Rare coding variants in ten genes confer substantial risk for schizophrenia

In the paper

“By meta-analyzing the whole-exomes of 24,248 cases and 97,322 controls, we implicate ultra-rare coding variants (URVs) in ten genes as conferring substantial risk for schizophrenia (odds ratios 3 – 50, P < 2.14 × 10−6), and 32 genes at a FDR < 5%.”

In the paper

“We observe an overlap of rare variant risk between schizophrenia, autism spectrum disorders (ASD)1, epilepsy and severe neurodevelopmental disorders (DD/ID)2, though in some shared genes different mutation types are implicated.”

What the sources say

• Not checked yetcites [1] 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 [2] Kaplanis, J. et al. Evidence for 28 genetic disorders discovered by combining healthcare and research data. Nature 586, 757–762 (2020). source

In the paper

“These genes have the greatest expression in central nervous system neurons and have diverse molecular functions that include the formation, structure, and function of the synapse.”

In the paper

“We found that missense variants with MPC > 3 have a global signal on par with PTVs in schizophrenia, autism spectrum disorders, and severe neurodevelopmental disorders, while variants with MPC 2 – 3 has a significant but weaker signal than PTVs and were therefore analyzed separately”

In the paper

“As expected, all ten genes are among the most constrained genes in the genome, with a substantial depletion of PTVs compared to chance expectation24.”

What the sources say

• Not checked yetcites [24] Lek, M. et al. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536, 285–291 (2016). source

In the paper

“Although confidence intervals are wide, URVs in these genes appear to confer substantial risk, with odds ratio of PTVs and Class I variants ranging from 3 to 50.”

In the paper

“Using Poisson rate tests based on expected mutation rate27, we found these de novo mutations are enriched for the 244 genes with P < 0.01 in our case-control analysis (Figure S13, Table S5), with limited or no signal in the remaining genes in the genome (Figure 1D).”

What the sources say

• Not checked yetcites [27] Hu, W., MacDonald, M. L., Elswick, D. E. & Sweet, R. A. The glutamate hypothesis of schizophrenia: evidence from human brain tissue studies. Ann. NY Acad. Sci. 1338, 38–57 (2015). source

In the paper

“We found a significant excess of URVs in schizophrenia cases compared to controls in the 299 DD/ID-associated genes (Pmeta = 1.5 × 10−14; ORClass I = 1.44, 1.3 – 1.6 95% CI), and in the 102 ASD-associated genes (Pmeta = 3.7 × 10−7; ORClass I = 1.45, 1.23 – 1.72 95% CI; Figure 5A; Table S12).”

In the paper

“We show for the first time that common regulatory variants from GWAS and ultra-rare coding variants disrupt an overlapping set of genes, including an allelic series in four genes in which common variants and rare coding variants increase risk to varying degrees.”

In the paper

“Nine of the ten schizophrenia genes showed limited de novo PTV signal in DD/ID, with a combined 8 de novo PTVs observed in these genes (Xexp = 4.98; PPois = 0.13; Figure 5B; Table S13).”

In the paper

“reaffirm that schizophrenia risk genes are involved in the postsynaptic density and broader synaptic function”

In the paper

“PTVs show consistent signals across the different cohorts, and synonymous variants do not deviate from expectation.”

In the paper

“individual genes like SETD1A, TRIO, and SP4 exhibited prenatal expression while GRIN2A and GRIA3 showed postnatal expression (Figure S22).”

In the paper

“PTVs in 9 of the 10 most confidently associated genes are associated with schizophrenia and not for DD/ID”

In the paper

“de novo missense mutations in GRIN2A cluster at the base of the ion channel with the most mutations in the exon encoding for the pore of the complex (Figure 5D).”

In the paper

“Furthermore, FAM120A and STAG1 resided in more complex GWAS-associated regions containing multiple genes but were prioritized among their neighbors as FDR < 5% in our sequencing study (Figure 4C, 4D).”

In the paper

“Statistical fine-mapping prioritized the likely underlying protein-coding gene at 64 of these associations (Table S11, Figure S18), and we found a case-control enrichment of URVs in these genes (Pmeta = 3.9 × 10−4; ORClass I = 1.46, 1.2 – 1.77 95% CI; Figure 4A, Table S12).”

In the paper

“we observe allelic series in GRIN2A, TRIO, and CACNA1G in which PTVs increase schizophrenia risk and de novo missense mutations confer strong DD/ID risk.”

In the paper

“De novo missense mutations in these genes clustered in specific domains and are associated with more severe neurodevelopmental, syndromic disorders with cognitive impairment”

In the paper

“Beyond the statistical enrichment, GRIN2A and SP4, two of the ten significant rare variant genes, had clear associations in schizophrenia GWAS (Figure 3A, Figure 4B).”

In the paper

“Following earlier reports studying heritability enrichment in GTEx tissues8,31, we found that genes with the highest specific expression in brain regions showed the strongest enrichment of risk URVs, most significantly in the human frontal cortex (P = 1.63 × 10−8) and with limited signal in the other tissue types (Extended Data Figure 4, Table S8, S9).”

What the sources say

• Not checked yetcites [8] Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). source
• Not checked yetcites [31] Koopmans, F. et al. SynGO: an evidence-based, expert-curated knowledge base for the synapse. Neuron 103, 217–234 (2019). source

In the paper

“implying that more risk genes await discovery using this approach.”

In the paper

“Earlier schizophrenia sequencing studies have established that ultra-rare and de novo mutations contribute to risk as a category, and have prioritized disease-relevant tissues and processes, specifically observing an enrichment in neuronal genes and synaptic processes9,11,19–23.”

What the sources say

• Not checked yetcites [9] Genovese, G. et al. Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia. Nat. Neurosci. 19, 1433–1441 (2016). source
• Not checked yetcites [11] 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
• Not checked yetcites [19] Purcell, S. M. et al. A polygenic burden of rare disruptive mutations in schizophrenia. Nature 506, 185–190 (2014). source
• Not checked yetcites [20] Singh, T. et al. Rare loss-of-function variants in SETD1A are associated with schizophrenia and developmental disorders. Nat. Neurosci. 19, 571–577 (2016). source
• Not checked yetcites [21] Howrigan, D. P. et al. Exome sequencing in schizophrenia-affected parent–offspring trios reveals risk conferred by protein-coding de novo mutations. Nat. Neurosci. 23, 185–193 (2020). source
• Not checked yetcites [22] Gulsuner, S. et al. Genetics of schizophrenia in the South African Xhosa. Science 367, 569–573 (2020). source
• Not checked yetcites [23] Karczewski, K. J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020). source

In the paper

“Several rare (MAF < 0.1%) recurrent copy number variants (CNVs) have also been robustly associated with schizophrenia, as exemplified by the dramatically higher rates of schizophrenia in 22q11.2 deletion carriers10,15.”

What the sources say

• Not checked yetcites [10] Marshall, C. R. et al. Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects. Nat. Genet. 49, 27–35 (2017). source
• Not checked yetcites [15] Zuk, O. et al. Searching for missing heritability: designing rare variant association studies. Proc. Natl Acad. Sci. USA 111, E455–E464 (2014).

In the paper

“Furthermore, these risk alleles are concentrated in genes with a near-complete depletion of protein-truncating variants in population studies, a result shared with other neurodevelopmental disorders9,11 and suggesting strong direct selection against such mutations.”

What the sources say

• Not checked yetcites [9] Genovese, G. et al. Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia. Nat. Neurosci. 19, 1433–1441 (2016). source
• Not checked yetcites [11] 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

In the paper

“Because causal variants in schizophrenia GWAS are predominantly non-coding, challenges related to fine-mapping and interpretation of intergenic and intronic elements limit our ability to confidently identify underlying genes, infer the mechanism by which they influence disease risk, and determine the direction of effect.”

In the paper

“After extracting SCHEMA samples from this callset, we performed quality control steps to ensure high quality of sequence data, exclude contaminated samples, identify parent-proband trios and other related individuals, and infer global ancestries”

In the paper

“Finally, we demonstrate that increased scale following this approach will uncover additional risk genes and help complete the genetic architecture of schizophrenia.”

In the paper

“Pathway analyses of common variants have prioritized disease-relevant tissues and cell types, and in some cases, independently recapitulating known biology8,30,31.”

What the sources say

• Not checked yetcites [8] Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). source
• Not checked yetcites [30] Finucane, H. K. et al. Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nat. Genet. 50, 621–629 (2018). source
• Not checked yetcites [31] Koopmans, F. et al. SynGO: an evidence-based, expert-curated knowledge base for the synapse. Neuron 103, 217–234 (2019). source

In the paper

“We attempted to control for technical and methodological batch effects that may arise from this approach in both variant calling and additionally via permutation testing described below.”

In the paper

“The most natural grouping for rare variants is within a gene, based on predicted functional consequence or evidence for deleteriousness16,17.”

What the sources say

• Not checked yetcites [16] Lee, S., Abecasis, G. R., Boehnke, M. & Lin, X. Rare-variant association analysis: study designs and statistical tests. Am. J. Hum. Genet. 95, 5–23 (2014). source
• Not checked yetcites [17] Rivas, M. A. et al. Effect of predicted protein-truncating genetic variants on the human transcriptome. Science 348, 666–669 (2015). source

In the paper

“Developed from neuropharmacological and neuropathological observations, the glutamatergic hypothesis postulates that the hypofunction of glutamatergic signaling through NMDA receptors is a possible mechanism of disease28 (Supplementary Note).”

What the sources say

• Not checked yetcites [28] Kang, H. J. et al. Spatio-temporal transcriptome of the human brain. Nature 478, 483–489 (2011). source

In the paper

“suggesting that more genes remain to be discovered (Figure 2B).”

In the paper

“Schizophrenia GWAS also identified a common variant at GRIN2A (OR = 1.057, P = 1.57 × 10−10), providing an allelic series in which different perturbation of gene function results in severity of disease risk (Figure 3A)8.”

What the sources say

• Not checked yetcites [8] Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). source

In the paper

“This has been borne out by genome-wide association studies (GWAS) which have now, in a companion paper, identified 270 common (minor allele frequency [MAF] > 1%) risk loci of individually small effect (median odds ratio [OR] < 1.05)13.”

What the sources say

• Not checked yetcites [13] Loh, P.-R. et al. Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis. Nat. Genet. 47, 1385–1392 (2015). source

In the paper

“It is well-established that schizophrenia has a substantial genetic component with contributions from across the allele frequency spectrum8–11.”

What the sources say

• Not checked yetcites [8] Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). source
• Not checked yetcites [9] Genovese, G. et al. Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia. Nat. Neurosci. 19, 1433–1441 (2016). source
• Not checked yetcites [10] Marshall, C. R. et al. Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects. Nat. Genet. 49, 27–35 (2017). source
• Not checked yetcites [11] 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

In the paper

“We subsequently applied site- and genotype-level filters to generate a robust set of coding SNPs and indels for a well-matched case-control analysis”

In the paper

“However, the analysis of URVs has had limited success in delivering individual gene discovery in schizophrenia because of power limitations, with only a single gene, SETD1A, identified as robustly associated16,21.”

What the sources say

• Not checked yetcites [16] Lee, S., Abecasis, G. R., Boehnke, M. & Lin, X. Rare-variant association analysis: study designs and statistical tests. Am. J. Hum. Genet. 95, 5–23 (2014). source
• Not checked yetcites [21] Howrigan, D. P. et al. Exome sequencing in schizophrenia-affected parent–offspring trios reveals risk conferred by protein-coding de novo mutations. Nat. Neurosci. 23, 185–193 (2020). source

In the paper

“which provides additional reassurance of the robustness of our case-control gene results.”

In the paper

“CNVs of large effect, on the other hand, often disrupt hundreds of kilobases of the genome and multiple genes simultaneously, limiting our ability to derive clear functional insights10.”

What the sources say

• Not checked yetcites [10] Marshall, C. R. et al. Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects. Nat. Genet. 49, 27–35 (2017). source

In the paper

“To ensure calibrated analyses, these samples were included in joint re-processing and variant calling using a standardized BWA-Picard-GATK pipeline as part of the larger Genome Aggregation Database (gnomAD) effort”

In the paper

“The NMDA receptor changes in composition during prenatal to postnatal neurodevelopment with GRIN2A predominantly expressed during late childhood and adolescence, recapitulating expected epidemiological observations on schizophrenia age-of-onset (Supplementary Methods, Figure 3B)29.”

What the sources say

• Not checked yetcites [29] Network and Pathway Analysis Subgroup of the Psychiatric Genetics Consortium. Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways. Nat. Neurosci. 18, 199–209 (2015). source

In the paper

“As a class of variation, common variants explain ~24% of the variance in disease liability14.”

What the sources say

• Not checked yetcites [14] Karayiorgou, M. et al. Schizophrenia susceptibility associated with interstitial deletions of chromosome 22q11. Proc. Natl Acad. Sci. USA 92, 7612–7616 (1995). source

In the paper

“suggesting that 0.86% of patients are carriers and ~35% of variants are de novo.”

In the paper

“Because schizophrenia as a trait is under strong selection39–41, we expect that URVs of large effect to be frequently de novo or of very recent origin and contribute to risk in only a fraction of diagnosed patients.”

What the sources say

• Not checked yetcites [39] Power, R. A. et al. Fecundity of patients with schizophrenia, autism, bipolar disorder, depression, anorexia nervosa, or substance abuse vs their unaffected siblings. Arch. Gen. Psychiat. 70, 22–30 (2013).
• Not checked yetcites [40] Endele, S. et al. Mutations in GRIN2A and GRIN2B encoding regulatory subunits of NMDA receptors cause variable neurodevelopmental phenotypes. Nat. Genet. 42, 1021–1026 (2010). source
• Not checked yetcites [41] Finn, R. D. et al. Pfam: the protein families database. Nucleic Acids Res. 42, D222–D230 (2014). source

In the paper

“The vast majority of risk alleles, their direction and magnitude of effect, mode of action, and responsible genes are yet to be discovered.”

In the paper

“Combined, these results suggest there is at least partial convergence in the genes and biological processes implicated by common and ultra-rare genetic variation, and that ultra-rare coding variants can be leveraged to prioritize genes within GWAS loci.”

In the paper

“These observations offer the possibility that certain properties may differentiate genes for adult psychiatric disorders and more severe DD/IDs.”

In the paper

“These observations suggest schizophrenia and childhood onset neurodevelopmental disorders share some genes and biological processes, but that at least in some cases, the severity or the nature of the functional impairment differs between disorders.”

In the paper

“These studies have established that the genetic signals were concentrated in constrained genes and shared between the two disorders35,36.”

What the sources say

• Not checked yetcites [35] The Deciphering Developmental Disorders Study. Large-scale discovery of novel genetic causes of developmental disorders. Nature 519, 223–228 (2015). source
• Not checked yetcites [36] Barbosa, S. et al. Opposite modulation of RAC1 by mutations in TRIO is associated with distinct, domain-specific neurodevelopmental disorders. Am. J. Hum. Genet. 106, 338–355 (2020). source

In the paper

“Most recently, the analysis of de novo mutations from 31,058 DD/ID trios implicated 299 genes, while the analysis of 11,986 ASD cases identified 102 genes at FDR < 10% (Table S11)1,37.”

What the sources say

• Not checked yetcites [1] 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 [37] Haukka, J., Suvisaari, J. & Lönnqvist, J. Fertility of patients with schizophrenia, their siblings, and the general population: a cohort study from 1950 to 1959 in Finland. Am. J. Psychiat. 160, 460–463 (2003). source

In the paper

“Efforts in the past decade are beginning to generate a more comprehensive view of the genetic architecture for schizophrenia, composed of common variants of small effects, large CNVs with elevated frequencies driven by genomic instability, and now, URVs of large effect implicating individual genes (Figure 6A)8,10.”

What the sources say

• Not checked yetcites [8] Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature 511, 421–427 (2014). source
• Not checked yetcites [10] Marshall, C. R. et al. Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects. Nat. Genet. 49, 27–35 (2017). source