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The relationship between rare CNV burden and neuropsychiatric traits in young, general populations is underexplored. A total of 6,807 children from the Avon Longitudinal Study of Parents and Children (ALSPAC) were studied. CNVs were inferred from single nucleotide polymorphism\u2010array data using PennCNV. After excluding children with known candidate CNVs for schizophrenia (SCZ), rare (&lt;1%) CNV burden (total number of genes affected by CNVs, total length of CNVs, and largest CNV carried) was analyzed in relation to: psychotic experiences (PEs) and anxiety\/depression in adolescence; autism spectrum disorder (ASD) and attention\u2010deficit hyperactivity disorder (ADHD), ASD and ADHD traits, and cognitive measures during childhood. Outcomes were also assessed in relation to known SCZ CNVs. The number of genes affected by rare CNVs was associated with a continuous measure of ASD: the standardized mean difference [SMD] per gene affected was increased by 0.018 [95%CI 0.011,0.025], <jats:italic>p<\/jats:italic>\u2009=\u20093e\u201007 for duplications and by 0.021 [95%CI 0.010, 0.032], <jats:italic>p<\/jats:italic>\u2009=\u20091e\u201004 for deletions. In line with our published results on educational attainment in ALSPAC, intelligence quotient (IQ) was associated with CNV burden: the SMD per gene affected was \u22120.017 [95%CI \u22120.025, \u22120.008] <jats:italic>p<\/jats:italic>\u2009=\u20091e\u201004 for duplications and \u22120.023 [95%CI \u22120.037, \u22120.009], <jats:italic>p<\/jats:italic>\u2009=\u2009.002 for deletions. Associations were also observed for measures of coherence, attention, memory, and social cognition. SCZ\u2010associated deletions were associated with IQ (SMD: \u22120.617 [95%CI \u22120.936, \u22120.298], <jats:italic>p<\/jats:italic>\u2009=\u20092e\u201004), but not with PEs or other traits. We found that rare CNV burden and known SCZ candidate CNVs are associated with neuropsychiatric phenotypes in a nonclinically ascertained sample of young people.<\/jats:p>","DOI":"10.1002\/ajmg.b.32637","type":"journal-article","created":{"date-parts":[[2018,4,24]],"date-time":"2018-04-24T09:59:18Z","timestamp":1524563958000},"page":"489-502","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":31,"title":["Association of copy number variation across the genome with neuropsychiatric traits in the general population"],"prefix":"10.1002","volume":"177","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1860-6337","authenticated-orcid":false,"given":"Anna L.","family":"Guyatt","sequence":"first","affiliation":[{"name":"MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol Bristol United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evie","family":"Stergiakouli","sequence":"additional","affiliation":[{"name":"MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol Bristol United Kingdom"},{"name":"Centre for Academic Mental Health, Population Health Sciences, University of Bristol Bristol United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joanna","family":"Martin","sequence":"additional","affiliation":[{"name":"MRC Centre for Neuropsychiatric Genetics and Genomics Cardiff University Cardiff United Kingdom"},{"name":"Department of Medical Epidemiology &amp; Biostatistics Karolinska Institutet Stockholm Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Walters","sequence":"additional","affiliation":[{"name":"MRC Centre for Neuropsychiatric Genetics and Genomics Cardiff University Cardiff United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"O'Donovan","sequence":"additional","affiliation":[{"name":"MRC Centre for Neuropsychiatric Genetics and Genomics Cardiff University Cardiff United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Owen","sequence":"additional","affiliation":[{"name":"MRC Centre for Neuropsychiatric Genetics and Genomics Cardiff University Cardiff United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anita","family":"Thapar","sequence":"additional","affiliation":[{"name":"MRC Centre for Neuropsychiatric Genetics and Genomics Cardiff University Cardiff United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Kirov","sequence":"additional","affiliation":[{"name":"MRC Centre for Neuropsychiatric Genetics and Genomics Cardiff University Cardiff United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Santiago","family":"Rodriguez","sequence":"additional","affiliation":[{"name":"MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol Bristol United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dheeraj","family":"Rai","sequence":"additional","affiliation":[{"name":"Centre for Academic Mental Health, Population Health Sciences, University of Bristol Bristol United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stan","family":"Zammit","sequence":"additional","affiliation":[{"name":"MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol Bristol United Kingdom"},{"name":"Centre for Academic Mental Health, Population Health Sciences, University of Bristol Bristol United Kingdom"},{"name":"MRC Centre for Neuropsychiatric Genetics and Genomics Cardiff University Cardiff United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tom R.","family":"Gaunt","sequence":"additional","affiliation":[{"name":"MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol Bristol United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2018,4,24]]},"reference":[{"key":"e_1_2_7_2_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13229-015-0063-7"},{"key":"e_1_2_7_3_1","doi-asserted-by":"publisher","DOI":"10.1111\/1469-7610.00388"},{"key":"e_1_2_7_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/ije\/dys064"},{"key":"e_1_2_7_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/mp.2017.127"},{"key":"e_1_2_7_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3406"},{"key":"e_1_2_7_7_1","first-page":"185","volume-title":"Temperament: Early developing personality traits","author":"Buss A. 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