The DOI matches its Crossref record; 103 of the 103 references it cites were found in a registry or an index; 4 of the 39 sources its claims cite were checked for support.
Mapping genomic loci implicates genes and synaptic biology in schizophrenia
Open accessPublished version of a preprint
Abstract
Schizophrenia has a heritability of 60–80%1, much of which is attributable to common risk alleles. Here, in a two-stage genome-wide association study of up to 76,755 individuals with schizophrenia and 243,649 control individuals, we report common variant associations at 287 distinct genomic loci. Associations were concentrated in genes that are expressed in excitatory and inhibitory neurons of the central nervous system, but not in other tissues or cell types. Using fine-mapping and functional genomic data, we identify 120 genes (106 protein-coding) that are likely to underpin associations at some of these loci, including 16 genes with credible causal non-synonymous or untranslated region variation. We also implicate fundamental processes related to neuronal function, including synaptic organization, differentiation and transmission. Fine-mapped candidates were enriched for genes associated with rare disruptive coding variants in people with schizophrenia, including the glutamate receptor subunit GRIN2A and transcription factor SP4, and were also enriched for genes implicated by such variants in neurodevelopmental disorders. We identify biological processes relevant to schizophrenia pathophysiology; show convergence of common and rare variant associations in schizophrenia and neurodevelopmental disorders; and provide a resource of prioritized genes and variants to advance mechanistic studies. A genome-wide association study including over 76,000 individuals with schizophrenia and over 243,000 control individuals identifies common variant associations at 287 genomic loci, and further fine-mapping analyses highlight the importance of genes involved in synaptic processes.
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48 Own result · 27 Not checked yet · 12 Own interpretation · 5 Own method · 1 Supported · 1 Supported so far · 1 Partly supported · 1 No basis given · accuracy not yet measured
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In the paper
“Of the 10 exome-wide significant genes identified by SCHEMA36, two were prioritised candidates from fine-mapping; GRIN2A encoding a glutamatergic NMDA receptor subunit, and SP4, a transcription factor highly expressed in brain and which is regulated by NMDA transmission, and also regulates NMDA receptor abundance37.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Convergence of Common and Rare Variant Associations
What the sources say
- Could not verifycites [36] Cheng, Y. et al. Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism. Nat. Commun. 12, 964 (2021). sourceExperimental — accuracy not yet measured
The Methods section describes rare-variant tests for urine metabolites, and the Results tables report metabolite-associated genes. Searches for SCHEMA, GRIN2A, SP4, and fine-mapping found no passage addressing whether GRIN2A and SP4 were among SCHEMA genes prioritised by fine-mapping. (LLM, conf=0.76)
- Partly supportedcites [37] Singh, T., Neale, B. M. & Daly, M. J. Exome sequencing identifies rare coding variants in 10 genes which confer substantial risk for schizophrenia. Preprint at https://doi.org/10.1101/2020.09.18.20192815 (2020). sourceExperimental — accuracy not yet measured
The 'Risk genes implicated by rare protein-coding variants' section identifies 10 significant genes, including GRIN2A and SP4. The 'Shared genes and processes' section says both had clear schizophrenia GWAS associations, but it does not state that both were among the genes prioritised by statistical fine-mapping. No page numbers are available in our copy. (LLM, conf=0.82)
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In the paper
“This is further supported by studies showing substantial effects on schizophrenia risk of CNVs39 and rare damaging coding variants in genes with similar functions, including some of the same genes (SCHEMA; companion paper).”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > DISCUSSION
What the sources say
- Supportedcites [39] Ripke, S. et al. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat. Genet. 45, 1150–1159 (2013). source
The citation is attached to the CNV portion of the sentence. The paper’s introductory passage (listed under Abstract) reports eight replicated rare copy number variants with strong effects on schizophrenia risk, giving genotypic relative risks of 4–20. The rare-coding-variant portion is attributed to other studies, not this citation. (LLM, conf=0.91)
- Not checked yetcites SCHEMA
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- Supported
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In the paper
“and were also enriched for genes implicated by such variants in neurodevelopmental disorders”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > Abstract
plaincorrelationaln = 76,755- Asserted: passes — The authors put it forward as true.
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In the paper
“we report common variant associations at 287 distinct genomic loci”
- Also stated in: § Association Meta-Analysis · plain
“identified 342 LD-independent significant SNPS (Supplementary Table 2) located in 287 loci”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > Abstract
plaincorrelationaln = 76,755- Asserted: passes — The authors put it forward as true.
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- Also stated in: § Association Meta-Analysis · plain
In the paper
“In the EUR sample, the SNP-based heritability (h2SNP) (i.e. proportion of variance in liability attributable to all measured SNPs) was estimated13 to be 0.24 (SE 0.007).”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > SNP-based heritability and Polygenic Prediction
What the sources say
- Not checked yetcites [13] Zeng, J. et al. Widespread signatures of natural selection across human complex traits and functional genomic categories. Nat. Commun. 12, 1164 (2021). source
hedged- Asserted: passes — The authors put it forward as true.
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In the paper
“show convergence of common and rare variant associations in schizophrenia and neurodevelopmental disorders”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > Abstract
plaincorrelationaln = 76,755- Asserted: passes — The authors put it forward as true.
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In the paper
“identified 342 LD-independent significant SNPS (Supplementary Table 2) located in 287 loci”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Association Meta-Analysis
plainn = 74,776- Asserted: passes — The authors put it forward as true.
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In the paper
“We also implicate fundamental processes related to neuronal function, including synaptic organisation, differentiation, and transmission.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > Abstract
plaincorrelationaln = 76,755- Asserted: passes — The authors put it forward as true.
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In the paper
“Using fine-mapping and functional genomic data, we identify 120 genes (106 protein-coding) as likely to underpin associations at some of these loci”
- Also stated in: § Prioritisation by Gene Expression · plain
“Combining all approaches, FINEMAP and SMR, we prioritised 120 genes of which 106 are protein-coding”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > Abstract
plainconditionaln = 76,755- Asserted: passes — The authors put it forward as true.
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- Also stated in: § Prioritisation by Gene Expression · plain
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In the paper
“Separate GWAS for males and females had a genetic correlation statistically indistinguishable from 1 (rg=0.992, SE 0.024).”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Association Meta-Analysis
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- Probably not a substantial claim. 11
- It may state two separate claims as one. 39
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In the paper
“A recent genome-wide association study (GWAS) reported 176 genomic loci containing common alleles associated with schizophrenia9”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > INTRODUCTION
What the sources say
- Supportedcites [9] Lam, M. et al. Comparative genetic architectures of schizophrenia in East Asian and European populations. Nat. Genet. 51, 1670–1678 (2019). source
The Results section (‘Schizophrenia genetic associations from the meta-analysis of EAS and EUR’; page not supplied) reports 208 independent schizophrenia-associated variants across 176 genetic loci. The paper also describes its findings as concerning common genetic variants, supporting the citing sentence’s characterization. (LLM, conf=0.93)
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In the paper
“This primary GWAS identified 313 independent SNPs (linkage disequilibrium (LD) r2 < 0.1) that exceeded genome-wide significance (p<5×10−8) (Extended Data Figure 1; Supplementary Table 1), spanning 263 distinct loci.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Association Meta-Analysis
plainn = 74,776- Asserted: passes — The authors put it forward as true.
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In the paper
“Associations were concentrated in genes expressed in CNS neurons, excitatory and inhibitory, but not other tissues or cell types.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > Abstract
plaincorrelationaln = 76,755- Asserted: passes — The authors put it forward as true.
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In the paper
“All were relevant to neuronal function including development, differentiation, and synaptic transmission, and involved multiple cellular components including ion channels, synapses, and both axon and dendritic annotations.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Gene Set Enrichments
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In the paper
“we further examined the synaptic signal and found that conditionally significant annotations were mainly within postsynaptic terms (Supplementary Tables 8, 9), although enrichment was also found for genes involved in synaptic organisation and signalling.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Gene Set Enrichments
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In the paper
“For 33 regions, the 95% credible set contained 5 or fewer SNPs (Supplementary Table 11c) and for 9, only a single SNP.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Fine-mapping
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In the paper
“Using the all ancestry primary GWAS as the discovery sample, polygenic risk score (PRS) analysis explained a median of 0.073 of variance in liability (SNPs with GWAS p<0.05), and 0.024 when restricted to genome-wide significant SNPs.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > SNP-based heritability and Polygenic Prediction
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In the paper
“Compared to the lowest centile of PRS, the highest centile of PRS has an OR for schizophrenia of 39 (95% CI=29–53), and 5.6 (CI 4.9–6.5) when the top centile is compared with the remaining 99% of individuals”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > SNP-based heritability and Polygenic Prediction
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In the paper
“we found associations were enriched in genes with high expression in excitatory glutamatergic neurons from cerebral cortex and hippocampus (pyramidal CA1 and CA3 cells, and granule cells of dentate gyrus) and also human cortical inhibitory interneurons”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Gene Set Enrichments
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In the paper
“Very strong enrichments were again seen for genes expressed in excitatory glutamatergic neurons of the cortex (especially the deep layers) and hippocampus but also the amygdala”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Gene Set Enrichments
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In the paper
“We highlight rs4766428 (PP>0.99) which is the only credible SNP in a locus that contains 25 genes and is located within ATP2A2.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Fine-mapping
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In the paper
“PRS explained most variance in liability in cohorts of European ancestry (again a result of the ancestry composition of the GWAS9) and in samples which by ascertainment likely include the most severe cases (hospitalised patients or those treated with clozapine)”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > SNP-based heritability and Polygenic Prediction
What the sources say
- Not checked yetcites [9] Lam, M. et al. Comparative genetic architectures of schizophrenia in East Asian and European populations. Nat. Genet. 51, 1670–1678 (2019). source
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In the paper
“Highly significant enrichments were also seen for other neuronal populations, including as above, inhibitory medium spiny neurones in striatum, but also both excitatory and inhibitory neurons from the midbrain, thalamus and hindbrain, and inhibitory cells from the hippocampus.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Gene Set Enrichments
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“Among the 70 FINEMAP prioritised genes (64 protein-coding) were 16 genes (protein-coding by definition) based on NS or UTR variants”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Fine-mapping
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In the paper
“For almost all cohorts, PRS had more explanatory power based on risk alleles derived from the larger combined ancestry GWAS than from the matched ancestry GWAS; given the ancestry specific sample sizes, unsurprisingly9, this effect was strongest for the non-EUR samples”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > SNP-based heritability and Polygenic Prediction
What the sources say
- Not checked yetcites [9] Lam, M. et al. Comparative genetic architectures of schizophrenia in East Asian and European populations. Nat. Genet. 51, 1670–1678 (2019). source
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In the paper
“After removing duplicates, there were 55 SMR/SMR-Hi-C prioritised genes (Supplementary Table 12) of which 46 were protein-coding.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Prioritisation by Gene Expression
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“Genes where putatively causal eQTLs captured a particularly high FINEMAP PP (>95%) (Supplementary Table 17g) include ACE encoding angiotensin converting enzyme, the target of a major class of anti-hypertensive drugs (schizophrenia under-expression), DCLK3 encoding a neuroprotective kinase29(schizophrenia under-expression) and SNAP91 (discussed below; schizophrenia over-expression).”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Prioritisation by Gene Expression
What the sources say
- Not checked yetcites [29] Galvan, L. et al. The striatal kinase DCLK3 produces neuroprotection against mutant huntingtin. Brain 141, 1434–1454 (2018). source
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In the paper
“Multiple genes encode receptors and ion channels, including voltage-gated calcium and chloride channels (CACNA1C, CLCN3), metabotropic receptors (glutamate (GRM1) and GABA (GABBR2)), and the ligand-gated NMDA receptor subunit (GRIN2A).”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Synaptic Location and Function of Prioritised Genes
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“Of the 106 proteins encoded, 15 have synaptic annotations (Supplementary Table 19); 7 postsynaptic, 5 both pre- and post- synaptic, 2 presynaptic, and 1 gene is not mapped to any specific compartment.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Synaptic Location and Function of Prioritised Genes
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“Missense and UTR variants prioritised interferon regulatory factor 3 (IRF3 while KLF6, a transcription factor, was highlighted by three variants in the 3’ UTR.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Fine-mapping
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In the paper
“Others involve proteins playing a role in endocytosis (SNAP91), synaptic organisation and differentiation (DLGAP2, LRRC4B, GPM6A, PAK6), including PTPRD a receptor protein tyrosine phosphatase presynaptic organizer that trans‐synaptically interacts with multiple postsynaptic cell adhesion molecules (e.g. IL1RAPL1), and modulation of chemical transmission (MAPK3, DCC, CLCN3, DLGAP2).”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Synaptic Location and Function of Prioritised Genes
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In the paper
“We found both sets of genes were enriched for common variant associations, as were more weakly associated SCHEMA genes down to uncorrected P<0.001”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Convergence of Common and Rare Variant Associations
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“FOXP1 and MYT1L are associated with both DD and ASD and met our fine-mapping prioritisation criteria in the core PGC dataset”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Convergence of Common and Rare Variant Associations
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In the paper
“Enrichment of common variant associations was restricted to genes expressed in CNS neurons, both excitatory and inhibitory, and fundamental biological processes related to neuronal function.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > DISCUSSION
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In the paper
“We have performed the largest GWAS of schizophrenia to date and in doing so, identify a substantial increase in the number of associated loci.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > DISCUSSION
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“RERE was prioritised by SMR and is associated with DD.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Convergence of Common and Rare Variant Associations
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“SNPs mapping to these genes had cumulative FINEMAP PP of 0.88 and 0.72 respectively”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Convergence of Common and Rare Variant Associations
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In the paper
“Schizophrenia has a heritability of 60–80%, much of which is attributable to common risk alleles.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > Abstract
What the sources say
- Not checked yetcites [5] International Schizophrenia Consortium. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 460, 748–752 (2009). source
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In the paper
“Much of the between-individual variation in risk is genetic, involving large numbers of common alleles,5 rare copy number variants (CNVs)6, and rare coding variants (RCVs)7,8.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > INTRODUCTION
What the sources say
- Not checked yetcites [5] International Schizophrenia Consortium. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 460, 748–752 (2009). source
- Not checked yetcites [6] Pocklington, A. J. et al. Novel findings from CNVs implicate inhibitory and excitatory signaling complexes in schizophrenia. Neuron 86, 1203–1214 (2015). source
- Not checked yetcites [7] Singh, T. et al. The contribution of rare variants to risk of schizophrenia in individuals with and without intellectual disability. Nat. Genet. 49, 1167–1173 (2017). source
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In the paper
“Mutations in ATP2A2 cause Darier Disease21, which co-segregates with bipolar disorder in several multiplex pedigrees and is associated with bipolar disorder and schizophrenia at a population level22.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Fine-mapping
What the sources say
- Not checked yetcites [21] Sakuntabhai, A. et al. Mutations in ATP2A2, encoding a Ca2+ pump, cause Darier disease. Nat. Genet. 21, 271–277 (1999). source
- Not checked yetcites [22] Cederlöf, M. et al. The association between Darier disease, bipolar disorder, and schizophrenia revisited: a population-based family study. Bipolar Disord. 17, 340–344 (2015). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“ATP2A2 encodes a sarcoplasmic/endoplasmic reticulum calcium pump, suggesting that its role in schizophrenia pathogenesis may be through regulating neuronal cytoplasmic calcium levels.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Fine-mapping
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In the paper
“Overall, the findings across all the datasets are consistent with the hypothesis that schizophrenia is primarily a disorder of neuronal function, but do not suggest that pathology is restricted to a circumscribed brain region.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Gene Set Enrichments
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In the paper
“The Schizophrenia Exome Sequencing Meta-Analysis (SCHEMA) consortium (companion paper) identified 32 genes with damaging ultra-rare mutations associated with schizophrenia (FDR<0.05), including 10 at exome-wide significance.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Convergence of Common and Rare Variant Associations
What the sources say
- Not checked yetcites companion paper
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In the paper
“Convergences between rare variants and fine-mapped GWAS signals have been previously observed in other traits e.g.,34,35”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Convergence of Common and Rare Variant Associations
What the sources say
- Not checked yetcites [34] Satterstrom, F. K. et al. Large-scale exome sequencing study implicates both developmental and functional changes in the neurobiology of autism. Cell 180, 568–584 (2020). source
- Not checked yetcites [35] Luo, Y. et al. Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7. Nat. Genet. 49, 186–192 (2017). source
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“SP4, a transcription factor highly expressed in brain and which is regulated by NMDA transmission, and also regulates NMDA receptor abundance37.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > RESULTS > Convergence of Common and Rare Variant Associations
What the sources say
- Not checked yetcites [37] Singh, T., Neale, B. M. & Daly, M. J. Exome sequencing identifies rare coding variants in 10 genes which confer substantial risk for schizophrenia. Preprint at https://doi.org/10.1101/2020.09.18.20192815 (2020). source
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In the paper
“This suggests that abnormal neuronal function in schizophrenia is not confined to a small number of brain structures, which in turn might explain its diverse psychopathology, association with a broad range of cognitive impairments, and lack of regional specificity in neuroimaging measures1.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > DISCUSSION
What the sources say
- Not checked yetcites [1] Owen, M. J., Sawa, A. & Mortensen, P. B. Schizophrenia. Lancet 388, 86–97 (2016). source
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In the paper
“Disrupted neuronal function in schizophrenia is unlikely to be restricted to the synapse, but the concentration of associations in genes with pre- and post-synaptic locations, and with functions related to synaptic organisation, differentiation and transmission, point to the pathophysiological importance of these neuronal compartments and their attendant functions.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > DISCUSSION
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In the paper
“We applied the HEIDI test37 to filter out SMR associations (PHEIDI < 0.01) due to linkage disequilibrium between SCZ-associated variants and eQTLs.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > ONLINE METHODS > Secondary analyses in core PGC dataset
What the sources say
- Not checked yetcites [37] Singh, T., Neale, B. M. & Daly, M. J. Exome sequencing identifies rare coding variants in 10 genes which confer substantial risk for schizophrenia. Preprint at https://doi.org/10.1101/2020.09.18.20192815 (2020). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“We used FUSION44 and EpiXcan45 as tests of robustness of the SMR results.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > ONLINE METHODS > Secondary analyses in core PGC dataset
What the sources say
- Not checked yetcites [44] Lam, M. et al. RICOPILI: Rapid Imputation for COnsortias PIpeLIne. Bioinformatics 36, 930–933 (2019). source
- Not checked yetcites [45] Purcell, S., Neale, B., Todd-Brown, K., Thomas, L. & Ferreira, M. A. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am. J. Hum. Genet. 81, 559–575 (2007). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“The study protocols were approved by the institutional review board at each centre involved with recruitment. Informed consent and permission to share the data were obtained from all subjects”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > DISCUSSION > Ethics
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“As fine-mapping requires data from all markers in the region36 we only performed fine-mapping on regions that attained genome-wide significance (GWS) in the core PGC GWAS.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > ONLINE METHODS > Secondary analyses in core PGC dataset
What the sources say
- Not checked yetcites [36] Cheng, Y. et al. Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism. Nat. Commun. 12, 964 (2021). source
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Within each gene set analysis, p-values were corrected for multiple testing using the Bonferroni procedure.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > ONLINE METHODS > Secondary analyses in core PGC dataset
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“we evaluated the effectiveness of the primary technical and genomic quality control parameters on the genome-wide inflation of test statistics using the lambda GC (median)5 and as necessary made the QC parameters more stringent until this value was between 1.0 and 1.4 (before inclusion of principal components as covariates) and/or between 1.0 and 1.15 after inclusion of PCA covariates.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > ONLINE METHODS > Association Analysis
What the sources say
- Not checked yetcites [5] International Schizophrenia Consortium. Common polygenic variation contributes to risk of schizophrenia and bipolar disorder. Nature 460, 748–752 (2009). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“We controlled for a set of 10,360 genes with detectable expression in brain tissue measured as Fragments Per Kilobase of transcript per Million mapped reads (FPKM)32 to detect synaptic signals above signals simply reflecting the property of brain expression.”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > ONLINE METHODS > Secondary analyses in core PGC dataset
What the sources say
- Not checked yetcites [32] Fromer, M. et al. De novo mutations in schizophrenia implicate synaptic networks. Nature 506, 179–184 (2014). source
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Technical Quality control was performed on the core PGC cohorts separately according to standards developed by the PGC3 including SNP missingness < 0.05 (before sample removal); subject missingness < 0.02; autosomal heterozygosity deviation (| Fhet | < 0.2); SNP missingness < 0.02 (after sample removal); difference in SNP missingness between cases and controls < 0.02; and SNP Hardy-Weinberg”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > ONLINE METHODS > Association Analysis
What the sources say
- Not checked yetcites [3] Momen, N. C. et al. Association between mental disorders and subsequent medical conditions. N. Engl. J. Med. 382, 1721–1731 (2020). source
plain- Asserted: passes — The authors put it forward as true.
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What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“We performed PCA for all 90 cohorts separately using SNPs with high imputation quality (INFO >0.8), low missingness (<1%), MAF>0.05 and in relative linkage equilibrium (LD) after 2 iterations of LD pruning (r2 < 0.2, 200 SNP windows).”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > ONLINE METHODS > Association Analysis
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. It may state two separate claims as one.
The paper relies on this without support.
The causal variants driving the reported GWAS associations and the biological consequences of those variants are largely unknown.
“but the causal variants driving these associations and the biological consequences of these variants are largely unknown”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The cited source says what the claim attributes to it.
In the citing paper
“Compared to GWAS of other psychiatric disorders in adults (e.g., major depressive disorder with more than 135,000 cases 62 , or schizophrenia with more than 76,000 cases 63 ), the five retained GWAS of child neurodevelopmental disorders are relatively small and underpowered to detect robustly associated common genetic risk factors related to these disorders.”
From Candidate diagnostic biomarkers for neurodevelopmental disorders in children and adolescents: a systematic review (2023) · cites this paper as [63]
In the citing paper
“suggesting that common and rare genetic risk factors at least partially converge on the same underlying pathogenic biological processes.”
From Rare coding variants in ten genes confer substantial risk for schizophrenia (2022) · cites this paper as [3]
In the citing paper
“we demonstrate that genes prioritized from common variant analyses of schizophrenia are enriched in rare variant risk3”
From Rare coding variants in ten genes confer substantial risk for schizophrenia (2022) · cites this paper as [3]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > ONLINE METHODS > Overview of Samples
“1249 LD – independent (r2 > 0.1) Variants showing evidence for association (P< 1×10−5) were further meta-analysed with an additional dataset of 1,979 cases and 142,626 controls of European ancestry obtained from deCODE genetics”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > ONLINE METHODS > Association Analysis
“We obtained summary association results from deCODE genetics for 1,228 index SNPs (P < 1×10−5) based on 1,979 cases and 142,626 controls of European ancestry.”
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > ONLINE METHODS > Overview of Samples
“1249 LD – independent (r2 > 0.1) Variants showing evidence for association (P< 1×10−5)”
§ Mapping genomic loci implicates genes and synaptic biology in schizophrenia > ONLINE METHODS > Association Analysis
“Index SNPs were LD independent and had r2 < 0.1 within 3 Mb windows.”
Citations
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The genetics of cognition in schizophrenia
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Genetic regulatory and biological implications of the 10q24.32 schizophrenia risk locus
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Self-citationPolygenic Scores Clarify the Relationship Between Mental Health and Gender Diversity
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Self-citationIncremental advances in psychiatric molecular genetics and nosology
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Regional Specificity of Cortical Layer 3 Dendritic Spine Deficits in Schizophrenia
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From variants to mechanisms: Neurogenomics in the post-GWAS era
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Analysis of the complement component C4 gene with schizophrenia subphenotypes
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Self-citationRelationship of metabolites and metabolic ratios with schizophrenia: a mendelian randomization study
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Self-citationNeuronal alterations in AKT isotype expression in schizophrenia
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Sexual Trauma, Polygenic Scores, and Mental Health Diagnoses and Outcomes
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Self-citationCross‐Sectional Brain Age Assessments Are Limited in Predicting Future Brain Change
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Self-citationIUPHAR review: Moving beyond dopamine-based therapeutic strategies for schizophrenia
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Genetic Architecture and Risk of Childhood Maltreatment Across 5 Psychiatric Diagnoses.
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Self-citation
Metadata
- Authors
- Trubetskoy, V., Pardiñas, A. F., Qi, T., Panagiotaropoulou, G., Awasthi, S., Bigdeli, T. B., Bryois, J., Chen, C.-Y., Dennison, C. A., Hall, L. S., Lam, M., Watanabe, K., Frei, O., Ge, T., Harwood, J. C., Koopmans, F., Magnusson, S., Richards, A. L., Sidorenko, J., Wu, Y., Zeng, J., Grove, J., Kim, M., Li, Z., Voloudakis, G., Zhang, W., Adams, M., Agartz, I., Atkinson, E. G., Agerbo, E., Al Eissa, M., Albus, M., Alexander, M., Alizadeh, B. Z., Alptekin, K., Als, T. D., Amin, F., Arolt, V., Arrojo, M., Athanasiu, L., Azevedo, M. H., Bacanu, S. A., Bass, N. J., Begemann, M., Belliveau, R. A., Bene, J., Benyamin, B., Bergen, S. E., Blasi, G., Bobes, J., Bonassi, S., Braun, A., Bressan, R. A., Bromet, E. J., Bruggeman, R., Buckley, P. F., Buckner, R. L., Bybjerg-Grauholm, J., Cahn, W., Cairns, M. J., Calkins, M. E., Carr, V. J., Castle, D., Catts, S. V., Chambert, K. D., Chan, R. C. K., Chaumette, B., Cheng, W., Cheung, E. F. C., Chong, S. A., Cohen, D., Consoli, A., Cordeiro, Q., Costas, J., Curtis, C., Davidson, M., Davis, K. L., de Haan, L., Degenhardt, F., DeLisi, L. E., Demontis, D., Dickerson, F., Dikeos, D., Dinan, T., Djurovic, S., Duan, J., Ducci, G., Dudbridge, F., Eriksson, J. G., Fañanás, L., Faraone, S. V., Fiorentino, A., Forstner, A., Frank, J., Freimer, N. B., Fromer, M., Frustaci, A., Gadelha, A., Genovese, G., Gershon, E. S., Giannitelli, M., Giegling, I., Giusti-Rodríguez, P., Godard, S., Goldstein, J. I., González Peñas, J., González-Pinto, A., Gopal, S., Gratten, J., Green, M. F., Greenwood, T. A., Guillin, O., Gülöksüz, S., Gur, R. E., Gur, R. C., Gutiérrez, B., Hahn, E., Hakonarson, H., Haroutunian, V., Hartmann, A. M., Harvey, C., Hayward, C., Henskens, F. A., Herms, S., Hoffmann, P., Howrigan, D. P., Ikeda, M., Iyegbe, C., Joa, I., Julià, A., Kähler, A. K., Kam-Thong, T., Kamatani, Y., Karachanak-Yankova, S., Kebir, O., Keller, M. C., Kelly, B. J., Khrunin, A., Kim, S.-W., Klovins, J., Kondratiev, N., Konte, B., Kraft, J., Kubo, M., Kučinskas, V., Kučinskiene, Z. A., Kusumawardhani, A., Kuzelova-Ptackova, H., Landi, S., Lazzeroni, L. C., Lee, P. H., Legge, S. E., Lehrer, D. S., Lencer, R., Lerer, B., Li, M., Lieberman, J., Light, G. A., Limborska, S., Liu, C.-M., Lönnqvist, J., Loughland, C. M., Lubinski, J., Luykx, J. J., Lynham, A., Macek, M., Mackinnon, A., Magnusson, P. K. E., Maher, B. S., Maier, W., Malaspina, D., Mallet, J., Marder, S. R., Marsal, S., Martin, A. R., Martorell, L., Mattheisen, M., McCarley, R. W., McDonald, C., McGrath, J. J., Medeiros, H., Meier, S., Melegh, B., Melle, I., Mesholam-Gately, R. I., Metspalu, A., Michie, P. T., Milani, L., Milanova, V., Mitjans, M., Molden, E., Molina, E., Molto, M. D., Mondelli, V., Moreno, C., Morley, C. P., Muntané, G., Murphy, K. C., Myin-Germeys, I., Nenadić, I., Nestadt, G., Nikitina-Zake, L., Noto, C., Nuechterlein, K. H., O’Brien, N. L., O’Neill, F. 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A., Pinto, D., Pochareddy, S., Polioudakis, D., Purcaro, M., Purcell, S., Pratt, H., Reddy, T., Rhie, S., Roussos, P., Rozowsky, J., Sanders, S., Sestan, N., Sethi, A., Shi, X., Shieh, A., Swarup, V., Szekely, A., Wang, D., Warrell, J., Weissman, S., Weng, Z., White, K., Wiseman, J., Witt, H., Won, H., Wood, S., Wu, F., Xu, X., Yao, L., Zandi, P., Psychosis Endophenotypes International Consortium, Arranz, M. J., Bakker, S., Bender, S., Bramon, E., Collier, D. A., Crepo-Facorro, B., Hall, J., Iyegbe, C., Kahn, R., Lawrie, S., Lewis, C., Lin, K., Linszen, D. H., Mata, I., McIntosh, A., Murray, R. M., Ophoff, R. A., van Os, J., Powell, J., Rujescu, D., Walshe, M., Weisbrod, M., The SynGO Consortium, Achsel, T., Andres-Alonso, M., Bagni, C., Bayés, À., Biederer, T., Brose, N., Brown, T. C., Chua, J. J. E., Coba, M. P., Cornelisse, L. N., de Jong, A. P. H., de Juan-Sanz, J., Dieterich, D. C., Feng, G., Goldschmidt, H. L., Gundelfinger, E. D., Hoogenraad, C., Huganir, R. L., Hyman, S. 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K., Malhotra, D., McIntosh, A., McQuillin, A., Menezes, P. R., Morgan, V. A., Morris, D. W., Mowry, B. J., Murray, R. M., Nimgaonkar, V., Nöthen, M. M., Ophoff, R. A., Paciga, S. A., Palotie, A., Pato, C. N., Qin, S., Rietschel, M., Riley, B. P., Rivera, M., Rujescu, D., Saka, M. C., Sanders, A. R., Schwab, S. G., Serretti, A., Sham, P. C., Shi, Y., St Clair, D., Stefánsson, H., Stefansson, K., Tsuang, M. T., van Os, J., Vawter, M. P., Weinberger, D. R., Werge, T., Wildenauer, D. B., Yu, X., Yue, W., Holmans, P. A., Pocklington, A. J., Roussos, P., Vassos, E., Verhage, M., Visscher, P. M., Yang, J., Posthuma, D., Andreassen, O. A., Kendler, K. S., Owen, M. J., Wray, N. R., Daly, M. J., Huang, H., Neale, B. M., Sullivan, P. F., Ripke, S., Walters, J. T. R., O’Donovan, M. C., Schizophrenia Working Group of the Psychiatric Genomics Consortium, de Haan, L., van Amelsvoort, T., van Winkel, R., Gareeva, A., Sham, P. C., Shi, Y., St Clair, D., & van Os, J.
- Affiliations
- Stiftung Charité (DE)
- Cardiff University (GB)
- The University of Queensland (AU)
- State University of New York (US)
- Biogen (United States) (US)
- Broad Institute (US)
- Amsterdam Neuroscience (NL)
- Oslo University Hospital (NO)
- Aarhus University (DK)
- University of California, Los Angeles (US)
- Qingdao University (CN)
- Icahn School of Medicine at Mount Sinai (US)
- Royal Edinburgh Hospital (GB)
- University of Oslo (NO)
- McLean Hospital (US)
- University Medical Center Groningen (NL)
- University of Münster (DE)
- Complejo Hospitalario Universitario de Santiago (ES)
- University of Coimbra (PT)
- Virginia Commonwealth University (US)
- University College London (GB)
- Max Planck Institute of Experimental Medicine (DE)
- University of Pecs (HU)
- University of South Australia (AU)
- Karolinska Institutet (SE)
- University of Bari Aldo Moro (IT)
- Universidad de Oviedo (ES)
- IRCCS San Raffaele Roma (IT)
- Universidade Federal de São Paulo (BR)
- Stony Brook University (US)
- University of Tennessee Health Science Center (US)
- Harvard University (US)
- University Medical Center Utrecht (NL)
- Hunter Medical Research Institute (AU)
- University of Pennsylvania (US)
- UNSW Sydney (AU)
- The University of Melbourne (AU)
- The University of Sydney (AU)
- Chinese Academy of Sciences (CN)
- Inserm (FR)
- University of North Carolina at Chapel Hill (US)
- Castle Peak Hospital (CN)
- National University of Singapore (SG)
- Centre National de la Recherche Scientifique (FR)
- Sorbonne Université (FR)
- Irmandade da Santa Casa de Misericórdia de São Paulo (BR)
- King's College London (GB)
- University of Nicosia (CY)
- University of Bonn (DE)
- Cambridge Health Alliance (US)
- Sheppard Pratt Health System (US)
- National and Kapodistrian University of Athens (GR)
- University College Cork (IE)
- Endeavor Health (US)
- ASL Roma (IT)
- University of Leicester (GB)
- University of Helsinki (FI)
- Centro de Investigación Biomédica en Red de Salud Mental (ES)
- SUNY Upstate Medical University (US)
- Heidelberg University (DE)
- Barnet Enfield and Haringey Mental Health Trust (GB)
- University of Chicago (US)
- Medical University of Vienna (AT)
- Massachusetts General Hospital (US)
- University of the Basque Country (ES)
- University of California San Diego (US)
- Maastricht University Medical Centre (NL)
- Universidad de Granada (ES)
- Charité – Universitätsmedizin Berlin (DE)
- Children's Hospital of Philadelphia (US)
- James J. Peters VA Medical Center (US)
- Western General Hospital (GB)
- University of Newcastle Australia (AU)
- University of Basel (CH)
- Fujita Health University (JP)
- Stavanger University Hospital (NO)
- Vall d'Hebron Institut de Recerca (ES)
- F. Hoffmann-La Roche AG (CH)
- RIKEN Center for Integrative Medical Sciences (JP)
- Medical University of Sofia (BG)
- University of Colorado Boulder (US)
- Chonnam National University (KR)
- Mental Health Research Center of Russian Academy of Medical Sciences (RU)
- Humboldt-Universität zu Berlin (DE)
- Vilnius University (LT)
- University of Indonesia (ID)
- General University Hospital in Prague (CZ)
- University of Pisa (IT)
- Stanford Medicine (US)
- Wright State University (US)
- Hadassah Medical Center (IL)
- Sun Yat-sen University (CN)
- Columbia University (US)
- Kurchatov Institute (RU)
- National Taiwan University (TW)
- Hunter New England Local Health District (AU)
- Utrecht University (NL)
- Johns Hopkins University (US)
- University Hospital Bonn (DE)
- Pitié-Salpêtrière Hospital (FR)
- Institut Pere Mata (ES)
- Dalhousie University (CA)
- VA Boston Healthcare System (US)
- Ollscoil na Gaillimhe – University of Galway (IE)
- University of Southern California (US)
- University of Tartu (EE)
- Alexandrovska Hospital (BG)
- Universidad Complutense de Madrid (ES)
- Universitat Pompeu Fabra (ES)
- Royal College of Surgeons in Ireland (IE)
- Philipps University of Marburg (DE)
- Queen's University Belfast (GB)
- Lawrence Berkeley National Laboratory (US)
- Oxford Health NHS Foundation Trust (GB)
- University of Washington (US)
- University of Utah (US)
- University of Würzburg (DE)
- Genethon (France) (FR)
- Finnish Institute for Health and Welfare (FI)
- Beth Israel Deaconess Medical Center (US)
- National Cancer Institute (US)
- Chinese University of Hong Kong (HK)
- Region Stockholm (SE)
- Lieber Institute for Brain Development (US)
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin (DE)
- Bulgarian Academy of Sciences (BG)
- University of Verona (IT)
- Istanbul University (TR)
- Norwegian University of Science and Technology (NO)
- Oulu University Hospital (FI)
- The University of Western Australia (AU)
- Sheba Medical Center (IL)
- Baker Heart and Diabetes Institute (AU)
- GGz centraal (NL)
- Centre for Addiction and Mental Health (CA)
- Shanghai Jiao Tong University (CN)
- First Affiliated Hospital of Xi'an Jiaotong University (CN)
- Ankara University (TR)
- Queen's University (CA)
- University of Iowa (US)
- Louisiana State University Health Sciences Center New Orleans (US)
- University of California, San Francisco (US)
- National Health Research Institutes (TW)
- Washington University in St. Louis (US)
- University of Colorado Denver (US)
- Ramsay Health Care (Australia) (AU)
- Centro San Giovanni di Dio Fatebenefratelli (IT)
- Statens Serum Institut (DK)
- Aarhus University Hospital (DK)
- University of Tasmania (AU)
- University of Copenhagen (DK)
- Rutgers, The State University of New Jersey (US)
- China Medical University (TW)
- Mayo Clinic (US)
- Duke University (US)
- Yale University (US)
- University of Illinois Chicago (US)
- University of Massachusetts Amherst (US)
- Sage Bionetworks (US)
- University of Massachusetts Chan Medical School (US)
- Universidad de Cantabria (ES)
- Leibniz Institute for Neurobiology (DE)
- Institut de Recerca Sant Pau (ES)
- McGovern Institute for Brain Research (US)
- Genentech (US)
- Korea Advanced Institute of Science and Technology (KR)
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (DE)
- Montreal Neurological Institute and Hospital (CA)
- Weill Cornell Medicine (US)
- Vrije Universiteit Amsterdam (NL)
- Howard Hughes Medical Institute (US)
- Amsterdam University Medical Centers (NL)
- Umeå University (SE)
- Forschungszentrum Jülich (DE)
- Queen Mary University of London (GB)
- University of Trento (IT)
- Russian Academy of Sciences (RU)
- Samsung Medical Center (KR)
- Feinstein Institute for Medical Research (US)
- Agency for Science, Technology and Research (SG)
- Universidade de São Paulo (BR)
- University of Wollongong (AU)
- University of Hong Kong (HK)
- deCODE Genetics (Iceland) (IS)
- University of California, Irvine (US)
- Chinese Academy of Medical Sciences & Peking Union Medical College (CN)
- Amsterdam UMC Location University of Amsterdam (NL)
- Corresponding author
- Ripke, Stephan
- Walters, James T. R.
- O’Donovan, Michael C.
- ORCID
- Trubetskoy, Vassily
- Pardiñas, Antonio F.
- Qi, Ting
- Panagiotaropoulou, Georgia
- Awasthi, Swapnil
- Bigdeli, Tim B.
- Chen, Chia-Yen
- Dennison, Charlotte A.
- Hall, Lynsey S.
- Lam, Max
- Watanabe, Kyoko
- Frei, Oleksandr
- Ge, Tian
- Harwood, Janet C.
- Richards, Alexander L.
- Sidorenko, Julia
- Wu, Yang
- Zeng, Jian
- Grove, Jakob
- Kim, Minsoo
- Li, Zhiqiang
- Voloudakis, Georgios
- Zhang, Wen
- Adams, Mark
- Agartz, Ingrid
- Atkinson, Elizabeth G.
- Agerbo, Esben
- Albus, Margot
- Alizadeh, Behrooz Z.
- Als, Thomas D.
- Arolt, Volker
- Arrojo, Manuel
- Athanasiu, Lavinia
- Azevedo, Maria Helena
- Bacanu, Silviu A.
- Bass, Nicholas J.
- Begemann, Martin
- Bene, Judit
- Benyamin, Beben
- Bergen, Sarah E.
- Blasi, Giuseppe
- Bobes, Julio
- Bonassi, Stefano
- Braun, Alice
- Bressan, Rodrigo Affonseca
- Bromet, Evelyn J.
- Bruggeman, Richard
- Buckley, Peter F.
- Buckner, Randy L.
- Cahn, Wiepke
- Cairns, Murray J.
- Calkins, Monica E.
- Carr, Vaughan J.
- Castle, David
- Catts, Stanley V.
- Chan, Raymond C. K.
- Chaumette, Boris
- Cheng, Wei
- Cheung, Eric F. C.
- Chong, Siow Ann
- Cohen, David
- Consoli, Angèle
- Cordeiro, Quirino
- Costas, Javier
- Curtis, Charles
- Davidson, Michael
- Davis, Kenneth L.
- Degenhardt, Franziska
- DeLisi, Lynn E.
- Demontis, Ditte
- Dickerson, Faith
- Dinan, Timothy
- Djurovic, Srdjan
- Duan, Jubao
- Ducci, Giuseppe
- Dudbridge, Frank
- Eriksson, Johan G.
- Fañanás, Lourdes
- Faraone, Stephen V.
- Fiorentino, Alessia
- Forstner, Andreas
- Frank, Josef
- Gadelha, Ary
- Genovese, Giulio
- Gershon, Elliot S.
- Giannitelli, Marianna
- Giegling, Ina
- Goldstein, Jacqueline I.
- González-Pinto, Ana
- Gopal, Srihari
- Gratten, Jacob
- Green, Michael F.
- Greenwood, Tiffany A.
- Gülöksüz, Sinan
- Gur, Raquel E.
- Gur, Ruben C.
- Gutiérrez, Blanca
- Hahn, Eric
- Hakonarson, Hakon
- Haroutunian, Vahram
- Harvey, Carol
- Hayward, Caroline
- Herms, Stefan
- Hoffmann, Per
- Howrigan, Daniel P.
- Ikeda, Masashi
- Joa, Inge
- Julià, Antonio
- Kähler, Anna K.
- Kamatani, Yoichiro
- Karachanak-Yankova, Sena
- Keller, Matthew C.
- Kelly, Brian J.
- Kim, Sung-Wan
- Konte, Bettina
- Kraft, Julia
- Kubo, Michiaki
- Kučinskas, Vaidutis
- Kuzelova-Ptackova, Hana
- Landi, Stefano
- Lazzeroni, Laura C.
- Legge, Sophie E.
- Lehrer, Douglas S.
- Lerer, Bernard
- Li, Miaoxin
- Lieberman, Jeffrey
- Light, Gregory A.
- Liu, Chih-Min
- Lönnqvist, Jouko
- Loughland, Carmel M.
- Luykx, Jurjen J.
- Lynham, Amy
- Mackinnon, Andrew
- Magnusson, Patrik K. E.
- Maher, Brion S.
- Malaspina, Dolores
- Marder, Stephen R.
- Marsal, Sara
- Martin, Alicia R.
- Martorell, Lourdes
- Mattheisen, Manuel
- McCarley, Robert W.
- McDonald, Colm
- McGrath, John J.
- Medeiros, Helena
- Meier, Sandra
- Melle, Ingrid
- Metspalu, Andres
- Michie, Patricia T.
- Milani, Lili
- Milanova, Vihra
- Mitjans, Marina
- Molden, Espen
- Molina, Esther
- Mondelli, Valeria
- Moreno, Carmen
- Morley, Christopher P.
- Muntané, Gerard
- Murphy, Kieran C.
- Nenadić, Igor
- Nestadt, Gerald
- Noto, Cristiano
- Nuechterlein, Keith H.
- O’Brien, Niamh Louise
- O’Neill, F. Anthony
- Ota, Vanessa Kiyomi
- Pantelis, Christos
- Papadimitriou, George N.
- Parellada, Mara
- Paunio, Tiina
- Pellegrino, Renata
- Periyasamy, Sathish
- Perkins, Diana O.
- Pfuhlmann, Bruno
- Pietiläinen, Olli
- Porteous, David
- Quattrone, Diego
- Quested, Digby
- Rampino, Antonio
- Rapaport, Mark H.
- Reichenberg, Abraham
- Roffman, Joshua L.
- Roth, Julian
- Rutten, Bart P. F.
- Salomaa, Veikko
- Santoro, Marcos Leite
- Savitz, Adam
- Schall, Ulrich
- Scott, Rodney J.
- Seidman, Larry J.
- Sharp, Sally Isabel
- Shi, Jianxin
- Sim, Kang
- Skarabis, Nora
- Slominsky, Petr
- So, Hon-Cheong
- Sobell, Janet L.
- Stain, Helen J.
- Steen, Nils Eiel
- Steixner-Kumar, Agnes A.
- Stögmann, Elisabeth
- Stone, William S.
- Straub, Richard E.
- Streit, Fabian
- Strengman, Eric
- Stroup, T. Scott
- Subramaniam, Mythily
- Sugar, Catherine A.
- Suvisaari, Jaana
- Swerdlow, Neal R.
- Szatkiewicz, Jin P.
- Ta, Thi Minh Tam
- Takahashi, Atsushi
- Terao, Chikashi
- Thibaut, Florence
- Toncheva, Draga
- Tooney, Paul A.
- Torretta, Silvia
- Tosato, Sarah
- Üçok, Alp
- Vaaler, Arne
- Waddington, John
- Walter, Henrik
- Waterreus, Anna
- Webb, Bradley T.
- Weiser, Mark
- Williams, Nigel M.
- Witt, Stephanie H.
- Wu, Jing Qin
- Xu, Zhida
- Yolken, Robert
- Zai, Clement C.
- Zhu, Feng
- Zimprich, Fritz
- Ayub, Muhammad
- Benner, Christian
- Bertolino, Alessandro
- Black, Donald W.
- Bray, Nicholas J.
- Breen, Gerome
- Buccola, Nancy G.
- Byerley, William F.
- Chen, Wei J.
- Cloninger, C. Robert
- Donohoe, Gary
- Freedman, Robert
- Galletly, Cherrie
- Gandal, Michael J.
- Gennarelli, Massimo
- Hougaard, David M.
- Hwu, Hai-Gwo
- Jablensky, Assen V.
- McCarroll, Steven A.
- Moran, Jennifer L.
- Mors, Ole
- Mortensen, Preben B.
- Neil, Amanda L.
- Nordentoft, Merete
- Pato, Michele T.
- Petryshen, Tracey L.
- Pirinen, Matti
- Schulze, Thomas G.
- Smoller, Jordan W.
- Stahl, Eli A.
- Tsuang, Debby W.
- Vilella, Elisabet
- Wang, Shi-Heng
- Xu, Shuhua
- Agiananda, Feranindhya
- Irmansyah, Irmansyah
- Lukman, Petrin R.
- Nasrun, Martina W.
- Siste, Kristiana
- Wiguna, Tjhin
- Wulandari, D.
- Reza, Muhammad
- Abyzov, Alexej
- Akbarian, Schahram
- Breen, Michael
- Brown, Miguel
- Carlyle, Becky
- Crawford, Gregory
- Dracheva, Stella
- Emani, Prashant
- Farnham, Peggy
- Galeev, Timur
- Gerstein, Mark
- Giase, Gina
- Girdhar, Kiran
- Goes, Fernando
- Gu, Mengting
- Hoffman, Gabriel
- Hyde, Thomas
- Jaffe, Andrew
- Jiang, Shan
- Jiang, Yan
- Kefi, Amira
- Kim, Yunjung
- Kitchen, Robert
- Lee, Donghoon
- Li, Mingfeng
- Liu, Chunyu
- Liu, Shuang
- Mattei, Eugenio
- Pan, Xinghua
- Peters, Mette A.
- Pinto, Dalila
- Pochareddy, Sirisha
- Purcaro, Michael
- Purcell, Shaun
- Pratt, Henry
- Rhie, Suhn
- Rozowsky, Joel
- Sanders, Stephan
- Sethi, Anurag
- Shi, Xu
- Shieh, Annie
- Swarup, Vivek
- Szekely, Anna
- Wang, Daifeng
- Warrell, Jonathan
- Weng, Zhiping
- White, Kevin
- Wiseman, Jennifer
- Witt, Heather
- Won, Hyejung
- Wu, Feinan
- Xu, Xuming
- Zandi, Peter
- Arranz, Maria J.
- Bender, Stephan
- Lawrie, Stephen
- Lewis, Cathryn
- Mata, Ignacio
- Walshe, Muriel
- Weisbrod, Matthias
- Achsel, Tilmann
- Bagni, Claudia
- Bayés, Àlex
- Biederer, Thomas
- Brose, Nils
- Brown, Tyler C.
- Chua, John Jia En
- Coba, Marcelo P.
- Cornelisse, L. Niels
- Dieterich, Daniela C.
- Feng, Guoping
- Goldschmidt, Hana L.
- Gundelfinger, Eckart D.
- Hoogenraad, Casper
- Huganir, Richard L.
- Imig, Cordelia
- Jahn, Reinhard
- Jung, Hwajin
- Kaeser, Pascal S.
- Kim, Eunjoon
- Kreutz, Michael R.
- Lipstein, Noa
- MacGillavry, Harold D.
- Malenka, Robert
- McPherson, Peter S.
- Pielot, Rainer
- Ryan, Timothy A.
- Sala, Carlo
- Sheng, Morgan
- Smalla, Karl-Heinz
- Smit, August B.
- Südhof, Thomas C.
- Thomas, Paul D.
- Toonen, Ruud F.
- Verpelli, Chiara
- Adolfsson, Rolf
- Arango, Celso
- Belangero, Sintia Iole
- Børglum, Anders D.
- Braff, David
- Buxbaum, Joseph D.
- Campion, Dominique
- Cervilla, Jorge A.
- Cichon, Sven
- Corvin, Aiden
- Curtis, David
- Forti, Marta Di
- Domenici, Enrico
- Ehrenreich, Hannelore
- Esko, Tõnu
- Fanous, Ayman H.
- Gawlik, Micha
- Gill, Michael
- Glatt, Stephen J.
- Hong, Kyung Sue
- Iwata, Nakao
- Jönsson, Erik G.
- Kennedy, James L.
- Kirov, George
- Krebs, Marie-Odile
- Lee, Jimmy
- Lencz, Todd
- Levinson, Douglas F.
- Li, Qingqin S.
- Liu, Jianjun
- Malhotra, Anil K.
- Malhotra, Dheeraj
- McQuillin, Andrew
- Menezes, Paulo R.
- Morgan, Vera A.
- Morris, Derek W.
- Mowry, Bryan J.
- Nimgaonkar, Vishwajit
- Nöthen, Markus M.
- Paciga, Sara A.
- Palotie, Aarno
- Pato, Carlos N.
- Qin, Shengying
- Rietschel, Marcella
- Riley, Brien P.
- Rivera, Margarita
- Saka, Meram C.
- Serretti, Alessandro
- Stefánsson, Hreinn
- Tsuang, Ming T.
- Vawter, Marquis P.
- Weinberger, Daniel R.
- Werge, Thomas
- Yu, Xin
- Yue, Weihua
- Holmans, Peter A.
- Pocklington, Andrew J.
- Vassos, Evangelos
- Visscher, Peter M.
- Yang, Jian
- Andreassen, Ole A.
- Kendler, Kenneth S.
- Owen, Michael J.
- Wray, Naomi R.
- Daly, Mark J.
- Huang, Hailiang
- Neale, Benjamin M.
- Sullivan, Patrick F.
- Ripke, Stephan
- Walters, James T. R.
- O’Donovan, Michael C.
- Venue
- Nature
- Published
- 2022-04-08
- Volume
- 604
- Issue
- 7906
- Pages
- 502-508
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC9392466
- OpenAlex
- W4223520055
- Semantic Scholar
- 5b68667ad8bf91c7b91a44dfca6564662b85eb17
- Cited by
- 2,964
- References
- 99
- Citations by year
- 2026: 534 · 2025: 701 · 2024: 731 · 2023: 533 · 2022: 331
- FWCI
- 377.30
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Nature (publishedVersion)
- medRxiv (acceptedVersion)
- UWA Profiles and Research Repository (UWA) (publishedVersion, other-oa)
- EUR Research Repository (Erasmus University Rotterdam) (publishedVersion, other-oa)
- PubMed (publishedVersion)
- Research Publications (Maastricht University) (publishedVersion, other-oa)
- Research Portal (King's College London) (publishedVersion, other-oa)
- Research at the University of Copenhagen (University of Copenhagen) (publishedVersion, other-oa)
- Amsterdam UMC (VU Amsterdam) - Institutional Repository (publishedVersion, other-oa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, other-oa)
- VU Research Portal (publishedVersion, other-oa)
- ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
- PubMed Central (acceptedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- Opin vísindi (Opin vísindi) (submittedVersion, cc-by-nc-sa)
- Repository of Digital Objects for Teaching Research and Culture (University of Valencia) (submittedVersion, cc-by-nc)
- Rovira & Virgili repository (submittedVersion, other-oa)
- RISalud Institutional Health Repository of Andalucía (submittedVersion, other-oa)
- UTAS Research Repository (submittedVersion)
- Research Online (University of Wollongong) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion, other-oa)
- Institutional Repository of Institute of Psychology, Chinese Academy of Sciences (Institute of Psychology, Chinese Academy of Sciences) (submittedVersion)
- HAL (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Cineca Institutional Research Information System (Tor Vergata University) (submittedVersion)
- Archivio istituzionale della ricerca (Alma Mater Studiorum Università di Bologna) (submittedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
- Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion, other-oa)
- DR-NTU (Nanyang Technological University) (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- ePrints Soton (University of Southampton) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Open access LMU (Ludwid Maxmilian's Universitat Munchen) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Figshare (submittedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Institutional Research Information System (Università degli Studi di Brescia) (submittedVersion)
- Nova Science Publishers (Nova Science Publishers, Inc.) (submittedVersion, other-oa)
- Iris (University of Trento) (submittedVersion)
- Lirias (submittedVersion, other-oa)
- Opin vísindi (Opin vísindi) (submittedVersion, other-oa)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
- Pure Amsterdam UMC (submittedVersion, cc-by)
- Research Portal (Queen's University Belfast) (submittedVersion)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
- STM:n Hallinnonalan avoin julkaisuarkisto (Julkari) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, other-oa)
- Research Publications (Maastricht University) (submittedVersion)
- NOVA (University of Newcastle Australia) (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion)
- Funders
- Johns Hopkins University
- Fundación Alicia Koplowitz (777394, SAM16PE07CP1, PI19/024, PI16/02012, B2017/BMD-3740 AGES-CM-2)
- South London and Maudsley NHS Foundation Trust
- National Alliance for Research on Schizophrenia and Depression (667302, 728018, 602805)
- Mental Health Research UK (G0901310, G1100583)
- Wellcome Trust (085475/Z/08/Z, 085475, MR/L010305/1, 777394, 085475/B/08/Z, 223273)
- Broad Institute
- National Institute for Health and Care Research (NIHR200756, PDA/02/06/016)
- Academy of Medical Sciences (AMS-SGCL5-Mondelli)
- King's College London
- University College London
- European Commission (747429, 248828, 2014‐2020, H2020 Program, EU-H2020, CZ.02.1.01, B2017/BMD-3740 AGES-CM-2, HORIZON2020, H2020, 728018, 248778, 667302, 777394, 847776, 115916, 602805, 283798)
- Cardiff University (MR/L010305/1, G0800509)
- Fundação de Amparo à Pesquisa do Estado de São Paulo (2010/08968- 6, 14/07280-1, 2014/, 11/50740-5, 07/58736-1, 2011/, 16/04983-7, Code 001)
- National Natural Science Foundation of China (XDB38000000, CZ.02, 31525014, 91731303, 32041008, 2017SHZDZX01, 31961130380, 31771388)
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior ((Code 001), 2011/50740-5)
- Chinese Academy of Sciences (2017SHZDZX01, XDB38000000, QYZDJ-SSW-SYS009)
- Lundbeckfonden (R155-2014-1724, R204-2015-4129, R341-2020-222, R248‐2017‐2003, R24-2008-3243, R364-2021-85)
- Ministerio de Ciencia e Innovación (728018)
- Shanghai Jiao Tong University
- Norges Forskningsråd (283798, #248980, 248828, 262656, 223273, 248778, 273 291, B2017/BMD-3740 AGES-CM-2, 777394)
- Centro de Investigación Biomédica en Red de Salud Mental (B2017/BMD‐3740 AGES‐CM‐2, AGES-CM-2, B2017/BMD-3740)
- University College London Hospitals NHS Foundation Trust
- Innovative Medicines Initiative (AIMS-2- TRIALS, 115916, H2020, 777394)
- Nemzeti Kutatási Fejlesztési és Innovációs Hivatal
- Qingdao University
- National Institutes of Health (NMRC/TCR/003/2008, 223273, 2017SHZDZX01, B2017/BMD-3740 AGES-CM-2, 777394, H2020)
- Horizon 2020 Framework Programme (115916, 667302, 777394, EU‐H2020, # 847776, 728018)
- Stanley Center for Psychiatric Research, Broad Institute
- Medical Research Council (G1100583, G0901310, EU H2020, 777394, MR/L010305/1, MC_UU_00007/10, G0800509, MR/W020238/1, NIHR200756)
- Economic and Social Research Council
- National Medical Research Council (NMRC/TCR/003/2008, NMRC/TCR/003)
- Instituto de Salud Carlos III (PI16/, PI16/02012, SAM16PE07CP1, 728018, B2017/BMD-3740 AGES-CM-2, PI19/024, H2020)
- European Regional Development Fund (02.1.01/0.0/0.0, 2014-2020’, H2020, 667302, CZ.02, CZ.02.1.01, CZ.02.1.01/0.0, CZ.02.1.01/0.0/0.0, B2017/BMD-3740 AGES-CM-2, 728018, B2017/BMD-3740)
- National Institute of Mental Health (U01MH109514, R01MH119243, K01MH121659, U01MH109536, R01MH116281, R01MH101519, B2017/BMD-3740 AGES-CM-2, NMRC/TCR/003/2008, 777394, R01MH124873, R01MH106575)
- National Institute of Neurological Disorders and Stroke (R37NS036715)
- Topics
- Health Sciences › Medicine › Psychiatry and Mental health › Schizophrenia research and treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- schizophrenia, genome-wide association study, fine mapping, common genetic variants, GRIN2A, Sp4, neurodevelopmental disorders, excitatory and inhibitory neurons, gene prioritization, synaptic transmission, schizophrenia pathophysiology
- MeSH terms
- Alleles, Humans, Schizophrenia, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Genomics, Genome-Wide Association Study
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
A language model drew the claims from the paper on 2026-10-05, under version 3 of the claim definition (model deepseek-v4.1-flash, prompt extract-v3).
A second model labelled each claim on 2026-10-05 (model jev-1.13-20260917, definition revision gold-guideline-v0.2).
Cited sources are checked with a language model’s help (gpt-6-sol).
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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