage findings (e.g., chromosome 7q, etc.; for review see Klauck, 2006). Additionally, above-threshold LOD scores were not significantly improved when diagnostic boundaries were changed or CNV carriers removed from the data. In fact, one of the most impressive features of the Sebat paper was the enlightened subdivision of the samples based not on phenotype, but rather by the nature of the inheritance patterns of autistic spectrum disorders within the families (the same may be true for the AGPC data, but the information is not explicitly categorized). This stratification into “simplex” (single case within the family) and “multiplex” (more than one affected individual) must be telling us something about the genetic architecture of complex genetic disorders. The results indicate that de novo CNVs were four times more common in the simplex families than multiplex. Let’s examine a hypothetical explanation for this finding. First, the simplex families may not be, or rather may not go on to be, true “families” in the genetic sense—their mutations are of the lower penetrance, “susceptibility altering” class. Such CNV mutations would not produce the densely affected families that are so attractive to gene mappers and so will never be collected and categorized as “multiplex.” The fact that three CNV regions (2q37.3, 3p14.2, and 20p13) are independently present twice in the Sebat simplex group adds weight to these CNVs being “common” risk variants—perhaps they are ripe candidates for a case-control association study in a larger simplex/sporadic cohort? The type of CNVs present in the multiplex families are, by definition, of sufficient penetrance for the multiplex classification to become possible: this class of mutations will probably be rarer. One supportive observation for the distinction between the two CNV types rests on the fact that there is no overlap between identified multiplex and simplex CNV regions—will that remain the case as further studies are carried out? Another, from the AGPC paper, is that many of their familial CNVs lie over previously identified linkage hotspots or known balanced chromosomal rearrangements (breakpoints, see below).

However, two mysteries remain: the predominance of CNV deletions in the Sebat paper compared to the stated overrepresentation of duplications in the AGPC paper. Whether this is a technical or family sample choice issue remains to be elucidated. Secondly, and perhaps more vague a problem, is the seldom addressed nature of the mutations identified in neuropsychiatric disorders. The archetypal mutations we learn about in undergraduate lectures, primarily in the context of neoplasms, include gain-of-function (oncogenes), loss-of-function (tumor suppressors), dominant negative and so on. Chromosome abnormalities in general, and CNVs in particular, seem to suggest that autism spectrum disorder (ASD), schizophrenia, and bipolar disorder are diseases in which gene dosage changes are the only pathological mechanism. Is this a real biological phenomenon or merely a methodological ascertainment bias? If the latter, how might we better adapt our gene hunting strategies to target other forms of mutation?

A Gene in the Hand Is Worth 50 Under a Linkage Peak
In the warm afterglow of an experimental tour-de-force, the biological ramifications can sometimes be sidelined. What genes have these CNVs affected and what does this tell us about the biology of autism spectrum disorder, we can ask, not forgetting that this work should be considered in the context of the history of other genetic and biological studies on ASD.

The first, and perhaps most impressive, finding is that of a CNV covering the Neurexin 1 (NRXN1) gene. The protein encoded by this gene interacts with a family of receptors called Neuroligins. Interestingly, Neuroligin 3 (NLGN3) and Neuroligin 4 (NLGN4) have been linked to ASD through chromosome abnormalities and mutations detected in rare cases. Moreover, SHANK3 has recently been identified as an ASD candidate through the study of cytogenetic abnormalities and several point mutations. SHANK3 protein has also been demonstrated to bind to neuroligins. This amazing convergence is reminiscent of another recent celebrity pairing in the schizophrenia field: the discovery of DISC1 and PDE4B through independent chromosome abnormalities followed by the discovery that their proteins functionally interact. The identification of these four ASD candidate genes is likely to stimulate much research into this nascent signaling pathway, particularly in the context of its supposed role in synaptogenesis.

Many of the CNVs affect gene clusters, and only by analyzing multiple overlapping deletions or systematically examining the gene candidates individually will the causative ASD genes be identified. This seems to be the case for the genes ZFP42 and PACRG, which have been found both in large CNVs with multiple genes affected and singly in smaller CNVs. Several additional CNVs were identified which were small enough, or within large enough genes (large size seems to be a anecdotally reported feature of genes identified through a variety of cytogenetic approaches) to implicate just that gene. These include SLC4A10, FLJ16237, A2BP1, NFIA, GAB2, PCDH7, PCDH9, CDH8, C18orf58, FHOD3, C2orf10, MAN2A1, CSMD1, and TRPM3 as a conservative selection. Two aspects of biology immediately spring to mind when viewing these genes. Firstly, the three members of the cadherin family identified fall into the same biological role as the neuroligins, namely cell adhesion. A related gene, FAT, has also been implicated in familial bipolar disorder. Secondly, the identification of MAN2A1 encoding a component enzyme in the pathway which post-translationally modifies proteins through glycosylation adds another gene from this process to a list including ALG9/DIBD1 and MGAT5 , both of which have been implicated in psychiatric illness. Together with the list of genes identified through CNV analysis, one can add USP6, NBEA, ST7, AUTS2, SSBP1, GRPR, and SHANK3, discovered in previous studies of autism spectrum disorder chromosome abnormalities. These candidates (and those identified in the psychoses) provide a wealth of resources for future functional and genetic studies. However, on the journey to a more rigorous biological definition of ASD, it may be a mistake to attempt to squeeze the functions of these genes into one unifying but unhelpfully vague cellular grouping, e.g., “signal transduction” or “metabolism.” Rather, biological investigations might benefit from trying to place these disparate genes in the context of their roles in the functioning of the brain regions or subsystems in which they are expressed. A hard task undoubtedly, but an endeavor that is likely to provide us with a more holistic understanding of the conditions.

View all comments by Ben Pickard

Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  Daniel Weinberger, SRF Advisor
Submitted 27 March 2008
Posted 27 March 2008

The paper by Walsh et al. is an important addition to the expanding literature on copy number variations in the human genome and their potential role in causing neuropsychiatric disorders. It is clear that copy number variations are important aspects of human genetic variation and that deletions and duplications in diverse genes throughout the genome are likely to affect the function of these genes and possibly the development and function of the human brain. So-called private variations, such as those described in this paper, i.e., changes in the genome found in only a single individual, as all of these variations are, are difficult to establish as pathogenic factors, because it is hard to know how much they contribute to the complex problem of human behavioral variation in a single individual. If the change is private, i.e., only in one case and not enriched in cases as a group, as are common genetic polymorphisms such as SNPs, how much they account for case status is very difficult to prove.

An assumption implicit in this paper is that these private variations may be major factors in the case status of the individuals who have them. The data of this paper suggest, however, this is actually not the case, at least for the childhood onset cases. Here’s why: mentioned in the paper is a statement that only two of the CNVs in the childhood cases are de novo, i.e., spontaneous and not inherited (and one of these is on the Y chromosome, making its functional implications obscure). If most of the CNVs are inherited, they can’t be causing illness per se as major effect players because they are coming from well parents.

Also, if you add up all CNVs in transmitted and non-transmitted chromosomes of the parents, it’s something like 31 gene-based CNVs in 154 parents (i.e., 20 percent of the parents have a gene-based deletion or duplication in the very illness-related pathways that are highlighted in the cases), which is at least as high a frequency as in the adult-onset schizophrenia sample in this study…and three times the frequency as found in the adult controls. This is not to say that such variants might not represent susceptibility genetic factors, or show variable penetrance between individuals, like other polymorphisms, and contribute to the complex genetic risk architecture, like other genetic variations that have been more consistently associated with schizophrenia. However, the CNV literature has tended to seek a more major effect connotation to the findings.

View all comments by Daniel Weinberger

Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  William Honer
Submitted 28 March 2008
Posted 28 March 2008
  I recommend the Primary Papers

As new technologies are applied to understanding the etiology and pathophysiology of schizophrenia, considering the clinical features of the cases studied and the implications of the findings is of value. The conclusion of the Walsh et al. paper, “these results suggest that schizophrenia can be caused by rare mutations….“ is worth considering carefully.

What evidence is needed to link an observation in the laboratory or clinic to cause? Recent recommendations for the content of papers in epidemiology (von Elm et al., 2008) remind us of the suggestions of A.V. Hill (Hill, 1965). To discern the implications of a finding, or association, for causality, Hill suggests assessment of the following:

1. Strength of the association: this is not the observed p-value, but a measure of the magnitude of the association. In the Walsh et al. study, the primary outcome measure, structural variants duplicating or deleting genes was observed in 15 percent of cases, and 5 percent of controls. But what is the association with? The diagnostic entity of schizophrenia, or some risk factor for the illness? Of interest, and noted in the Supporting Online Material, these variants were present in 7/15 (47 percent) of the cases with presumed IQ <80, but only 15/135 (11 percent) of the cases with IQ >80. Are the structural variants more strongly associated with mental retardation (within schizophrenia 47 percent vs. 11 percent) than with diagnosis (11 percent vs. 5 percent of controls, assuming normal IQ)? This is of particular interest in the context of the speculation in the paper concerning the importance of genes putatively involved with brain development in the etiology of schizophrenia.

2. Consistency of results in the literature across studies and research groups: there are now several papers examining copy number variation in schizophrenia, including a report from our group (Wilson et al., 2006). The authors of the present paper state that each variant observed was unique, and so consistency of the specific findings could be argued to be irrelevant, if the model is of novel mutations (more on models below). Undoubtedly, future meta-analyses and accumulating databases help determine if there is anything consistent in the findings, other than a higher frequency of any abnormalities in cases rather than controls.

3. Specificity of the findings to the illness in question: this was not addressed experimentally in the paper. However, the findings of more abnormalities in the putative low IQ cases, and the similarity of the findings to reports in autism and mental retardation, suggest that this criterion for supporting causality is unlikely to be met.

4. Temporality: the abnormalities should precede the illness. If DNA from terminally differentiated neurons harbors the same variants as DNA from constantly renewed populations of lymphocytes, then clearly this condition is met. While it seems highly likely that this is the case, it is worthwhile considering the possibility that DNA structure may vary between tissue types, or between cell populations. Even within human brain there is some evidence for chromosomal heterogeneity (Rehen et al., 2005).

5. Biological gradient: presence of a “dose-response” curve strengthens the likelihood of a causal relationship. This condition is not met within cases: only 1/115 appeared to have more than one variant. However, in the presumably more severe childhood onset form of schizophrenia, four individuals carried multiple variants, and the observation of a higher prevalence of variants overall. Still, the question of what the observations of CNV are associated with is relevant, since one of the inclusion/exclusion criteria for COS allowed IQ 65-80, and it is uncertain how many of these cases had some degree of intellectual deficit.

6. Plausibility: biological likelihood—quite difficult to satisfy as a criterion, in the context of the limits of knowledge concerning the mechanisms of illness of schizophrenia.

7. Coherence of the observation with known facts about the illness: the genetic basis of schizophrenia is quite well studied, and there is no dearth of theories concerning genetic architecture. However, a coherent model remains lacking. As examples, the suggestion is made that the observations concerning inherited CNVs in the COS cases are linked with a severe family history in this type of illness. This appears inconsistent with a high penetrance model for CNVs as suggested in the opening of the paper (presuming the parents in COS families are unaffected, as would seem likely). Elsewhere, CNVs are proposed by the authors to be related to de novo events, and an interaction with an environmental modifier, folate (and exposure to famine), is posited (McClellan et al., 2006). A model of the effects of CNVs, which generates falsifiable hypotheses is needed.

8. Experiment: the ability to intervene clinically to modify the effects of CNVs disrupting genes seems many years away.

9. Analogy: the novelty of the CNV findings is both intriguing, but limiting in understanding the likelihood of causal relationships.

The intersection of clinical realities and novel laboratory technologies will fuel the need for better translational research in schizophrenia for many, many more years.

References:

von Elm E, Altman DG, Egger M, Pocock SJ, Gøtzsche PC, Vandenbroucke JP. Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies. J Clin Epidemiol. 2008 Apr 1;61(4):344-349. Abstract

HILL AB. THE ENVIRONMENT AND DISEASE: ASSOCIATION OR CAUSATION? Proc R Soc Med. 1965 May 1;58():295-300. Abstract

Wilson GM, Flibotte S, Chopra V, Melnyk BL, Honer WG, Holt RA. DNA copy-number analysis in bipolar disorder and schizophrenia reveals aberrations in genes involved in glutamate signaling. Hum Mol Genet. 2006 Mar 1;15(5):743-9. Abstract

Rehen SK, Yung YC, McCreight MP, Kaushal D, Yang AH, Almeida BSV, Kingsbury MA, Cabral KMS, McConnell MJ, Anliker B, Fontanoz M, Chun J: Constitutional aneuploidy in the normal human brain. J Neurosci 2005; 25:2176-2180. Abstract

McClellan JM, ESusser E, King M-C: Maternal famine, de novo mutations, and schizophrenia. JAMA 2006; 296:582-584. Abstract

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Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  Todd LenczAnil Malhotra (SRF Advisor)
Submitted 30 March 2008
Posted 30 March 2008

The new study by Walsh et al. (2008), as well as recent data from other groups working in schizophrenia, autism, and mental retardation, make a strong case for including copy number variants as an important source of risk for neurodevelopmental phenotypes. These findings raise several intriguing new questions for future research, including: the degree of causality/penetrance that can be attributed to individual CNVs; diagnostic specificity; and recency of their origins. While these questions are difficult to address in the context of private mutations, one potential source of additional information is the examination of common, recurrent CNVs, which have not yet been systematically studied as potential risk factors for schizophrenia.

Still, the association of rare CNVs with schizophrenia provides additional evidence that genetic transmission patterns may be a complex hybrid of common, low-penetrant alleles and rare, highly penetrant variants. In diseases ranging from Parkinson's to colon cancer, the literature demonstrates that rare penetrant loci are frequently embedded within an otherwise complex disease. Perhaps the most well-known example involves mutations in amyloid precursor protein and the presenilins in Alzheimer’s disease (AD). Although extremely rare, accounting for <1 percent of all cases of AD, identification of these autosomal dominant subtypes greatly enhanced understanding of pathophysiology. Similarly, a study of consanguineous families in Iran has very recently identified a rare autosomal recessive form of mental retardation (MR) caused by glutamate receptor (GRIK2) mutations, thereby opening new avenues of research (Motazacker et al., 2007). In schizophrenia, we have recently employed a novel, case-control approach to homozygosity mapping (Lencz et al., 2007), resulting in several candidate loci that may harbor highly penetrant recessive variants. Taken together, these results suggest that a diversity of methodological approaches will be needed to parse genetic heterogeneity in schizophrenia.

References:

Motazacker MM, Rost BR, Hucho T, Garshasbi M, Kahrizi K, Ullmann R, Abedini SS, Nieh SE, Amini SH, Goswami C, Tzschach A, Jensen LR, Schmitz D, Ropers HH, Najmabadi H, Kuss AW. (2007) A defect in the ionotropic glutamate receptor 6 gene (GRIK2) is associated with autosomal recessive mental retardation. Am J Hum Genet. 81(4):792-8. Abstract

Lencz T, Lambert C, DeRosse P, Burdick KE, Morgan TV, Kane JM, Kucherlapati R,Malhotra AK (2007). Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia. Proc Natl Acad Sci U S A. 104(50):19942-7. Abstract

View all comments by Todd Lencz
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Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  Ben Pickard
Submitted 31 March 2008
Posted 31 March 2008

In my mind, the study of CNVs in autism (and likely soon in schizophrenia/bipolar disorder, which are a little behind) is likely to put biological meat on the bones of illness etiology and finally lay to rest the annoyingly persistent taunts that genetics hasn’t delivered on its promises for psychiatric illness.

I don’t think it’s necessary at the moment to wring our hands at any inconsistencies between the Walsh et al. and previous studies of CNV in schizophrenia (e.g., Kirov et al., 2008). There are a number of factors which I think are going to influence the frequency, type, and identity of CNVs found in any given study.

1. CNVs are going to be found at the rare/penetrant/familial end of the disease allele spectrum—in direct contrast to the common risk variants which are the targets of recent GWAS studies. In the short term, we are likely to see a large number of different CNVs identified. The nature of this spectrum, however, is that there will be more common pathological CNVs which should be replicated sooner—NRXN1, APBA2 (Kirov et al., 2008), CNTNAP2 (Friedman et al., 2008)—and may be among some of these “low hanging fruit.” For the rarer CNVs, proving a pathological role is going to be a real headache. Large studies or meta-analyses are never going to yield significant p-values for rare CNVs which, nevertheless, may be the chief causes of illness for those few individuals who carry them. Showing clear segregation with illness in families is likely to be the only means to judge their role. However, we must not expect a pure cause-and-effect role for all CNVs: even in the Scottish t(1;11) family disrupting the DISC1 gene, there are several instances of healthy carriers.

2. Sample selection is also likely to be critical. In the Kirov paper, samples were chosen to represent sporadic and family history-positive cases equally. In the Walsh paper, samples were taken either from hospital patients (the majority) or a cohort of childhood onset schizophrenia. Detailed evidence for family history on a case-by-case basis was not given but appeared far stronger in the childhood onset cases. CNVs appeared to be more prevalent, and as expected, more familial, in the latter cohort. A greater frequency was also observed in the Kirov study familial subset.

3. Inclusion criteria are likely to be important—particularly in the more sporadic cases without family history. This is because CNVs found in this group may be commoner and less penetrant—they will be more frequent in cases than in controls but not exclusively found in cases. Any strategy, such as that used in the Kirov paper, which discounts a CNV based on its presence—even singly—in the control group is likely to bias against this class.

4. Technical issues. Certainly, the coverage/sensitivity of the method of choice for the “event discovery” stage is going to influence the minimum size of CNV detectable. However, a more detailed coverage often comes with a greater false-positive rate. Technique choice may also have more general issues. In both of the papers, the primary detection method is based on hybridization of case and pooled control genomes prior to detection on a chip. Thus, a more continuously distributed output may result—and the extra round of hybridization might bias against certain sequences. More direct primary approaches such as Illumina arrays or a second-hand analysis of SNP genotyping arrays may provide a more discrete copy number output, but these, too, can suffer from interpretational issues.

The other major implication of these and other CNV studies is the observation that certain genes “ignore” traditional disease boundaries. For example, NRXN1 CNVs have now been identified in autism and schizophrenia, and CNTNAP2 translocations/CNVs have been described in autism, Gilles de la Tourette syndrome, and schizophrenia/epilepsy. This mirrors the observation of common haplotypes altering risk across the schizophrenia-bipolar divide in numerous association studies. It might be the case that these more promiscuous genes are likely to be involved in more fundamental CNS processes or developmental stages—with the precise phenotypic outcome being defined by other variants or environment. The presence of mental retardation comorbid with psychiatric diagnoses in a number of CNV studies suggests that this might be the case. I look forward to the Venn diagrams of the future which show us the shared neuropsychiatric and disease-specific genes/gene alleles. It will also be interesting to see if the large deletions/duplications involving numerous genes give rise to more severe, familial, and diagnostically more defined syndromes or, alternatively, a more diffuse phenotype. Certainly, it has not been easy to dissect out individual gene contributions to phenotype in VCFS or the minimal region in Down syndrome.

References:

Friedman JI, Vrijenhoek T, Markx S, Janssen IM, van der Vliet WA, Faas BH, Knoers NV, Cahn W, Kahn RS, Edelmann L, Davis KL, Silverman JM, Brunner HG, van Kessel AG, Wijmenga C, Ophoff RA, Veltman JA. CNTNAP2 gene dosage variation is associated with schizophrenia and epilepsy. Mol Psychiatry. 2008 Mar 1;13(3):261-6. Abstract

View all comments by Ben Pickard

Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  Christopher RossRussell L. Margolis
Submitted 3 April 2008
Posted 3 April 2008

We agree with the comments of Weinberger, Lencz and Malhotra, and Pickard, and the question raised by Honer about the extent to which the association may be more to mental retardation than schizophrenia. These new studies of copy number variation represent important advances, but need to be interpreted carefully.

We are now getting two different kinds of data on schizophrenia, which can be seen as two opposite poles. The first is from association studies with common variants, in which large numbers of people are required to see significance, and the strengths of the associations are quite modest. These kinds of vulnerability factors would presumably contribute a very modest increase in risk, and many taken together would cause the disease. By contrast, the “private” mutations, as identified by the Sebat study, could potentially be completely causative, but because they are present in only single individuals or very small numbers of individuals, it is difficult to be certain of causality. Furthermore, since some of them in the early-onset schizophrenia patients were present in unaffected parents, one might have to assume the contribution of a common variant vulnerability (from the other parent) as well.

If a substantial number of the private structural mutations are causal, then one might expect to have seen multiple small Mendelian families segregating a structural variant. The situation would then be reminiscent of the autosomal dominant spinocerebellar ataxis, in which mutations (currently about 30 identified loci) in multiple different genes result in similar clinical syndromes. The existence of many small Mendelian families would be less likely if either 1) structural variants that cause schizophrenia nearly always abolish fertility, or 2) some of the SVs detected by Walsh et al. are risk factors, but are usually not sufficient to cause disease. The latter seems more likely.

We think these two poles highlight the continued importance of segregation studies, as have been used for the DISC1 translocation. In order to validate these very rare “private” copy number variations, we believe that it would be important to look for sequence variations in the same genes in large numbers of schizophrenia and control subjects, and ideally to do so in family studies.

One very exciting result of the new copy number studies is the implication of whole pathways rather than just single genes. This highlights the importance of a better understanding of pathogenesis. The study of candidate pathways should help facilitate better pathogenic understanding, which should result in better biomarkers and potentially improve classification and treatment. In genetic studies, development of pathway analysis will be fruitful. Convergent evidence can come from studies of pathogenesis in cell and animal models, but this will need to be interpreted with caution, as it is possible to make a plausible story for so many different pathways (Ross et al., 2006). The genetic evidence will remain critical.

References:

Ross CA, Margolis RL, Reading SA, Pletnikov M, Coyle JT. Neurobiology of schizophrenia. Neuron. 2006 Oct 5;52(1):139-53. Abstract

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Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  Michael Owen, SRF AdvisorMichael O'Donovan (SRF Advisor)George Kirov
Submitted 15 April 2008
Posted 15 April 2008

The idea that a proportion of schizophrenia is associated with rare chromosomal abnormalities has been around for some time, but it has been difficult to be sure whether such events are pathogenic given that most are rare. Two instances where a pathogenic role seems likely are first, the balanced ch1:11 translocation that breaks DISC1, where pathogenesis seems likely due to co-segregation with disease in a large family, and second, deletion of chromosome 22q11, which is sufficiently common for rates of psychosis to be compared with that in the general population. This association came to light because of the recognizable physical phenotype associated with deletion of 22q11, and the field has been waiting for the availability of genome-wide detection methods that would allow the identification of other sub-microscopic chromosomal abnormalities that might be involved, but whose presence is not predicted by non-psychiatric syndromal features. This technology is now upon us in the form of various microarray-based methods, and we can expect a slew of studies addressing this hypothesis in the coming months.

Structural chromosomal abnormalities can take a variety of forms, in particular, deletions, duplication, inversions, and translocations. Generally speaking, these can disrupt gene function by, in the case of deletions, insertions and unbalanced translocations, altering the copy number of individual genes. These are sometimes called copy number variations (CNVs). Structural chromosomal abnormalities can also disrupt a gene sequence, and such disruptions include premature truncation, internal deletion, gene fusion, or disruption of regulatory or promoter elements.

It is, however, worth pointing out that structural chromosomal variation in the genome is common—it has been estimated that any two individuals on average differ in copy number by a total of around 6 Mb, and that the frequency of individual duplications or deletions can range from common through rare to unique, much in the same way as other DNA variation. Also similar to other DNA variation, many structural variants, indeed almost certainly most, may have no phenotypic effects (and this includes those that span genes), while others may be disastrous for fetal viability. Walsh and colleagues have focused upon rare structural variants, and by rare they mean events that might be specific to single cases or families. For this reason, they specifically targeted CNVs that had not previously been described in the published literature or in the Database of Genomic Variants. The reasonable assumption was made that this would enrich for CNVs that are highly penetrant for the disorder. Indeed, Walsh et al. favor the hypothesis that genetic susceptibility to schizophrenia is conferred not by relatively common disease alleles but by a large number of individually rare alleles of high penetrance, including structural variants. As we have argued elsewhere (Craddock et al., 2007), it seems entirely plausible that schizophrenia reflects a spectrum of alleles of varying effect sizes including common alleles of small effect and rare alleles of larger effect, but data from genetic epidemiology do not support the hypothesis that the majority of the disorder reflects rare alleles of large effect.

Walsh et al. found that individuals with schizophrenia were >threefold more likely than controls to harbor rare CNVs that impacted on genes, but in contrast, found no significant difference in the proportions of cases and controls carrying rare mutations that did not impact upon genes. They also found a similar excess of rare structural variants that deleted or duplicated one or more genes in an independent series of cases and controls, using a cohort with childhood onset schizophrenia (COS).

The results of the Walsh study are important, and clearly suggest a role for structural variation in the etiology of schizophrenia. There are, however, a number of caveats and issues to consider. First, it would be unwise on the basis of that study to speculate on the likely contribution of rare variants to schizophrenia as a whole. It is likely correct that, due to selection pressures, highly penetrant alleles for disorders (like schizophrenia) that impair reproductive fitness are more likely to be of low frequency than they are to be common, but this does not imply that the converse is true. That is, one cannot assume that the penetrance of low frequency alleles is more likely to be high than low. Thus, and as pointed out by Walsh et al., it is not possible to know which or how many of the unique events observed in their study are individually pathogenic. Whether individual loci contribute to pathogenesis (and their penetrances) is, as we have seen, hard to establish. Estimating penetrance by association will require accurate measurement of frequencies in case and control populations, which for rare alleles, will have to be very large. Alternatively, more biased estimates of penetrance can be estimated from the degree of co-segregation with disease in highly multiplex pedigrees, but these are themselves fairly rare in schizophrenia, and pedigrees segregating any given rare CNV obviously even more so.

As Weinberger notes, the case for high penetrance (at the level of being sufficient to cause the disorder) is also undermined by their data from COS, where the majority of variants were inherited from unaffected parents. This accords well with the observation that 22q11DS, whilst conferring a high risk of schizophrenia, is still only associated with psychosis in ~30 percent of cases. It also accords well with the relative rarity of pedigrees segregating schizophrenia in a clearly Mendelian fashion, though the association of CNVs with severe illness of early onset might be expected to reduce the probability of transmission.

Third, there are questions about the generality of the findings. Cases in the case control series were ascertained in a way that enriched for severity and chronicity. Perhaps more importantly, the CNVs were greatly overrepresented in people with low IQ. Thus, one-third of all the potentially pathogenic CNVs in the case control series were seen in the tenth of the sample with IQ less than 80. The association between structural variants and low IQ is well known, as is the association between low IQ and psychotic symptoms, and it seems plausible to assume that forms of schizophrenia accompanied by mental retardation (MR) are likely to be enriched for this type of pathogenesis. The question that arises is whether the CNVs in such cases act simply by influencing IQ, which in turn has a non-specific effect on increasing risk of schizophrenia, or whether there are specific CNVs for MR plus schizophrenia, and some which may indeed increase risk of schizophrenia independent of IQ. In the case of 22q11 deletion, risk of schizophrenia does not seem to be dependent on risk of MR, but more work is needed to establish that this applies more generally.

Another reason to caution about the generality of the effect is that Walsh et al. found that cases with onset of psychotic symptoms at age 18 or younger were particularly enriched for CNVs, being greater than fourfold more likely than controls to harbor such variants. There did remain an excess of CNVs in cases with adult onset, supporting a more general contribution, although it should be noted that even in this group with severe disorder, this excess was not statistically significant (Fisher’s exact test, p = 0.17, 2-tailed, our calculation). The issue of age of onset clearly impacts upon assessing the overall contribution CNVs may make upon psychosis, since onset before 18, while not rare, is also not typical. A particular contribution of CNVs to early onset also appears supported by the second series studied, which had COS. However, this is a particularly unusual form of schizophrenia which is already known to have high rates of chromosomal abnormalities. Future studies of more typical samples will doubtless bear upon these issues.

Even allowing for the fact that many more CNVs may be detected as resolution of the methodology improves, the above considerations suggest it is premature to conclude a substantial proportion of cases of schizophrenia can be attributed to rare, highly penetrant CNVs. Nevertheless, even if it turns out that only a small fraction of the disorder is attributable to CNVs, as seen for other rare contributors to the disorder (e.g., DISC1 translocation), such uncommon events offer enormous opportunities for advancing our knowledge of schizophrenia pathogenesis.

References:

Craddock N, O'Donovan MC, Owen MJ. Phenotypic and genetic complexity of psychosis. Invited commentary on ... Schizophrenia: a common disease caused by multiple rare alleles.Br J Psychiatry. 2007 90:200-3. Abstract

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Related News: Copy Number Variations in Schizophrenia: Rare But Powerful?

Comment by:  Ridha JooberPatricia Boksa
Submitted 2 May 2008
Posted 4 May 2008

Walsh et al. claim that rare and severe chromosomal structural variants (SVs) (i.e., not described in the literature or in the specialized databases as of November 2007) are highly penetrant events each explaining a few, if not singular, cases of schizophrenia.

However, their definition of rareness is questionable. Indeed, it is unclear why SVs that are rare (<1 percent) but previously described should be omitted from their analysis. In addition, contrary to their own definition of rareness, the authors included in the COS sample several SVs that have been previously mentioned in the literature (e.g. “115 kb deletion on chromosome 2p16.3 disrupting NRXN1”). Furthermore, some of these SVs (entire Y chromosome duplication) are certainly not rare (by the authors’ definition), nor highly penetrant with regard to psychosis (Price et al., 1967). Finally, as their definition of rareness depends on a specific date, the results of this study will change over time.

As to the assessment of severity, it can equally be concluded from table 2 and using their statistical approach that "patients with schizophrenia are significantly more likely to harbor rare structural variants (6/150) that do not disrupt any gene compared to controls(2/268) (p = 0.03)", thus contradicting their claim. In fact, had they used criteria in the literature (Lee et al., 2007; (Brewer et al., 1999) (i.e., deletion SVs are more likely than duplications to be pathogenic) and appropriate statistical contrasts, deletions are significantly (p = 0.02) less frequent in patients (5/23) than in controls (9/13) who have SVs. In addition, the assumption of high penetrance is questionable given the high level (13 percent) of non-transmitted SVs in parents of COS patients. Is the rate of psychosis proportionately high in the parents? From the data presented, we know that only 2/27 SVs in COS patients are de novo and that “some” SVs are transmitted. Adding this undetermined number of transmitted SVs to the reported non-transmitted SVs will lead to an even larger proportion of parents carrying SVs. Disclosing the inheritance status of SVs in COS patients along with information on diagnoses in parents from this “rigorously characterised cohort,” represents a major criterion for assessing the risk associated with these SVs.

Consequently, it appears that the argument of rareness is rather idiosyncratic and contains inconsistencies, and the one of severity is very open to interpretation. Most importantly, it should be emphasized that amalgamated gene effects at the population level do not allow one to conclude that any single SV actually contributes to schizophrenia in an individual. Thus it is unclear how this study of grouped events differs from the thousands of controversial and underpowered association studies of single genes.

References:

Price WH, Whatmore PB. Behaviour Disorders and Pattern of Crime among XYY males Identified at a Maximum Security Hospital. Brit Med J 1967;1:533-6.

Lee C, Iafrate AJ, Brothman AR. Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet 2007 July;39(7 Suppl):S48-S54.

Brewer C, Holloway S, Zawalnyski P, Schinzel A, FitzPatrick D. A chromosomal duplication map of malformations: regions of suspected haplo- and triplolethality--and tolerance of segmental aneuploidy--in humans. Am J Hum Genet 1999 June;64(6):1702-8.

View all comments by Ridha Joober
View all comments by Patricia Boksa

Related News: Mixed Message: 15q13.3 Deletions Confer Risk, But for What?

Comment by:  Ben Pickard
Submitted 21 January 2009
Posted 21 January 2009

Before Christmas, an insightful discussion between SRF's Pete Farley and researchers Heather Mefford and Evan Eichler delved into the complex interplay between genotype (copy number variant status at 1q21.1) and phenotype (psychiatric illness, autism, mental retardation, and congenital abnormalities) (see SRF related news story). The upshot was that although deletions at this locus were statistically associated with pathologies, the severity and nature of those pathologies was extremely variable. This raised questions about whether researchers and clinicians should focus on the disease or the deletion, and what the mechanisms that determine the clinical endpoint might be. This is becoming a clear trend. Another CNV region at 16p11.2 has also been variously associated with both autism and schizophrenia. Deletions of just a single gene, CNTNAP2, as opposed to a gene cluster, have also shown this phenomenon of variable phenotype expression—deletion carriers have been diagnosed with autism, Gilles de la Tourette/obsessive compulsive disorder, schizophrenia/epilepsy, or remain entirely healthy (Bakkaloglu et al., 2008; Friedman et al., 2008; Verkerk et al., 2003; Belloso et al., 2007).

In the same vein, this new paper by Helbig and colleagues describes yet another example of a discrete copy number variant (microdeletion) that was originally linked with psychiatric phenotypes but is now also shown to give rise to idiopathic generalized epilepsy (IGE). The deletion is at 15q13.3, which encompasses the candidate neurotransmitter receptor gene, CHRNA7, among others. In fact, with a frequency of 1 percent in the IGE population and absence in controls, the deletion is the strongest genetic risk factor for this condition and is more prevalent in IGE than in either mental retardation or schizophrenia.

Although the study of CNVs has highlighted this genotype-phenotype issue, it has been observed previously in the context of the overlap of linkage hotspots between schizophrenia and bipolar disorder (Berrettini, 2003), in case-control association studies linking the same gene to multiple disorders (Chubb et al., 2008), and in the case of the Scottish family with the t(1;11) translocation disrupting DISC1, in which carrier phenotypes ranged from healthy to major depression, bipolar disorder, and schizophrenia (Blackwood et al., 2001).

So we are now faced with complex genetic disorders that really live up to their name. As such, two particular issues warrant further discussion.

The first issue is that clinicians seem to observe discrete rather than continuous disorder phenotypes. Despite the current diagnostic manuals leaving little room for diagnostic leeway, it seems that the majority of case phenotypes tend toward a limited number of outcomes such as schizophrenia, bipolar disorder, mental retardation, autism, and epilepsy. Moreover, no psychiatrist can distinguish DISC1 schizophrenia from 1q21.1 schizophrenia or NRG1 schizophrenia without recourse to genetic methodologies, suggesting that there is a positive biological drive towards the endpoint. To borrow what may be a useful analogy from physics, the system is “chaotic” (in terms of its genetic input and its effect on cellular biology) but tends toward “strange attractors” (a limited set of diagnoses) [http://en.wikipedia.org/wiki/Attractor]. Why might this be so? It may be that there are several higher order functional bottlenecks within the brain such as synaptic transmission efficiency, cortical development, astrocyte/oligodendrocyte function, hippocampal neurogenesis, higher order communication between brain regions, etc. These act to “sum” the expected environmental, genetic, and cellular complexity present within an individual and transform it into a limited set of potential outcomes—in essence, these are the strange attractors.

The next issue is how the same mutation can give rise to two (or more) different conditions. It may be useful to think of the Knudson “two-hit” hypothesis of cancer in which environment and other genetic factors act subsequent to a “deep” genetic fault (Knudson, 1971).

The CNV examples above may represent such fundamental disruptions and most probably impinge on neurodevelopmental pathways, priming the brain to be tipped over the threshold into a disease state. In fact, the t(1:11) translocation carriers present evidence for such a phenomenon as both healthy and affected carriers show abnormal P300 brain response activities suggesting this endophenotype highlights an underlying brain dysfunction (Blackwood et al., 2001).

We have to postulate that the additional genetic or environmental influences (modifiers) not only determine entry into the disease state but also dictate the final outcome. Possible candidates for modifiers of the deletions above are the remaining single copy alleles at the CNV locus—exposed recessive mutations, imprinting, or epigenetic modification could all alter expressivity and penetrance of the deletion phenotype. However, limited studies by Eichler’s group seem to discount this possibility (Mefford et al., 2008).

In any case, genomewide association and CNV studies suggest that there is plenty of scope for a sufficient burden of genetic modifiers outside the CNV region. This may also fit in with the seemingly disparate concepts of rare/familial variants exposed by linkage and common/low odds ratio variants revealed by association. Both act causally with the former potentially acting as the “first hit.”

As time progresses, we will move towards the definition of the range of phenotypes potentially resulting from each genotype and the spectrum of genotypes causing each phenotype. CNVs represent a pretty blunt tool to dissect finer relationships between genotype and phenotype, so it is to be expected that rare but penetrant point mutations that emerge from resequencing projects will be of greater use in dissecting function-phenotype links—as has been seen with the connexin gene family, for example (Rabionet et al., 2002).

In summary, it is to be hoped that the clinical and research communities are able to embrace these complexities for what they offer—a deeper understanding of these disorders, one that is intimately linked to the development and function of the brain.

References:

Bakkaloglu B, O'roak BJ, Louvi A, Gupta AR, Abelson JF, Morgan TM, Chawarska K, Klin A, Ercan-Sencicek AG, Stillman AA, Tanriover G, Abrahams BS, Duvall JA, Robbins EM, Geschwind DH, Biederer T, Gunel M, Lifton RP, State MW. Molecular cytogenetic analysis and resequencing of contactin associated protein-like 2 in autism spectrum disorders. Am J Hum Genet. 2008 Jan 1;82(1):165-73. Abstract

Friedman JI, Vrijenhoek T, Markx S, Janssen IM, van der Vliet WA, Faas BH, Knoers NV, Cahn W, Kahn RS, Edelmann L, Davis KL, Silverman JM, Brunner HG, van Kessel AG, Wijmenga C, Ophoff RA, Veltman JA. CNTNAP2 gene dosage variation is associated with schizophrenia and epilepsy. Mol Psychiatry. 2008 Mar 1;13(3):261-6. Abstract

Verkerk AJ, Mathews CA, Joosse M, Eussen BH, Heutink P, Oostra BA, . CNTNAP2 is disrupted in a family with Gilles de la Tourette syndrome and obsessive compulsive disorder. Genomics. 2003 Jul 1;82(1):1-9. Abstract

Belloso JM, Bache I, Guitart M, Caballin MR, Halgren C, Kirchhoff M, Ropers HH, Tommerup N, Tümer Z. Disruption of the CNTNAP2 gene in a t(7;15) translocation family without symptoms of Gilles de la Tourette syndrome. Eur J Hum Genet. 2007 Jun 1;15(6):711-3. Abstract

Berrettini W. Evidence for shared susceptibility in bipolar disorder and schizophrenia. Am J Med Genet C Semin Med Genet. 2003 Nov 15;123C(1):59-64. Abstract

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

Blackwood DH, Fordyce A, Walker MT, St Clair DM, Porteous DJ, Muir WJ. Schizophrenia and affective disorders--cosegregation with a translocation at chromosome 1q42 that directly disrupts brain-expressed genes: clinical and P300 findings in a family. Am J Hum Genet. 2001 Aug 1;69(2):428-33. Abstract

Knudson AG. Mutation and cancer: statistical study of retinoblastoma. Proc Natl Acad Sci U S A. 1971 Apr 1;68(4):820-3. Abstract

Mefford HC, Sharp AJ, Baker C, Itsara A, Jiang Z, Buysse K, Huang S, Maloney VK, Crolla JA, Baralle D, Collins A, Mercer C, Norga K, de Ravel T, Devriendt K, Bongers EM, de Leeuw N, Reardon W, Gimelli S, Bena F, Hennekam RC, Male A, Gaunt L, Clayton-Smith J, Simonic I, Park SM, Mehta SG, Nik-Zainal S, Woods CG, Firth HV, Parkin G, Fichera M, Reitano S, Lo Giudice M, Li KE, Casuga I, Broomer A, Conrad B, Schwerzmann M, Räber L, Gallati S, Striano P, Coppola A, Tolmie JL, Tobias ES, Lilley C, Armengol L, Spysschaert Y, Verloo P, De Coene A, Goossens L, Mortier G, Speleman F, van Binsbergen E, Nelen MR, Hochstenbach R, Poot M, Gallagher L, Gill M, McClellan J, King MC, Regan R, Skinner C, Stevenson RE, Antonarakis SE, Chen C, Estivill X, Menten B, Gimelli G, Gribble S, Schwartz S, Sutcliffe JS, Walsh T, Knight SJ, Sebat J, Romano C, Schwartz CE, Veltman JA, de Vries BB, Vermeesch JR, Barber JC, Willatt L, Tassabehji M, Eichler EE. Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med. 2008 Oct 16;359(16):1685-99. Abstract

Rabionet R, López-Bigas N, Arbonès ML, Estivill X. Connexin mutations in hearing loss, dermatological and neurological disorders. Trends Mol Med. 2002 May 1;8(5):205-12. Abstract

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Related News: Schizophrenia-associated Variant in ZNF804A Gene Affects Brain Connectivity

Comment by:  James WaltersMichael Owen (SRF Advisor)
Submitted 3 June 2009
Posted 3 June 2009

Andreas Meyer-Lindenberg’s group examine the association between a single nucleotide polymorphism (SNP), rs1344706 in gene ZNF804A, recently identified as a risk factor for schizophrenia in a genome-wide association study (GWAS) (O'Donovan et al., 2008) and functional connectivity as measured by fMRI. The attraction of this polymorphism for a study of this kind is twofold. First, statistically speaking it is the most robust SNP association with schizophrenia reported to date. Second, because a single variant shows strong evidence for association, which is not the case for other reported associations, it is possible to specify a priori for the gene in question directional hypotheses in relation to potential neurocognitive correlates. This militates against the generation of false positives through the testing of multiple SNPs and haplotypes which has rendered problematic the interpretation of at least some previous genetic imaging studies (Walters and Owen, 2007). The function of ZNF804A is unknown but the fact that it contains a zinc finger domain suggests that it may be a transcription factor. It is hoped that the characterization of the actions of SNPs identified by GWAS will identify new pathogenic mechanisms of psychosis. One way in which this can be achieved is via approaches such as that taken in this article.

Esslinger et al. report variations in functional connectivity in 115 healthy individuals according to rs1344706 risk variant status. Given the association of ZNF804A with both schizophrenia and bipolar disorder they employed two fMRI tasks thought to be sensitive to altered function in these disorders: the N Back (2back) task is sensitive to deficits of dorsolateral prefrontal cortex (DLPFC) function in schizophrenia and an emotional face-matching task is linked with amygdala function and thought to be relevant to mood disorder. They compared the activity in these regions and functional connectivity (using time-series correlation) between the three rs1344706 genotype groups.

No differences between genotype groups were found for activation, but the authors did identify altered connectivity with the most activated DLPFC locale. Risk-allele carriers were shown to exhibit a lack of uncoupling of activity (increased functional connectivity) between the right DLPFC and left hippocampus during the 2-back task as well as decreased connectivity within right DLPFC and between right and left DLPFC. Risk variant carriers also showed wide ranging increased connectivity between right amygdala and other anatomical regions. The majority of these findings showed a risk allele dose effect.

The increased DLPFC/hippocampus functional connectivity in carriers of the risk allele is potentially the most interesting finding given that Meyer-Lindenberg’s group has previously shown that those with schizophrenia show increased functional connectivity between DLPFC and hippocampus during working memory (Meyer-Lindenberg et al., 2005). Notes of caution in this regard are that 1) the biological, anatomical or functional significance of fMRI determined functional connectivity is yet to be established and 2) other functional connectivity studies in schizophrenia have produced conflicting results Lawrie et al., 2002. Nonetheless, it is interesting that rs1344706 may affect co-ordination of activity between these two brain regions given their seeming importance in psychotic conditions. The significance of these findings to cognitive deficits and other symptom domains needs further investigation particularly as others have postulated dysconnectivity has more relevance to first rank psychotic symptoms (Stephan et al., 2009).

It is likely that genome-wide association approaches will continue to identify genes with unknown neural function and so approaches such as this are likely to be a valuable way of identifying the biological/neural pathways that involve these genes. It is also imperative that as in this study methodology is employed to allow for multiple testing and also that negative findings are reported. We would also suggest caution until these findings are replicated. As well as such approaches in humans, it is also important to investigate the effects of identified variants at other levels of analysis from gene expression to behavioural genetics work. Finally we find it reassuring that GWAS approaches seem to be successful in identifying risk variants whose functions can be investigated using methods such as that taken by Esslinger et al.

References:

O'Donovan MC, Craddock N, Norton N, et al. Identification of loci associated with schizophrenia by genome-wide association and follow-up. Nature Genetics. 2008;40(9):1053-1055. Abstract

Walters JT, Owen MJ. Endophenotypes in psychiatric genetics. Mol Psychiatry. 2007;12(10):886-890. Abstract

Meyer-Lindenberg AS, Olsen RK, Kohn PD, et al. Regionally Specific Disturbance of Dorsolateral Prefrontal-Hippocampal Functional Connectivity in Schizophrenia. Archives of General Psychiatry. 2005;62(4):379-386. Abstract

Lawrie SM, Buechel C, Whalley HC, Frith CD, Friston KJ, Johnstone EC. Reduced frontotemporal functional connectivity in schizophrenia associated with auditory hallucinations. Biological Psychiatry. 2002;51(12):1008-1011. Abstract

Stephan KE, Friston KJ, Frith CD. Dysconnection in Schizophrenia: From Abnormal Synaptic Plasticity to Failures of Self-monitoring. Schizophr Bull. 2009;35(3):509-527. Abstract

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Related News: Largest GWAS Analysis to Date Offers Only Two New Candidate Genes

Comment by:  Todd LenczAnil Malhotra (SRF Advisor)
Submitted 3 July 2009
Posted 3 July 2009

The three companion papers published in Nature provide important new evidence for a role of the MHC complex and common variation across the genome in risk for schizophrenia. These studies have exploited the availability of comprehensive genotyping technologies, coupled with large cohorts of cases and controls, to identify candidate loci for disease susceptibility.

A notable feature of these papers is the clear willingness of each of the groups to share its data, and to provide overlapping presentations of each others’ results. The combination of datasets permitted the statistical significance of the MHC findings to emerge, thereby increasing confidence in results. The implication that immune processes may interact with genetic risk to influence schizophrenia risk is consistent with several lines of evidence, including our own small GWAS study (Lencz et al., 2007) implicating cytokine receptors in schizophrenia susceptibility.

Perhaps most intriguing is the finding from the International Schizophrenia Consortium demonstrating that a “score” test—combining information from many thousands of common variants—can reliably differentiate patients and controls across multiple psychiatric cohorts. These results indicate that hundreds, if not thousands, of genes of small effect may contribute to schizophrenia risk. Moreover, these same genes were shown to contribute to bipolar risk (but not risk for non-psychiatric disorders such as diabetes).

Much more work remains to be done in psychiatric genetics. While the score test accounted for about 3 percent of the observed case-control variance, statistical modeling suggested that common variation could explain as much as one-third or more of the total risk. Nevertheless, there remains a substantial proportion of genetic “dark matter” (unexplained variance), given the high heritability of a disorder such as schizophrenia. Complementary approaches are needed to further parse the source of the common genetic variance, as well as to identify rare yet highly penetrant mutations. Additional techniques, such as pharmacogenetic studies and endophenotypic research, will help to explicate the functionality and clinical significance of observed risk alleles.

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Related News: Largest GWAS Analysis to Date Offers Only Two New Candidate Genes

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 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.

References:

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: 19910–19914. 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: 12387–12392. 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

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Related News: Largest GWAS Analysis to Date Offers Only Two New Candidate Genes

Comment by:  Irving Gottesman, SRF Advisor
Submitted 3 July 2009
Posted 3 July 2009
  I recommend the Primary Papers

The synthesis and extraction of the essence of the 3 Nature papers by Heimer and Farley represents science reporting at its best. Completion of the task while the ink was still wet shows that SRF is indeed in good hands. Congratulations on being concise, even-handed, non-judgmental, and challenging under the pressure of time.

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Related News: Largest GWAS Analysis to Date Offers Only Two New Candidate Genes

Comment by:  Christopher RossRussell L. Margolis
Submitted 6 July 2009
Posted 6 July 2009

Schizophrenia Genetics: Glass Half Full?
While it may be disappointing that the GWAS described above did not identify more genes, they nevertheless represent a landmark in psychiatric genetics and suggest a dual approach for the future: continued large-scale genetic association studies along with alternative genetic approaches leading to the discovery of new genetic etiologies, and more functional investigations to identify pathways of pathogenesis—which may themselves suggest new etiologies.

The consistent identification of an association with the MHC locus reinforces (without proving, as pointed out in the SRF news story) long-standing interest in the involvement of infectious or immune factors in schizophrenia pathogenesis (Yolken and Torrey, 2008). Epidemiologic and neuropathological studies that include patients selected for the presence or absence of immunologic genetic risk variants could potentially clarify etiology; cell and mouse model studies could clarify pathogenesis (Ayhan et al., 2009). It is striking that a major genetic finding in schizophrenia serves to reinforce the concept of environmental risk factors.

The two specific genes identified by the SGENE consortium, NRGN and TCF4, offer intriguing new leads into schizophrenia. This should foster a number of further genetic and neurobiological studies. Deep resequencing (and CNV analysis) can detect rare causative mutations, as exemplified by TCF4 mutations leading to Pitt-Hopkins syndrome. Neurogranin already has clear connections to interesting signaling pathways related to glutamate transmission. A hope is that further studies of both gene products and their interactions will identify pathogenic pathways.

The ISC used common genetic variants “en masse” to generate a “polygene score” from discovery samples of patients; that score was able to predict case status in test populations. The success of this approach provides very strong evidence that a portion of schizophrenia risk status is attributable to common genetic variants acting in concert and that schizophrenia shares genetic factors with bipolar disorder, but not with other diseases. This analysis has multiple practical implications for the direction of research. First, since polygenic factors explain only a portion of the genetic risk, the search for other genetic factors—rare mutations of major effect detectable by deep sequencing, CNVs, variations in tandem repeats (Bruce et al., 2009, in press), and other genomic lesions—takes on new importance. Second, a meaningful integration of polygenic factors in a way that facilitates understanding of schizophrenia pathogenesis and the discovery of therapeutic targets will require identification of relevant pathways. Examination of patient-derived material—such as neurons differentiated from induced pluripotent stem cells taken from well-characterized, patient populations—may be of great value.

The remarkable overlap between the genetic factors of schizophrenia and bipolar disorder suggests the need for further and more inclusive clinical studies—not just of “endophenotypes,” but also of the phenotypes themselves, together, rather than in isolation (Potash and Bienvenu, 2009). For instance, it is only within the past few years that the importance of cognitive dysfunction in schizophrenia has been appreciated. Cognition in bipolar disorder is even less well studied.

How much is really known about the longitudinal course of both disorders? Do genetic factors predict disease outcome? It is only recently that studies have focused intensively on the early course of schizophrenia and its prodrome. Much more is still to be learned, and even less is known about bipolar disorder. In conjunction with this greater understanding of clinical phenotype, it will clearly be necessary to refine the approach to phenotype by establishing the biological framework for these diseases and by establishing biomarkers, such as disruption in white matter (Karlsgodt et al., 2009) or abnormalities in functional networks (Demirci et al., 2009), that cut across current nosological categories. In turn, longitudinal study of clinical, imaging, and functional outcomes of schizophrenia and bipolar disorders should facilitate both focused candidate genetic studies and GWAS of large populations.

References:

Yolken RH, Torrey EF. Are some cases of psychosis caused by microbial agents? A review of the evidence. Mol Psychiatry. 2008 May;13(5):470-9. Abstract

Ayhan Y, Sawa A, Ross CA, Pletnikov MV. Animal models of gene-environment interactions in schizophrenia. Behav Brain Res. 2009 Apr 18. Abstract

Potash JB, Bienvenu OJ. Neuropsychiatric disorders: Shared genetics of bipolar disorder and schizophrenia. Nat Rev Neurol. 2009 Jun;5(6):299-300. Abstract

Karlsgodt KH, Niendam TA, Bearden CE, Cannon TD. White matter integrity and prediction of social and role functioning in subjects at ultra-high risk for psychosis. Biol Psychiatry. 2009 May 6. Epub ahead of print. Abstract

Demirci O, Stevens MC, Andreasen NC, Michael A, Liu J, White T, Pearlson GD, Clark VP, Calhoun VD. Investigation of relationships between fMRI brain networks in the spectral domain using ICA and Granger causality reveals distinct differences between schizophrenia patients and healthy controls. Neuroimage. 2009 Jun;46(2):419-31. Abstract

Bruce HA, Sachs NA, Rudnicki DD, Lin SG, Willour VL, Cowell JK, Conroy J, McQuaid D, Rossi M, Gaile DP, Nowak NJ, Holmes SE, Sklar P, Ross CA, DeLisi LE, Margolis RL. Long tandem repeats as a form of genomic copy number variation: structure and length polymorphism of a chromosome 5p repeat in control and schizophrenia populations. Psychiatric Genetics, in press.

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Related News: Largest GWAS Analysis to Date Offers Only Two New Candidate Genes

Comment by:  David Collier
Submitted 6 July 2009
Posted 6 July 2009
  I recommend the Primary Papers

This report is unnecessarily negative, from my point of view. The three studies show not only that GWAS can identify susceptibility alleles for schizophrenia, but that the majority of risk comes from common variants of small effect. These can be found, but as in other complex traits and diseases, such as obesity and height, considerable power is needed, because effect sizes are small, meaning greater samples sizes. This approach works: there are now almost 60 variants influencing height (Hirschhorn et al., 2009; Soranzo et al., 2009; Sovio et al., 2009). Furthermore, the genes identified so far from both traditional mapping, CNV analysis and GWAS, point to two biological pathways, the integrity of the synapse (neurexin 1, neurogranin, etc.) and the wnt/GSK3β signaling pathway (DISC1, TCF4, etc.), which is involved in functions such as neurogenesis in the brain. The identification of disease pathways for schizophrenia has major implications and should not be underestimated. It would be daft to lose nerve now and turn away from GWAS just as they are bearing fruit.

I would like to correct/expand on my comments to Peter Farley, to say that while statistical significance for some markers may be reached sooner, significance for many of the hundreds if not thousands of common schizophrenia susceptibility alleles of small effect might not emerge until samples of 100,000 cases and more than 100,000 controls have been collected. Another point is that organizations such the Wellcome Trust are already assembling case samples for schizophrenia as well as control samples.

Also, I would like to clarify that I believe the remainder of genetic variation, after common variation has been taken into account, will come from some combination of rare CNVs, other rare variants such as SNPs and other types of genetic marker such as variable number of tandem repeats (VNTRs) and of course the much neglected contribution from gene-environment interactions, in which main genetic effects may be obscured.

References:

Hirschhorn JN, Lettre G. Progress in genome-wide association studies of human height. Horm Res. 2009 Apr 1 ; 71 Suppl 2():5-13. Abstract

Soranzo N, Rivadeneira F, Chinappen-Horsley U, Malkina I, Richards JB, Hammond N, Stolk L, Nica A, Inouye M, Hofman A, Stephens J, Wheeler E, Arp P, Gwilliam R, Jhamai PM, Potter S, Chaney A, Ghori MJ, Ravindrarajah R, Ermakov S, Estrada K, Pols HA, Williams FM, McArdle WL, van Meurs JB, Loos RJ, Dermitzakis ET, Ahmadi KR, Hart DJ, Ouwehand WH, Wareham NJ, Barroso I, Sandhu MS, Strachan DP, Livshits G, Spector TD, Uitterlinden AG, Deloukas P. Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. PLoS Genet. 2009 Apr 1 ; 5(4):e1000445. Abstract

Sovio U, Bennett AJ, Millwood IY, Molitor J, O'Reilly PF, Timpson NJ, Kaakinen M, Laitinen J, Haukka J, Pillas D, Tzoulaki I, Molitor J, Hoggart C, Coin LJ, Whittaker J, Pouta A, Hartikainen AL, Freimer NB, Widen E, Peltonen L, Elliott P, McCarthy MI, Jarvelin MR. Genetic determinants of height growth assessed longitudinally from infancy to adulthood in the northern Finland birth cohort 1966. PLoS Genet. 2009 Mar 1 ; 5(3):e1000409. Abstract

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Related News: Largest GWAS Analysis to Date Offers Only Two New Candidate Genes

Comment by:  Michael O'Donovan, SRF AdvisorNick CraddockMichael Owen (SRF Advisor)
Submitted 9 July 2009
Posted 9 July 2009

Some commentators in their reflections take a rather negative view on what has been achieved through the application of GWAS technology to schizophrenia and psychiatric disorders more generally. We strongly disagree with this position. Below, we give examples of a number of statements that can be made about the aetiology of schizophrenia and bipolar disorder that could not be made at high levels of confidence even two years ago that are based upon evidence deriving from the application of GWAS.

1. We know with confidence that the role of rare copy number variants in schizophrenia is not limited to 22q11DS (VCFS) (reviewed recently in O’Donovan et al., 2009). We do not yet know how much of a contribution, but we know the identity of an increasing number of these. Most span multiple genes so it may prove problematic as it has in 22q11DS to identify the relevant molecular mechanisms. However, for one locus, the CNVs are limited to a single gene: Neurexin1 (Kirov et al., 2008; Rujescu et al., 2009). Genetic findings are merely the start of the journey to a deeper biological understanding, but no doubt many neurobiological researchers have already embarked on that journey in respect of neurexin1.

2. Although we have argued in this forum that some of the major pre-GWAS findings in schizophrenia very likely reflect true susceptibility genes (DTNBP1, NRG1, etc), we now have at least 4 novel loci where the evidence is more definitive (ZNF804A, MHC, NRGN, TCF4), (O’Donovan et al., 2008a; ISC, 2009; Shi et al., 2009; Stefansson et al., 2009) and two novel loci (Ferreira et al., 2008) in bipolar disorder (ANK3 and CACNA1C), at least one of which (CACNA1C) additionally confers risk of schizophrenia (Green et al., 2009). This is obviously a small part of the picture, but it is certainly better than no picture at all. These findings also offer a much more secure foundation than the earlier findings upon which to build follow up studies, for example brain imaging, and cognitive phenotypes (Esslinger et al., 2009), and even candidate gene studies. We would not regard the first convincing evidence that altered calcium channel function is a primary aetiological event in at least some forms of psychosis as a trivial gain in knowledge.

3. We can say with confidence that common alleles of small effect are abundant in schizophrenia, and that they contribute to a substantial part of the population risk (ISC, 2009). Identifying any one of these at stringent levels of statistical significance may be challenging in terms of sample sizes. As we have pointed out before, merging multiple datasets may indeed obscure some true associations because of sometimes unpredictable relationships between risk alleles and those assayed indirectly in GWAS studies (Moskvina and O’Donovan, 2007). Nevertheless, that many of the same alleles are overrepresented in multiple independent GWAS datasets from different countries (ISC, 2009) means that larger samples offer the prospect of identifying many more of these. This is not to say that large samples are the only approach; genetic heterogeneity may well underpin some aspects of clinical heterogeneity (Craddock et al., 2009a). However, with the exception of individual large pedigrees, it is not yet evident which type of clinical sample one should base a small scale study on. It should also be self-evident that the analysis of multiple samples, each with a different phenotypic structure, will pose major problems in respect of multiple testing and subsequent replication. Moreover, ascertaining special samples that represent putative subtypes of the clinical (and endophenotypic) spectrum of psychosis will first require large samples to be carefully assessed and the relevant subjects extracted. Subsequently, downstream, evaluation of specific genotype-phenotype relationships will require the remainder of the clinical population to be genotyped in a suitably powered way to show that those effects are specific to some clinical features of the disorder. Increasingly, it is ascertainment and assessment that dominate the cost of GWAS studies so it is not clear this approach will achieve any economies. We must also remember that after a GWAS study, there remains the opportunity to look in a controlled manner for relatively specific associations in the context of the heterogeneous clinical picture. For example we are aware of a number of papers in development that will exploit the sorts of multi-locus tests reported by the ISC to refine diagnostics, and no doubt many other applications of this will emerge in the next year or so.

Critics should bear in mind that the GWAS data are not just there for the ‘headline’ genome-wide findings, but that the data will be available to mine for years to come. The findings reported to date are based on only the simplest analyses.

4. If it were the case that the thousands of SNPs of small effect were randomly distributed across biological systems, none being of more relevance to pathophysiology than another, identifying them would probably be a pointless endeavour. However, there is no reason to believe this will be the case. We have recently shown that in bipolar disorder, the GWAS signals are enriched in particular biological pathways (Holmans et al., 2009) and we also published strong evidence for a relatively selective involvement of the GABAergic system in schizoaffective disorder (Craddock et al., 2009b). We are aware of an as-yet unpublished independent sample with similar findings. We would not regard the first convincing evidence that altered GABA function is a primary aetiological event in at least some forms of psychosis as a trivial gain in knowledge.

Incidentally it is a common misconception that the identification of risk alleles of small effect necessarily confers no useful insights into pathogenesis and possible drug targets. For example, common alleles in PPARG and KCNJ11 have been robustly shown to confer risk to Type 2 diabetes (T2D) but with odds ratios in the region of only 1.14 (of similar magnitude to those revealed by GWAS of schizophrenia). PPARG encodes the target for the thiazolidinedione class of drugs used to treat T2D. KCNJ11 encodes part of the target for another class of diabetes drug, the sulphonylureas (Prokopenko et al., 2008). Moreover, studies of novel associated variants identified in T2D GWAS in healthy, non-diabetic, populations have demonstrated that for most, the primary effect on T2D susceptibility is mediated through deleterious effects on insulin secretion, rather than insulin action (Prokopenko et al., 2008). Further examples of insights into the biology of common diseases coming from the identification of loci of small effect are the implication of the complement system in age-related macular degeneration and autophagy in Crohn’s disease (Hirschhorn, 2009). Already, efforts are under way to translate the new recognition of the role of autophagy in Crohn’s disease into new therapeutic leads (Hirschhorn, 2009). Of course many of the loci identified in GWAS implicate genes whose functions are as yet largely or completely unknown, and determining those functions is a prerequisite of translating those findings. Nevertheless, we believe that the greatest benefits that will accrue from the continued discovery of risk loci through GWAS will come from the assembly of that information into novel disease pathways leading to novel therapeutic targets.

5. We can say with confidence that bipolar disorder and schizophrenia substantially overlap, at least in terms of polygenic risk (ISC, 2009). As clinicians, we do not regard that knowledge as a trivial achievement.

6. We can say with confidence from studies of CNVs that schizophrenia and autism share at least some risk factors in common (O’Donovan et al., 2009). We believe that is also an important insight.

The above are major achievements in what we expect to be a long but accelerating process of picking apart the origins of schizophrenia and other psychotic disorders. We do not think that any other research discipline in psychiatry has done more to advance that knowledge in the past 100 years.

Like that other common familial diseases, the genetics of schizophrenia and bipolar disorder is a “mixed economy” of common alleles of small effect and rare alleles of large and small effects, including CNVs. Those who are concerned at the cost of collecting large samples for GWAS studies must bear in mind that the robust identification of both types of mutation will require similarly large samples; we will just have to get used to that fact if we want to make progress. Collecting samples like this may be expensive, but as clinicians, we know those costs are trivial compared with the human and economic costs of psychotic disorders.

The question of phenotype definition is one which we have repeatedly addressed (Craddock et al., 2009a). Unquestionably, if we knew the true pathophysiological basis of these disorders, we could do better. The fact is that we don’t. Given that, it must be extremely encouraging that despite the problems, risk loci can be robustly identified by GWAS using samples defined by current diagnostic criteria. Moreover, armed with GWAS data in these heterogeneous populations, additional risk genes can be identified through strategies aimed at refining the phenotype that are not constrained by the current dichotomous view of the functional psychoses. We have shown at least one way in which this might be achieved without imposing a further burden of multiple testing (Craddock et al., 2009b), and have little doubt that others will emerge. We agree that approaches to phenotyping that more directly index underlying pathophysiology are highly appealing, and will ultimately be necessary for understanding the mechanistic relationships between gene and disorder. However, the two cardinal assumptions upon which the use of endophenotypes is predicated for gene discovery are questionable. First, there is little good evidence that putative endophenotypes are substantially simpler genetically than “exophenotypes” (Flint and Munafo, 2007). Second, there is rarely good evidence that the current crop of popular putative endophenotypes lie on the disease pathway, indeed there seems to be substantial pleiotropy in the genetics of complex traits, psychosis included (Prokopenko et al., 2008; O’Donovan et al., 2008b).

Finally, we reiterate that while only small parts of the heritability of any complex disorder have been accounted for, large-scale genetic approaches have been extremely successful in studies of non-psychiatric diseases (Manolio et al., 2008) and have led to substantial advances in our understanding of pathogenesis, even for diseases like Crohn’s disease where there was already prior knowledge of pathogenesis from other research methods (Mathew, 2008).

Psychiatry starts from a situation in which there is no robust prior knowledge of pathogenesis for the major phenotypes. Recent findings suggest that mental illness may be the medical field that will actually benefit most over the coming years from application of these powerful molecular genetic technologies.

References:
Craddock N, O'Donovan MC, Owen MJ. (2009a) Psychosis Genetics: Modeling the Relationship between Schizophrenia, Bipolar Disorder, and Mixed (or "Schizoaffective") Psychoses. Schizophrenia Bulletin 35(3):482-490. Abstract

Craddock N, Jones L, Jones IR, Kirov G, Green EK, Grozeva D, Moskvina V, Nikolov I, Hamshere ML, Vukcevic D, Caesar S, Gordon-Smith K, Fraser C, Russell E, Norton N, Breen G, St Clair D, Collier DA, Young AH, Ferrier IN, Farmer A, McGuffin P, Holmans PA, Wellcome Trust Case Control Consortium (WTCCC), Donnelly P, Owen MJ, O’Donovan MC. Strong genetic evidence for a selective influence of GABAA receptors on a component of the bipolar disorder phenotype. Molecular Psychiatry advanced online publication 1 July 2008; doi:10.1038/mp.2008.66. (b) Abstract

Esslinger C, Walter H, Kirsch P, Erk S, Schnell K, Arnold C, Haddad L, Mier D, Opitz von Boberfeld C, Raab K, Witt SH, Rietschel M, Cichon S, Meyer-Lindenberg A. (2009) Neural mechanisms of a genome-wide supported psychosis variant. Science 324(5927):605. Abstract

Ferreira MAR, O’Donovan MC, Meng YA, Jones IR, Ruderfer DM, Jones L, Fan J, Kirov G, Perlis RH, Green EK, Smoller JW, Grozeva D, Stone J, Nikolov I, Chambert K, Hamshere ML, Nimgaonkar V, Moskvina V, Thase ME, Caesar S, Sachs GS, Franklin J, Gordon-Smith K, Ardlie KG, Gabriel SB, Fraser C, Blumenstiel B, Defelice M, Breen G, Gill M, Morris DW, Elkin A, Muir WJ, McGhee KA, Williamson R, MacIntyre DJ, McLean A, St Clair D, VanBeck M, Pereira A, Kandaswamy R, McQuillin A, Collier DA, Bass NJ, Young AH, Lawrence J, Ferrier IN, Anjorin A, Farmer A, Curtis D, Scolnick EM, McGuffin P, Daly MJ, Corvin AP, Holmans PA, Blackwood DH, Wellcome Trust Case Control Consortium (WTCCC), Gurling HM, Owen MJ, Purcell SM, Sklar P and Craddock NJ. (2008) Collaborative genome-wide association analysis of 10,596 individuals supports a role for Ankyrin-G (ANK3) and the alpha-1C subunit of the L-type voltage-gated calcium channel (CACNA1C) in bipolar disorder. Nature Genetics 40:1056-1058. Abstract

Flint J, Munafò MR. (2007) The endophenotype concept in psychiatric genetics. Psychological Medicine 37(2):163-180. Abstract

Green EK, Grozeva D, Jones I, Jones L, Kirov G, Caesar S, Gordon-Smith K, Fraser C, Forty L, Russell E, Hamshere ML, Moskvina V, Nikolov I, Farmer A, McGuffin P, Wellcome Trust Case Consortium, Holmans PA, Owen MJ, O’Donovan MC and Craddock N. (2009) Bipolar disorder risk allele at CACNA1C also confers risk to recurrent major depression and to schizophrenia. Molecular Psychiatry (in press).

Hirschhorn JN. (2009) Genomewide association studies--illuminating biologic pathways. New England Journal of Medicine 360(17):1699-1701. Abstract

Holmans P, Green E, Pahwa J, Ferreira M, Purcell S, Sklar P, Owen M, O’Donovan M, Craddock N. Gene ontology analysis of GWAS datasets provide insights into the biology of bipolar disorder. The American Journal of Human Genetics 2009 Jun 17 [Epub ahead of print]. International Schizophrenia Consortium. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 2009 Jul 1 [Epub ahead of print]. Abstract

Kirov G, Gumus D, Chen W, Norton N, Georgieva L, Sari M, O'Donovan MC, Erdogan F, Owen MJ, Ropers HH, Ullmann R. (2008) Comparative genome hybridization suggests a role for NRXN1 and APBA2 in schizophrenia. Human Molecular Genetics 17(3):458-465. Abstract

Manolio TA, Brooks LD, Collins FS. (2008) A HapMap harvest of insights into the genetics of common disease. Journal of Clinical Investigation 118(5):1590-1605. Abstract

Mathew CG. (2008) New links to the pathogenesis of Crohn disease provided by genome-wide association scans. Nature Review Genetics 9(1):9-14. Abstract

Moskvina V and O'Donovan MC. (2007) Detailed analysis of the relative power of direct and indirect association studies and the implications for their interpretation. Human Heredity 64(1):63-73. Abstract

O’Donovan MC, Kirov G, Owen MJ. (2008a) Phenotypic variations on the theme of CNVs. Nature Genetics 40(12):1392-1393. Abstract

O’Donovan MC, Craddock N, Norton N, Williams H, Peirce T, Moskvina V, Nikolov I, Hamshere M, Carroll L, Georgieva L, Dwyer S, Holmans P, Marchini JL, Spencer C, Howie B, Leung H-T, Hartmann AM, Möller H-J, Morris DW, Shi Y, Feng G, Hoffmann P, Propping P, Vasilescu C, Maier W, Rietschel M, Zammit S, Schumacher J, Quinn EM, Schulze TG, Williams NM, Giegling I, Iwata N, Ikeda M, Darvasi A, Shifman S, He L, Duan J, Sanders AR, Levinson DF, Gejman P, Molecular Genetics of Schizophrenia Collaboration , Cichon S, Nöthen MM, Gill M, Corvin A, Rujescu D, Kirov G, Owen MJ. (2008b) Identification of novel schizophrenia loci by genome-wide association and follow-up. Nature Genetics 40:1053-1055. Abstract

O’Donovan MC, Craddock N, Owen MJ. Genetics of psychosis; Insights from views across the genome. Human Genetics 2009 Jun 12 [Epub ahead of print]. Abstract

Prokopenko I, McCarthy MI, Lindgren CM. (2008) Type 2 diabetes: new genes, new understanding. Trends in Genetics 24(12):613-621. Abstract

Rujescu D, Ingason A, Cichon S, Pietiläinen OP, Barnes MR, Toulopoulou T, Picchioni M, Vassos E, Ettinger U, Bramon E, Murray R, Ruggeri M, Tosato S, Bonetto C, Steinberg S, Sigurdsson E, Sigmundsson T, Petursson H, Gylfason A, Olason PI, Hardarsson G, Jonsdottir GA, Gustafsson O, Fossdal R, Giegling I, Möller HJ, Hartmann AM, Hoffmann P, Crombie C, Fraser G, Walker N, Lonnqvist J, Suvisaari J, Tuulio-Henriksson A, Djurovic S, Melle I, Andreassen OA, Hansen T, Werge T, Kiemeney LA, Franke B, Veltman J, Buizer-Voskamp JE; GROUP Investigators, Sabatti C, Ophoff RA, Rietschel M, Nöthen MM, Stefansson K, Peltonen L, St Clair D, Stefansson H, Collier DA. (2009) Disruption of the neurexin 1 gene is associated with schizophrenia. Human Molecular Genetics 18(5):988-996. Abstract

Shi J, Levinson DF, Duan J, Sanders AR, Zheng Y, Pe'er I, Dudbridge F, Holmans PA, Whittemore AS, Mowry BJ, Olincy A, Amin F, Cloninger CR, Silverman JM, Buccola NG, Byerley WF, Black DW, Crowe RR, Oksenberg JR, Mirel DB, Kendler KS, Freedman R & Gejman PV. (2009) Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature doi:10.1038/nature08192. Abstract

Stefansson H, Ophoff RA, Steinberg S, Andreassen OA, Cichon S, Rujescu D, Werge T, Pietiläinen OPH, Mors O, Mortensen PB, Sigurdsson E, Gustafsson O, Nyegaard M, Tuulio-Henriksson A, Ingason A, Hansen T, Suvisaari J, Lonnqvist J, Paunio T, Børglum AD, Hartmann A, Fink-Jensen A, Nordentoft M, Hougaard D, Norgaard-Pedersen B, Böttcher Y, Olesen J, Breuer R, Möller H-J, Giegling I, Rasmussen HB, Timm S, Mattheisen M, Bitter I, Réthelyi JM, Magnusdottir BB, Sigmundsson T, Olason P, Masson G, Gulcher JR, Haraldsson M, Fossdal R, Thorgeirsson TE, Thorsteinsdottir U, Ruggeri M, Tosato S, Franke B, Strengman E, Kiemeney LA, GROUP†, Melle I, Djurovic S, Abramova L, Kaleda V, Sanjuan J, de Frutos R, Bramon E, Vassos E, Fraser G, Ettinger U, Picchioni M, Walker N, Toulopoulou T, Need AC, Ge D, Yoon JL, Shianna KV, Freimer NB, Cantor RM, Murray R, Kong A, Golimbet V, Carracedo A, Arango C, Costas J, Jönsson EG, Terenius L, Agartz I, Petursson H, Nöthen MM, Rietschel M, Matthews PM, Muglia P, Peltonen L, St Clair D, Goldstein DB, Stefansson K, Collier DA & Genetic Risk and Outcome in Psychosis (GROUP). (2009) Common variants conferring risk of schizophrenia. Nature doi:10.1038/nature08186. Abstract

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Related News: Largest GWAS Analysis to Date Offers Only Two New Candidate Genes

Comment by:  Kevin J. Mitchell
Submitted 9 July 2009
Posted 9 July 2009

GWAS Results: Is the Glass Half Full or 95 Percent Empty?
The publication of the latest schizophrenia GWAS papers represents the culmination of a tremendous amount of work and unprecedented cooperation among a large number of researchers, for which they should be applauded. In addition to the hope of finding new “schizophrenia genes,” GWAS have been described by some of the researchers involved as, more fundamentally, a stern test of the common variants hypothesis. Based on the meagre haul of common variants dredged up by these three studies and their forerunners, this hypothesis should clearly now be resoundingly rejected—at least in the form that suggests that there is a large, but not enormous, number of such variants, which individually have modest, but not minuscule, effects. There are no common variants of even modest effect.

However, Purcell and colleagues now argue for a model involving vast numbers of variants, each of almost negligible effect alone. The authors show that an aggregate score derived from the top 10-50 percent of a set of 74,000 SNPs from the association results in a discovery sample can predict up to 3 percent of the variance in a target group. Simply put, a set of putative “risk alleles” can be defined in one sample and shown, collectively, to be very slightly (though highly significantly in a statistical sense) enriched in the test sample, compared to controls. This is consistent across several different schizophrenia samples and even in two bipolar disorder samples. The authors go on to perform a set of control analyses that suggest that these results are not due to obvious population stratification or genotype rate effects (although effects at this level are obviously prone to cryptic artifacts).

If taken at face value, what do these results mean? They imply some kind of polygenic effect on risk, but of what magnitude? The answer to that depends on the interpretation of the additional simulations performed by the authors. They argue that the risk allele set inevitably contains very many false positives, which dilute the predictive power of the real positives hidden among them. Based on this logic, if we only knew which were the real variants to look at, then the variance explained in the target group would be much greater.

To try and estimate the magnitude of the effect of the polygenic load of “true risk” alleles, the authors conducted a series of simulations, varying parameters such as allele frequencies, genotype relative risks, and linkage disequilibrium with genotyped markers. They claim that these analyses converge on a set of models that recapitulate the observed data and that all converge on a true level of variance explained of around 34 percent, demonstrating a large polygenic component to the genetic architecture of schizophrenia.

These simulations adopt a level of statistical abstraction that should induce a healthy level of skepticism or at least reserved judgment on their findings. Most fundamentally, they rely explicitly for their calculations of the true variance on a liability-threshold model of the genetic architecture of schizophrenia. In effect, the “test” of the model incorporates the assumption that the model is correct.

The liability-threshold model is an elegant statistical abstraction that allows the application of the powerful statistics of normal distributions. Unfortunately, it suffers from the fact that it has no support whatsoever and makes no biological sense. First, there is no justification for assuming a normal distribution of “underlying liability,” whatever that term is taken to mean. Second, as usual when it is invoked, the nature of this putative threshold is not explained, though it surreptitiously implies some form of very strong epistasis (to explain the difference in risk between someone with x liability alleles and someone else with x+1 alleles). If this model is not correct, then these simulations are fatally flawed.

Even if the model were correct, the calculations are far from convincing. From a starting set of 560 models, the authors arrive at seven that are consistent with the observed degree of prediction in the target samples. According to the authors, the fact that these seven models converge on a small range of values for the underlying variance explained by the markers is evidence that this value (around 34 percent) represents the true situation. What is not highlighted is the fact that the values for the actual additive genetic variance (taking into account incomplete linkage disequilibrium between the markers and the assumed causal variants) across these models ranges from 34 percent to 98 percent and that the number of SNPs assumed to be having an effect ranges from 4,625 to 74,062. This extreme variation in the derived models hardly inspires confidence in the authors’ claim that their data “strongly support a polygenic basis to schizophrenia that (1) involves common SNPs, [and] (2) explains at least one-third of the total variation in liability.” (italics added)

From a more theoretical perspective, it should be noted that a polygenic model involving thousands of common variants of tiny effect cannot explain and will not contribute to the observed heightened familial relative risks. Such risk can only be explained by a variant of large effect or by an oligogenic model involving at most two to three loci (Bodmer and Bonilla, 2008; Hemminki et al., 2008; Mitchell and Porteous, in preparation). It seems much more likely that the observed predictive power in the target samples represents a modest “genetic background” effect, which could influence the penetrance and expressivity of rare, causal mutations. However, if the point of GWAS is to find genetic variants that are predictive of risk or that shed light on the pathogenic mechanisms of the disease, then clearly, even if such variants can be found by massively increasing sample sizes, their identification alone would not achieve or even appreciably contribute to either of these goals.

References:

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

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

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Related News: Largest GWAS Analysis to Date Offers Only Two New Candidate Genes

Comment by:  David J. Porteous, SRF Advisor
Submitted 9 July 2009
Posted 10 July 2009
  I recommend the Primary Papers

Thumbs up or down on schizophrenia GWAS?
The triumvirate of schizophrenia GWAS studies just published in Nature gives cause for thought, and bears close scrutiny and reflection. To my reading, these three studies individually and collectively lead to an unambiguous conclusion—there is a lot of genetic heterogeneity and not one individual variant of common ancient origin accounts for a significant fraction of the genetic liability. To put it another way, there is no ApoE equivalent for schizophrenia. Strong past claims for ZNF804A and others look to have fallen by the statistical wayside. Putting the results of all three studies together does appear to provide support for a long known, pre-GWAS association with HLA, but otherwise it is hard to give a strong "thumbs up" to any specific result, not least because of the lack of replication between studies. The results are nevertheless important because the common disease, common variant model, on which GWAS are based and the associated cost justified, is strongly rejected as the main contributor to the genetic variance.

The ISC proposes a highly polygenic model with thousands of variants having an additive effect on both schizophrenia and bipolar disorder. I find no fault with their evidence, but its meaning and interpretation remains speculative. Simply consider the fact that SNPs carefully selected to tag half the genome account for about a third of the variance. It follows that the lion's share has gone undetected and will, by design and limitation, remain impervious to the GWAS strategy.

Part of the GWAS appeal is that the genotyping is technically facile and it is easier to collect lots of cases than it is families, but for as long as a diagnosis of schizophrenia or BP depends upon DSM-IV or ICD-10 classification, then diagnostic uncertainty will have a major effect on true power and validity of statistical association, both positive or negative. Indeed, the longstanding evidence from variable psychopathology amongst related individuals, the recent epidemiology evidence for shared genetic risk for schizophrenia and BP, and the further evidence supporting this from the ISC GWAS, all suggest that we should be returning more to family-based studies as a strategy to reduce genetic heterogeneity and find explanatory genetic variants. Plainly, adding ever more uncertainty through ever larger sample sizes is neither smart nor efficient.

I would certainly give the thumbs up to the full and unencumbered release of the primary data to the community as a whole, as this could usefully recoup some of the GWAS investment. It would facilitate a range of statistical and bioinformatics analyses and, who knows, there might be hidden nuggets of statistical support for independent genetic and biological studies.

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Related News: Largest GWAS Analysis to Date Offers Only Two New Candidate Genes

Comment by:  Sagiv Shifman
Submitted 11 July 2009
Posted 11 July 2009

The main question that arises from the three large genomewide association studies published in Nature is, What should we do next?

One important way forward would be to follow up the association findings in the MHC region. We need to understand the biological mechanism underlying this association. If the association signal is indeed related to infectious diseases, this line of inquiry may lead to the highly desired development of a treatment that might prevent the diseases in some cases.

One possible explanation for the association between schizophrenia and the MHC region (6p22.1) is that infection during pregnancy leads to disturbances of fetal brain development and increases the risk of schizophrenia later in life. A possible test for the theory of infectious diseases as risk factors for schizophrenia would be to study the associated SNPs in 6p22.1 in fathers and mothers of subjects with schizophrenia relative to parents of control subjects. If the 6p22.11 region is related to the tendency of mothers to be infected by viruses during pregnancy, we would expect the SNPs in 6p22.1 to be most strongly associated with being a mother to a subject with schizophrenia.

Another broader and more complicated part of the question is: What would be the best strategy for continued study of the genetic causes of schizophrenia? There shouldn’t be only one way to proceed. Testing samples that are 10 times larger seems likely to lead to the identification of more genes, but with much smaller effect size. Testing the association of common variants with schizophrenia is unlikely to lead to the development of genetic diagnostic tools in the near future. If we want to understand the biology of the disease, it might be easier to concentrate our efforts on the identification of rare inherited and non-inherited variants with large effect on the phenotype. Such rare variants are easier to model in animals (relative to common variants with very small functional effect) and might even account for a larger proportion of cases.

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Related News: Largest GWAS Analysis to Date Offers Only Two New Candidate Genes

Comment by:  Alan BrownPaul Patterson
Submitted 17 July 2009
Posted 17 July 2009

The three companion papers in this week’s issue of Nature, in our view, support the case for investigating interaction between susceptibility genes and infectious exposures in schizophrenia. We and others have argued previously that genetic studies conducted in isolation from environmental factors, and studies of environmental influences in the absence of genetic data, are necessarily limited. Maternal influenza, rubella, toxoplasmosis, herpes simplex virus, and other infections have each been associated with an increased risk of schizophrenia, with effect sizes ranging from twofold to over fivefold. While these epidemiologic findings clearly require replication in independent cohorts, two new developments provide further support for the hypothesis. First, a growing number of animal studies of maternal immune activation have documented behavioral and brain phenotypes in offspring that are analogous to findings from clinical research in schizophrenia, and these findings are mediated in large part by specific cytokines (Meyer et al., 2009; Patterson, 2008). Second, recent evidence indicates that maternal infection is also related to deficits in executive and other cognitive functions and neuropathology thought to arise from disruptions in brain development (Brown et al., 2009a; Brown et al., 2009b).

While the MHC region contains genes not involved in the immune system, in light of the epidemiologic findings on maternal infection, it is intriguing to see that this region is once more implicated in genetic studies of schizophrenia as the importance of this region in the response to infectious insults cannot be ignored. Although it is heartening to see that the potential implications of these findings for infectious etiologies were raised in the article from the SGENE plus group, an analysis of the frequency of SNPs by season of birth falls well short of the type of research that will yield definitive findings on the relationships between susceptibility genes and infectious insults. Hence, we advocate a strategy aimed at large scale genetic analyses of schizophrenia cases using birth cohorts with infectious exposures documented from prospectively collected biological samples from the prenatal period. If the schizophrenia-related pathogenic mechanisms by which MHC-related genetic variants operate involve interactions with prenatal infection, we would expect that studies of gene-infection interaction will yield larger effect sizes than those found in these new papers. The evidence from these papers and the epidemiologic literature should also facilitate narrowing of the number of candidate genes to be tested for interactions with infectious insults, thereby ameliorating the potential for type I error due to multiple comparisons.

References:

Meyer U, Feldon J, Fatemi SH. In-vivo rodent models for the experimental investigation of prenatal immune activation effects in neurodevelopmental brain disorders. Neurosci Biobehav Rev . 2009 Jul 1; 33(7):1061-79. Abstract

Patterson PH. Immune involvement in schizophrenia and autism: Etiology, pathology and animal models. Behav Brain Res. 2008 Dec 24; Abstract

Brown AS, Vinogradov S, Kremen WS, Poole JH, Deicken RF, Penner JD, McKeague IW, Kochetkova A, Kern D, Schaefer CA. Prenatal exposure to maternal infection and executive dysfunction in adult schizophrenia. Am J Psychiatry . 2009a Jun 1 ; 166(6):683-90. Abstract

Brown AS, Deicken RF, Vinogradov S, Kremen WS, Poole JH, Penner JD, Kochetkova A, Kern D, Schaefer CA. Prenatal infection and cavum septum pellucidum in adult schizophrenia. Schizophr Res . 2009b Mar 1 ; 108(1-3):285-7. Abstract

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Related News: Largest GWAS Analysis to Date Offers Only Two New Candidate Genes

Comment by:  Javier Costas
Submitted 17 July 2009
Posted 17 July 2009
  I recommend the Primary Papers

Two hundred years after Darwin’s birth and 150 years after the publication of On the Origin of Species, these three papers in Nature show the important role of natural selection in shaping the genetic architecture of schizophrenia susceptibility. If we compare the GWAS results for schizophrenia with those obtained for other diseases, it seems that there are less common risk alleles and/or lower effect sizes in schizophrenia than in many other complex diseases (see, for instance, the online catalog of published GWAS at NHGRI). This fact strongly suggests that negative selection limits the spread of susceptibility alleles, as expected due to the decreased fertility of schizophrenic patients.

Interestingly, the MHC region may be an exception. This region represents a classical example of balancing selection, i.e., the presence of several variants at a locus maintained in a population by positive natural selection (Hughes and Nei, 1988). In the case of the MHC, this balancing selection seems to be related to pathogen resistance or MHC-dependent mating choice. Therefore, the presence of common schizophrenia susceptibility alleles at this locus might be explained by antagonistic pleiotropic effects of alleles maintained by natural selection.

If negative selection limits the spread of schizophrenia risk alleles, most of the genetic susceptibility to schizophrenia is likely due to rare variants. Resequencing technologies will allow the identification of many of these variants in the near future. In the meantime, it would be interesting to focus our attention on non-synonymous SNPs at low frequency. Based on human-chimpanzee comparisons and human sequencing data, Kryukov et al. (2008) have shown that a large fraction of de novo missense mutations are mildly deleterious (i.e., they are subject to weak negative selection) and therefore they can still reach detectable frequencies. Assuming that most of these mildly deleterious alleles may be detrimental (i.e., they confer risk for disease) the authors conclude that numerous rare functional SNPs may be major contributors to susceptibility to common diseases Kryukov et al., 2008. Similar conclusions were obtained by the analysis of the relative frequency distribution of non-synonymous SNPs depending on their probability to alter protein function (Barreiro et al., 2008; Gorlov et al., 2008). As shown by Evans et al. (2008), genomewide scans of non-synonymous SNPs might complement GWAS, being able to identify rare non-synonymous variants of intermediate penetrance not detectable by current GWAS panels.

References:

Barreiro LB, Laval G, Quach H, Patin E, Quintana-Murci L (2008) Natural selection has driven population differentiation in modern humans. Nat Genet 40: 340-5. Abstract

Evans DM, Barrett JC, Cardon LR (2008) To what extent do scans of non-synonymous SNPs complement denser genome-wide association studies? Eur J Hum Genet 16: 718-23. Abstract

Gorlov IP, Gorlova OY, Sunyaev SR, Spitz MR, Amos CI (2008) Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. Am J Hum Genet 82: 100-12. Abstract

Hughes AL, Nei M (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335: 167-70. Abstract

Kryukov GV, Pennacchio LA, Sunyaev SR (2007) Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet 80: 727-39. Abstract

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Related News: Schizophrenia Genetics 2: The Rise of GWAS

Comment by:  Chris Carter
Submitted 7 April 2010
Posted 8 April 2010

I wonder whether the relative lack of success in schizophrenia GWAS may be because the origin of schizophrenia may lie not so much in the genetic make-up of people with schizophrenia themselves, but in their prenatal experience, and possibly with the genes of the mother rather than with those of the offspring. Famine, rubella, influenza, herpes (HSV1 and HSV2), and poliovirus infection as well as high fever during pregnancy have all been listed as risk factors for the offspring developing schizophrenia in later life, as have maternal preeclampsia and obstetric complications. (See page at Polygenic Pathways for the many references.)

Maternal resistance to these effects is likely to be gene-dependent. Is it worth considering GWAS in the mothers rather than in the offspring?

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