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Family Study Replicates Genetic Signals for Schizophrenia

19 April 2013. A new, family-based study identifies many of the same genetic sites already implicated in schizophrenia by other methods, lending support to their status as targets for more intensive study. Published online April 9 in JAMA Psychiatry and led by Edwin van den Oord of Virginia Commonwealth University in Richmond, the study probed over 8,000 single nucleotide polymorphisms (SNPs) in 3,286 people with schizophrenia and 3,012 related controls. The SNPs found to be significantly associated with schizophrenia had the usual small effects on risk, but these were in the right direction: 89 percent had the same influence on risk (i.e., increase or decrease) as that found for the same SNPs in a meta-analysis of 18 previous genomewide association studies (GWAS).

In a second paper in JAMA Psychiatry, published online April 3, a much smaller study of five families turns up protein-altering mutations in genes linked to glutamate signaling. Both studies attest to the usefulness of family-based samples, which have faded from the limelight in recent years as large case-control studies held center stage.

The replication results, reported earlier at a meeting in 2011 (see SRF related conference story), suggest that the quest to discover the genes involved in schizophrenia is on the right track. Although confirming a genetic signal in a completely different sample is something that has often eluded schizophrenia geneticists, the new study, as well as one published last year, suggests that replications are forthcoming for the field (see SRF related news story). Still, as the first, tepid findings from GWAS are being replaced with significant ones from larger sample sizes (see SRF related news story and SRF conference story), a concern has lingered that population stratification could explain these results. This means that, for example, an overrepresentation of a certain allele in a schizophrenia group compared to a control group may not be related to the disorder at all, but instead to something else, such as undetected differences in ethnic background between the two groups. A family-based study sidesteps this complication because cases and controls come from the same families; thus, variety in the genetic background in one group should be matched in the other.

The family study reinforces the notion that shared risk for schizophrenia within families mainly reflects shared genetics, rather than shared environment, writes John Hardy of University College London, U.K., in an accompanying editorial. He concludes, “…after this study, we can be confident that we are on a road that will lead to dissection of some of the pathogenesis of this major disorder.”

Select SNPs
To choose which SNPs were worth trying to replicate, first authors Karolina Åberg and Youfang Liu weighed several kinds of evidence. These included the significant hits in a meta-analysis they conducted of 18 GWAS, which considered over one million SNPs in 21,953 people; candidate gene studies from the SZGene database (Allen et al., 2008); a meta-analysis of 32 linkage studies (Ng et al., 2009); a meta-analysis of gene expression studies done in postmortem brain (Higgs et al., 2006); the Online Mendelian Inheritance of Man database; human versions of mouse genes implicated in neuropsychiatric-like behaviors (Konneker et al., 2008); and SNPs associated with transcript levels in the cortex, as tracked by a University of Chicago database. Using a special algorithm to evaluate the likelihood that each SNP would be related to schizophrenia, the researchers came up with a list of 9,380 SNPs. Of these, 8,107 were successfully genotyped in their family samples, which, importantly, did not overlap with samples used in the previous studies.

Many SNPs were associated with schizophrenia in this sample, and the number of small P values was greater than expected by chance. Of those with P <0.01, 89 percent had the same direction of effect on risk as found in the GWAS meta-analysis—something extremely unlikely to occur by chance (P = 2.20 x 10-16). Taking into account multiple kinds of data when initially selecting their SNPs worked in the researchers' favor: SNPs that weren’t top hits in their GWAS meta-analysis, but which were implicated by other types of data, were among the replicated SNPs.

Defining a replication as an SNP with a significant association with schizophrenia at the P <0.005 level and with the same direction of effect as the GWAS meta-analysis, Åberg and Liu and colleagues replicated 23 SNPs, some of which tagged familiar schizophrenia suspects such as TCF4 and NOTCH4, as well as newer genes such as AS3MT (see SRF related news story), CNNM2, and NT5C2 (see SRF related news story and SRF news story), which have recently surfaced in GWAS. Schizophrenia-related SNPs tagging the major histocompatibility region also were replicated in the European subset of the sample, but not in African or Asian subsets, which jibes with ethnic differentiation in this region.

Paths leading to NMDA receptors?
In the second study, a much smaller collection of families points to rare variants of large effect at work in schizophrenia. A team led by Debby Tsuang of the Veterans Affairs Puget Sound Health Care System in Seattle, Washington, sequenced the exomes of five families with multiple cases of schizophrenia. In each family, the researchers detected rare, protein-changing mutations that seemed to connect to the N-methyl-D-aspartate (NMDA) receptor, which is thought to be underactive in schizophrenia (see SRF Hypothesis). One variant was found in GRM5, which encodes a metabotropic glutamate receptor (mGluR5) that influences signals through NMDA receptors; another was found in PPEF2, which encodes a phosphatase that the researchers show regulates mGluR5 levels. The remaining three families had different variants in a gene—LRP1B—which encodes a lipoprotein receptor that binds to the postsynaptic density complex that contains NMDA receptors. Though tenuous, the link to NMDA receptors suggests that a subset of people who may have schizophrenia because of glutamate-altering mutations might benefit most from glutamate therapeutics.—Michele Solis.

Åberg KA, Liu Y, Bukszár J, McClay JL, Khachane AN, Andreassen OA, Blackwood D, Corvin A, Djurovic S, Gurling H, Ophoff R, Pato CN, Pato MT, Riley B, Webb T, Kendler K, O'Donovan M, Craddock N, Kirov G, Owen M, Rujescu D, St Clair D, Werge T, Hultman CM, Delisi LE, Sullivan P, van den Oord EJ. A comprehensive family-based replication study of schizophrenia genes. JAMA Psychiatry. 2013 Feb 1;70(2):1-9. Abstract

Timms AE, Dorschner MO, Wechsler J, Choi KY, Kirkwood R, Girirajan S, Baker C, Eichler EE, Korvatska O, Roche KW, Horwitz MS, Tsuang DW. Support for the N -Methyl-D-Aspartate Receptor Hypofunction Hypothesis of Schizophrenia From Exome Sequencing in Multiplex Families. JAMA Psychiatry. 2013 Apr 3:1-9. Abstract

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