Genetic copy number variants, cognition and psychosis: a meta-analysis and a family study.
Journal
Molecular psychiatry
ISSN: 1476-5578
Titre abrégé: Mol Psychiatry
Pays: England
ID NLM: 9607835
Informations de publication
Date de publication:
09 2021
09 2021
Historique:
received:
07
08
2018
accepted:
11
06
2020
revised:
11
06
2020
pubmed:
29
7
2020
medline:
1
2
2022
entrez:
29
7
2020
Statut:
ppublish
Résumé
The burden of large and rare copy number genetic variants (CNVs) as well as certain specific CNVs increase the risk of developing schizophrenia. Several cognitive measures are purported schizophrenia endophenotypes and may represent an intermediate point between genetics and the illness. This paper investigates the influence of CNVs on cognition. We conducted a systematic review and meta-analysis of the literature exploring the effect of CNV burden on general intelligence. We included ten primary studies with a total of 18,847 participants and found no evidence of association. In a new psychosis family study, we investigated the effects of CNVs on specific cognitive abilities. We examined the burden of large and rare CNVs (>200 kb, <1% MAF) as well as known schizophrenia-associated CNVs in patients with psychotic disorders, their unaffected relatives and controls (N = 3428) from the Psychosis Endophenotypes International Consortium (PEIC). The carriers of specific schizophrenia-associated CNVs showed poorer performance than non-carriers in immediate (P = 0.0036) and delayed (P = 0.0115) verbal recall. We found suggestive evidence that carriers of schizophrenia-associated CNVs had poorer block design performance (P = 0.0307). We do not find any association between CNV burden and cognition. Our findings show that the known high-risk CNVs are not only associated with schizophrenia and other neurodevelopmental disorders, but are also a contributing factor to impairment in cognitive domains such as memory and perceptual reasoning, and act as intermediate biomarkers of disease risk.
Identifiants
pubmed: 32719466
doi: 10.1038/s41380-020-0820-7
pii: 10.1038/s41380-020-0820-7
pmc: PMC8589646
doi:
Types de publication
Journal Article
Meta-Analysis
Research Support, Non-U.S. Gov't
Systematic Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
5307-5319Subventions
Organisme : Department of Health
ID : PDF-2010-03-047
Pays : United Kingdom
Organisme : Medical Research Council
ID : G0901310
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/L010305/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 085475/B/08/Z
Pays : United Kingdom
Organisme : Medical Research Council
ID : MC_PC_16014
Pays : United Kingdom
Organisme : Wellcome Trust
Pays : United Kingdom
Organisme : Wellcome Trust (Wellcome)
ID : 085475/Z/08/Z
Organisme : Wellcome Trust (Wellcome)
ID : 200589/Z/16/Z
Informations de copyright
© 2020. The Author(s).
Références
McCarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, et al. Common deletion polymorphisms in the human genome. Nat Genet. 2006;38:86–92.
pubmed: 16468122
Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, et al. Global variation in copy number in the human genome. Nature. 2006;444:444–54.
pubmed: 17122850
pmcid: 2669898
Pinto D, Marshall C, Feuk L, Scherer SW. Copy-number variation in control population cohorts. Hum Mol Genet. 2007;16:168–73.
Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, et al. Large-scale copy number polymorphism in the human genome. Science. 2004;305:525–8.
pubmed: 15273396
Foong J, Girdea M, Stavropoulos J, Brudno M. Prioritizing clinically relevant copy number variation from genetic interactions and gene function data. PLoS ONE. 2015;10:1–15.
Kirov G, Rees E, Walters JTR, Escott-Price V, Georgieva L, Richards AL, et al. The penetrance of copy number variations for schizophrenia and developmental delay. Biol Psychiatry. 2014;75:378–85.
pubmed: 23992924
Giaroli G, Bass N, Strydom A, Rantell K, McQuillin A. Does rare matter? Copy number variants at 16p11.2 and the risk of psychosis: a systematic review of literature and meta-analysis. Schizophr Res. 2014;159:340–6.
pubmed: 25311781
Levinson DF, Duan J, Oh S, Wang K, Sanders AR, Shi J, et al. Copy number variants in schizophrenia: confirmation of five previous finding sand new evidence for 3q29 microdeletions and VIPR2 duplications. Am J Psychiatry. 2011;168:302–16.
pubmed: 21285140
pmcid: 4441324
Malhotra D, Sebat J. CNVs: harbingers of a rare variant revolution in psychiatric genetics. Cell. 2012;148:1223–41.
pubmed: 22424231
pmcid: 3351385
Rees E, Walters JTR, Georgieva L, Isles AR, Chambert KD, Richards AL, et al. Analysis of copy number variations at 15 schizophrenia-associated loci. Br J Psychiatry. 2014;204:108–14.
pubmed: 24311552
pmcid: 3909838
Stefansson H, Rujescu D, Cichon S, Pietiläinen OPH, Ingason A, Steinberg S, et al. Large recurrent microdeletions associated with schizophrenia. Nature. 2008;455:232–6.
pubmed: 18668039
pmcid: 2687075
Marshall CR, Howrigan DP, Merico D, Thiruvahindrapuram B, Wu W, Greer DS, et al. Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects. Nat Genet. 2017;49:27–35.
pubmed: 27869829
Vassos E, Collier DA, Holden S, Patch C, Rujescu D, St. Clair D, et al. Penetrance for copy number variants associated with schizophrenia. Hum Mol Genet. 2010;19:3477–81.
pubmed: 20587603
Schneider M, Debbané M, Bassett AS, Chow EWC, Fung WLA, van den Bree M, et al. Psychiatric disorders from childhood to adulthood in 22q11.2 deletion syndrome: results from the International Consortium on Brain and Behavior in 22q11.2 deletion syndrome. Am J Psychiatry. 2014;171:627–39.
pubmed: 24577245
pmcid: 4285461
Walsh T, McClellan JM, McCarthy SE, Addington AM, Pierce SB, Cooper GM, et al. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science. 2008;320:539–43.
pubmed: 18369103
Stone JL, O’Donovan MC, Gurling H, Kirov GK, Blackwood DHR, Corvin A, et al. Rare chromosomal deletions and duplications increase risk of schizophrenia. Nature. 2008;455:237–41.
Szatkiewicz JP, O’Dushlaine C, Chen G, Chambert K, Moran JL, Neale BM, et al. Copy number variation in schizophrenia in Sweden. Mol Psychiatry. 2014;19:762–73.
pubmed: 24776740
pmcid: 4271733
Kirov G, Grozeva D, Norton N, Ivanov D, Mantripragada KK, Holmans P, et al. Support for the involvement of large copy number variants in the pathogenesis of schizophrenia. Hum Mol Genet. 2009;18:1497–503.
pubmed: 19181681
pmcid: 2664144
Gottesman II, Gould TD. The endophenotype concept in psychiatry: Etymology and strategic intentions. Am J Psychiatry. 2003;160:636–45.
pubmed: 12668349
Blakey R, Ranlund S, Zartaloudi E, Cahn W, Calafato S, Colizzi M, et al. Associations between psychosis endophenotypes across brain functional, structural, and cognitive domains. Psychol Med. 2017;2:1325–40.
Keefe RSE, Fenton WS. How should DSM-V criteria for schizophrenia include cognitive impairment? Schizophr Bull. 2007;33:912–20.
pubmed: 17567627
pmcid: 2632322
Leeson VC, Sharma P, Harrison M, Ron MA, Barnes TRE, Joyce EM. IQ trajectory, cognitive reserve, and clinical outcome following a first episode of psychosis: a 3-year longitudinal study. Schizophr Bull. 2011;37:768–77.
pubmed: 19934212
Saykin AJ, Shtasel DL, Gur RE, Kester DB, Mozley LH, Stafiniak P, et al. Neuropsychological deficits in neuroleptic naive patients with first-episode schizophrenia. Arch Gen Psychiatry. 1994;51:124–31.
pubmed: 7905258
Reichenberg A, Weiser M, Rabinowitz J, Caspi A, Schmeidler J, Mark M, et al. A population-based cohort study of premorbid intellectual, language, and behavioral functioning in patients with schizophrenia, schizoaffective disorder, and nonpsychotic bipolar disorder. Am J Psychiatry. 2002;159:2027–35.
pubmed: 12450952
Woodberry KA, Giuliano AJ, Seidman LJ. Premorbid IQ in Schizophrenia: a meta-analytic review. Am J Psychiatry. 2008;165:579–87.
pubmed: 18413704
Snitz BE, MacDonald AW, Carter CS. Cognitive deficits in unaffected first-degree relatives of schizophrenia patients: a meta-analytic review of putative endophenotypes. Schizophr Bull. 2006;32:179–94.
pubmed: 16166612
pmcid: 2632195
Mark W, Toulopoulou T. Cognitive intermediate phenotype and genetic risk for psychosis. Curr Opin Neurobiol. 2016;36:23–30.
pubmed: 26363129
Blokland GAM, del Re EC, Mesholam-Gately RI, Jovicich J, Trampush JW, Keshavan MS, et al. The Genetics of Endophenotypes of Neurofunction to Understand Schizophrenia (GENUS) consortium: a collaborative cognitive and neuroimaging genetics project. Schizophr Res. 2017;195:306–17.
pubmed: 28982554
pmcid: 5882601
Savage JE, Jansen PR, Stringer S, Watanabe K, Bryois J, de Leeuw CA, et al. Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence. Nat Genet. 2018;50:912–9.
pubmed: 29942086
pmcid: 6411041
Martin AK, Robinson G, Reutens D, Mowry B. Copy number deletion burden is associated with cognitive, structural, and resting-state network differences in patients with schizophrenia. Behav Brain Res. 2014;272:324–34.
pubmed: 25036426
Yeo RA, Gangestad SW, Liu J, Ehrlich S, Thoma RJ, Pommy J, et al. The impact of copy number deletions on general cognitive ability and ventricle size in patients with schizophrenia and healthy control subjects. Biol Psychiatry. 2013;73:540–5.
pubmed: 23237311
Bouchard TJ, McGue M. Genetic and environmental influences on human psychological differences. J Neurobiol. 2003;54:4–45.
pubmed: 12486697
Deary IJ, Johnson W, Houlihan LM. Genetic foundations of human intelligence. Hum Genet. 2009;126:215–32.
pubmed: 19294424
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, et al. Diversity of human copy number variation and multicopy genes. Science. 2010. https://doi.org/10.1126/science.1197005 .
Bagshaw ATM, Horwood LJ, Liu Y, Fergusson DM, Sullivan PF, Kennedy MA. No effect of genome-wide copy number variation on measures of intelligence in a New Zealand Birth Cohort. PLoS ONE. 2013;8:1–6.
Männik K, Mägi R, Macé A, Cole B, Guyatt AL, Shihab HA, et al. Copy number variations and cognitive phenotypes in unselected populations. Jama. 2015;313:2044–54.
pubmed: 26010633
pmcid: 4684269
Kendall KM, Rees E, Escott-Price V, Einon M, Thomas R, Hewitt J, et al. Cognitive performance among carriers of pathogenic copy number variants: analysis of 152,000 UK Biobank subjects. Biol Psychiatry. 2016:103–10.
Ziats MN, Goin-Kochel RP, Berry LN, Ali M, Ge J, Guffey D, et al. The complex behavioral phenotype of 15q13.3 microdeletion syndrome. Genet Med. 2016;18:1111–8. https://doi.org/10.1038/gim.2016.9 .
doi: 10.1038/gim.2016.9
pubmed: 26963284
Hippolyte L, Maillard AM, Rodriguez-Herreros B, Pain A, Martin-Brevet S, Ferrari C, et al. The number of genomic copies at the 16p11.2 locus modulates language, verbal memory, and inhibition. Biol Psychiatry. 2016;80:129–39.
pubmed: 26742926
D’Angelo D, Lebon S, Chen Q, Martin-Brevet S, Snyder LG, Hippolyte L, et al. Defining the effect of the 16p11.2 duplication on cognition, behavior, and medical comorbidities. JAMA Psychiatry. 2016;73:20–30.
pubmed: 26629640
pmcid: 5894477
Simon TJ, Bearden CE, Mc-Ginn DM, Zackai E. Visuospatial and numerical cognitive deficits in children with chromosome 22q11.2 deletion syndrome. Cortex. 2005;41:145–55.
pubmed: 15714897
pmcid: 4318636
Stefansson H, Meyer-Lindenberg A, Steinberg S, Magnusdottir B, Morgen K, Arnarsdottir S, et al. CNVs conferring risk of autism or schizophrenia affect cognition in controls. Nature. 2014;505:361–6.
pubmed: 24352232
Kirkpatrick RM, McGue M, Iacono WG, Miller MB, Basu S, Pankratz N. Low-frequency copy-number variants and general cognitive ability: no evidence of association. Intelligence. 2014;42:98–106.
pubmed: 24497650
Yeo RA, Gangestad SW, Liu J, Calhoun VD, Hutchison KE. Rare copy number deletions predict individual variation in intelligence. PLoS ONE. 2011;6:1–8.
McRae AF, Wright MJ, Hansell NK, Montgomery GW, Martin NG. No association between general cognitive ability and rare copy number variation. Behav Genet. 2013;43:202–7.
pubmed: 23417127
van Scheltinga AFT, Bakker SCC, van Haren NEM, Derks EMM, Buizer-Voskamp JEE, Cahn W, et al. Schizophrenia genetic variants are not associated with intelligence. Psychol Med. 2013;43:2563–70.
pubmed: 23410598
MacLeod AK, Davies G, Payton A, Tenesa A, Harris SE, Liewald D, et al. Genetic copy number variation and general cognitive ability. PLoS ONE. 2012;7:e37385.
pubmed: 23300510
pmcid: 3530597
Gialluisi A, Visconti A, Willcutt EG, Smith SD, Pennington BF, Falchi M, et al. Investigating the effects of copy number variants on reading and language performance. J Neurodev Disord. 2016;8:17.
pubmed: 27186239
pmcid: 4868026
Bramon E, Pirinen M, Strange A, Lin K, Freeman C, Bellenguez C, et al. A genome-wide association analysis of a broad psychosis phenotype identifies three loci for further investigation. Biol Psychiatry. 2014;75:386–97.
pubmed: 23871474
Burdick KE, Gunawardane N, Woodberry K, Malhotra AK. The role of general intelligence as an intermediate phenotype for neuropsychiatric disorders. Cogn Neuropsychiatry. 2009;14:299–311.
pubmed: 19634032
pmcid: 2727853
Singh-Manoux A, Ferrie JE, Lynch JW, Marmot M. The role of cognitive ability (intelligence) in explaining the association between socioeconomic position and health: evidence from the Whitehall II prospective cohort study. Am J Epidemiol. 2005;161:831–9.
pubmed: 15840615
Huguet G, Schramm C, Douard E, Jiang L, Labbe A, Tihy F, et al. Measuring and estimating the effect sizes of copy number variants on general intelligence in community-based samples. JAMA Psychiatry. 2018;75:447–57. https://doi.org/10.1001/jamapsychiatry.2018.0039 .
doi: 10.1001/jamapsychiatry.2018.0039
StatsDirect Ltd. StatsDirect statistical software. https://www.statsdirect.com .
Rupinski MT, Dunlap WP. Approximating Pearson product-moment correlations from Kendall’s Tau and Spearman’s Rho. Educ Psychol Meas. 1996;v56 n3:419–29.
Peterson RA, Brown SP. On the use of beta coefficients in meta-analysis. J Appl Psychol. 2005;90:175–81.
pubmed: 15641898
Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SFA, et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007;17:1665–74.
pubmed: 17921354
pmcid: 2045149
Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, et al. Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms. Nucleic Acids Res. 2008;36:1–12.
Kirov G, Rujescu D, Ingason A, Collier DA, O’Donovan MC, Owen MJ. Neurexin 1 (NRXN1) deletions in schizophrenia. Schizophr Bull. 2009;35:851–4.
pubmed: 19675094
pmcid: 2728827
Wechsler D. Wechsler adult intelligence scale—Revised manual. New York: Psychological Corporation; 1981.
Wechsler D. Wechsler adult intelligence scale, third edition: Administration and scoring manual. London: Psychological Corporation; 1997.
Speed D, Cai N, Johnson MR, Nejentsev S, Balding DJ. Reevaluation of SNP heritability in complex human traits. Nat Genet. 2017;49:986–92. https://doi.org/10.1038/ng.3865 .
doi: 10.1038/ng.3865
pubmed: 28530675
pmcid: 5493198
R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2018. https://www.R-project.org/ .
Ziyatdinov A, Vázquez-Santiago M, Brunel H, Martinez-Perez A, Aschard H, Soria JM. lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals. BMC Bioinform. 2018;19:68. https://doi.org/10.1186/s12859-018-2057-x .
doi: 10.1186/s12859-018-2057-x
Li M-X, Yeung JMY, Cherny SS, Sham PC. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Hum Genet. 2012;131:747–56.
pubmed: 22143225
Southam L, Gilly A, Süveges D, Farmaki A-E, Schwartzentruber J, Tachmazidou I, et al. Whole genome sequencing and imputation in isolated populations identify genetic associations with medically-relevant complex traits. Nat Commun. 2017;8:15606.
pubmed: 28548082
pmcid: 5458552
Langley K, Martin J, Agha SS, Davies C, Stergiakouli E, Holmans P, et al. Clinical and cognitive characteristics of children with attention-deficit hyperactivity disorder, with and without copy number variants. Br J Psychiatry. 2011;199:398–403.
pubmed: 22045946
pmcid: 3205349
Guyatt AL, Stergiakouli E, Martin J, Walters J, O’Donovan M, Owen M, et al. Association of copy number variation across the genome with neuropsychiatric traits in the general population. Am J Med Genet B Neuropsychiatr Genet. 2018;177:489–502.
pubmed: 29687944
pmcid: 6099375
Valsesia A, Macé A, Jacquemont S, Beckmann JS, Kutalik Z. The growing importance of CNVs: new insights for detection and clinical interpretation. Front Genet. 2013;4:92.
pubmed: 23750167
pmcid: 3667386
Rees E, Kirov G, Sanders A, Walters JTR, Chambert KD, Shi J, et al. Evidence that duplications of 22q11.2 protect against schizophrenia. Mol Psychiatry. 2014;19:37–40.
pubmed: 24217254
Guimond S, Chakravarty MM, Bergeron-Gagnon L, Patel R, Lepage M. Verbal memory impairments in schizophrenia associated with cortical thinning. NeuroImage Clin. 2016;11:20–9. https://doi.org/10.1016/j.nicl.2015.12.010 .
pubmed: 26909322
Fernandez VG, Asarnow R, Narr KL, Subotnik KL, Kuppinger H, Fogelson D, et al. Temporal lobe thickness and verbal memory in first-degree relatives of individuals with schizophrenia. Schizophr Res. 2018;199:221–5. https://doi.org/10.1016/j.schres.2018.02.038 .
doi: 10.1016/j.schres.2018.02.038
pubmed: 29499968
pmcid: 6110998
Fett AKJ, Viechtbauer W, Dominguez M de G, Penn DL, van Os J, Krabbendam L. The relationship between neurocognition and social cognition with functional outcomes in schizophrenia: a meta-analysis. Neurosci Biobehav Rev. 2011;35:573–88.
pubmed: 20620163
Faerden A, Barrett EA, Nesvåg R, Friis S, Finset A, Marder SR, et al. Apathy, poor verbal memory and male gender predict lower psychosocial functioning one year after the first treatment of psychosis. Psychiatry Res. 2013;210:55–61. https://doi.org/10.1016/j.psychres.2013.02.007 .
doi: 10.1016/j.psychres.2013.02.007
pubmed: 23489592
Zhang X, Du R, Li S, Zhang F, Jin L, Wang H. Evaluation of copy number variation detection for a SNP array platform. BMC Bioinform. 2014;15:50.
Pinto D, Darvishi K, Shi X, Rajan D, Rigler D, Fitzgerald T, et al. Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol. 2011;29:512–20.
pubmed: 21552272
pmcid: 3270583
Itsara A, Cooper GM, Baker C, Girirajan S, Li J, Absher D, et al. Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet. 2009;84:148–61.
pubmed: 19166990
pmcid: 2668011
Bergen SE, Gardner CO, Kendler KS. Age-related changes in heritability of behavioral phenotypes over adolescence and young adulthood: a meta-analysis. Twin Res Hum Genet. 2007;10:423–33.
pubmed: 17564500
Haworth CMA, Wright MJ, Luciano M, Martin NG, de Geus EJC, van Beijsterveldt CEM, et al. The heritability of general cognitive ability increases linearly from childhood to young adulthood. Mol Psychiatry. 2010;15:1112–20.
pubmed: 19488046
Clifton NE, Pocklington AJ, Scholz B, Rees E, Walters JTR, Kirov G, et al. Schizophrenia copy number variants and associative learning. Mol Psychiatry. 2017;22:178–82. https://doi.org/10.1038/mp.2016.227 .
doi: 10.1038/mp.2016.227
pubmed: 27956746