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Männik K, Mägi R, Macé A, Cole B, Guyatt A, Shihab HA, Maillard AM, Alavere H, Kolk A, Reigo A, Mihailov E, Leitsalu L, Ferreira AM, Nõukas M, Teumer A, Salvi E, Cusi D, McGue M, Iacono WG, Gaunt TR, Beckmann JS, Jacquemont S, Kutalik Z, Pankratz N, Timpson N, Metspalu A, Reymond A. Copy number variations and cognitive phenotypes in unselected populations. JAMA 2015; 313:2044-54. [PMID: 26010633 PMCID: PMC4684269 DOI: 10.1001/jama.2015.4845] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
IMPORTANCE The association of copy number variations (CNVs), differing numbers of copies of genetic sequence at locations in the genome, with phenotypes such as intellectual disability has been almost exclusively evaluated using clinically ascertained cohorts. The contribution of these genetic variants to cognitive phenotypes in the general population remains unclear. OBJECTIVE To investigate the clinical features conferred by CNVs associated with known syndromes in adult carriers without clinical preselection and to assess the genome-wide consequences of rare CNVs (frequency ≤0.05%; size ≥250 kilobase pairs [kb]) on carriers' educational attainment and intellectual disability prevalence in the general population. DESIGN, SETTING, AND PARTICIPANTS The population biobank of Estonia contains 52,000 participants enrolled from 2002 through 2010. General practitioners examined participants and filled out a questionnaire of health- and lifestyle-related questions, as well as reported diagnoses. Copy number variant analysis was conducted on a random sample of 7877 individuals and genotype-phenotype associations with education and disease traits were evaluated. Our results were replicated on a high-functioning group of 993 Estonians and 3 geographically distinct populations in the United Kingdom, the United States, and Italy. MAIN OUTCOMES AND MEASURES Phenotypes of genomic disorders in the general population, prevalence of autosomal CNVs, and association of these variants with educational attainment (from less than primary school through scientific degree) and prevalence of intellectual disability. RESULTS Of the 7877 in the Estonian cohort, we identified 56 carriers of CNVs associated with known syndromes. Their phenotypes, including cognitive and psychiatric problems, epilepsy, neuropathies, obesity, and congenital malformations are similar to those described for carriers of identical rearrangements ascertained in clinical cohorts. A genome-wide evaluation of rare autosomal CNVs (frequency, ≤0.05%; ≥250 kb) identified 831 carriers (10.5%) of the screened general population. Eleven of 216 (5.1%) carriers of a deletion of at least 250 kb (odds ratio [OR], 3.16; 95% CI, 1.51-5.98; P = 1.5e-03) and 6 of 102 (5.9%) carriers of a duplication of at least 1 Mb (OR, 3.67; 95% CI, 1.29-8.54; P = .008) had an intellectual disability compared with 114 of 6819 (1.7%) in the Estonian cohort. The mean education attainment was 3.81 (P = 1.06e-04) among 248 (≥250 kb) deletion carriers and 3.69 (P = 5.024e-05) among 115 duplication carriers (≥1 Mb). Of the deletion carriers, 33.5% did not graduate from high school (OR, 1.48; 95% CI, 1.12-1.95; P = .005) and 39.1% of duplication carriers did not graduate high school (OR, 1.89; 95% CI, 1.27-2.8; P = 1.6e-03). Evidence for an association between rare CNVs and lower educational attainment was supported by analyses of cohorts of adults from Italy and the United States and adolescents from the United Kingdom. CONCLUSIONS AND RELEVANCE Known pathogenic CNVs in unselected, but assumed to be healthy, adult populations may be associated with unrecognized clinical sequelae. Additionally, individually rare but collectively common intermediate-size CNVs may be negatively associated with educational attainment. Replication of these findings in additional population groups is warranted given the potential implications of this observation for genomics research, clinical care, and public health.
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Affiliation(s)
- Katrin Männik
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Aurélien Macé
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ben Cole
- University of Minnesota Medical School, Department of Laboratory Medicine & Pathology, 420 Delaware St. SE, Minneapolis, MN 55455, USA
| | - Anna Guyatt
- Bristol Genetic Epidemiology Laboratories, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Hashem A. Shihab
- Bristol Genetic Epidemiology Laboratories, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Anne M. Maillard
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Helene Alavere
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Anneli Kolk
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Department of Neurology and Neurorehabilitation, Children's Clinic, Tartu University Hospital, Tartu, Estonia
| | - Anu Reigo
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Department of Neurology and Neurorehabilitation, Children's Clinic, Tartu University Hospital, Tartu, Estonia
| | - Liis Leitsalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Anne-Maud Ferreira
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Margit Nõukas
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Erika Salvi
- Deparment of Health Sciences, University of Milan, Italy
| | - Daniele Cusi
- Deparment of Health Sciences, University of Milan, Italy
- Institute of Biomedical Technologies, Italian National Research Council, Milan, Italy
| | - Matt McGue
- University of Minnesota Department of Psychology, 75 E. River Rd, Minneapolis, MN 55455, USA
| | - William G. Iacono
- University of Minnesota Department of Psychology, 75 E. River Rd, Minneapolis, MN 55455, USA
| | - Tom R. Gaunt
- Bristol Genetic Epidemiology Laboratories, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | | | | | - Zoltán Kutalik
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute of Social and Preventive Medicine, Lausanne University Hospital (CHUV), Switzerland
| | - Nathan Pankratz
- University of Minnesota Medical School, Department of Laboratory Medicine & Pathology, 420 Delaware St. SE, Minneapolis, MN 55455, USA
| | - Nicholas Timpson
- Bristol Genetic Epidemiology Laboratories, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu, Estonia
- Department of Neurology and Neurorehabilitation, Children's Clinic, Tartu University Hospital, Tartu, Estonia
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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