Copy number variants in the population: Unselected does not mean unaffected

Copy Number Variations and Cognitive Phenotypes in Unselected Populations

Männik K, Mägi R, Macé A, Cole B, Guyatt AL, Shihab HA, Maillard AM, Alavere H, Kolk A, Reigo A, Mihailov E, Leitsalu L, Ferreira A, 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. JAMA 2015;313:2044–2054.

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.

Commentary

Copy number variants (CNVs; deletions or duplications of a stretch of chromosomal DNA) first came to attention as an important source of genomic variation in 2004 (1, 2). Since that time, numerous studies have been carried out to either 1) catalog CNVs that are found in normal, healthy individuals or 2) identify CNVs that are unique to or enriched in individuals with disease. The latter category of studies highlight CNVs that cause or increase risk of disease when present in an individual's genome. Studies of healthy individuals provide a basis for comparison when studying disease populations. Combined, these studies help delineate what types of CNVs are most likely to be pathogenic (large, de novo, gene-rich) and which are more likely to have no appreciable clinical effect (smaller, inherited, gene-depleted). Of course, there are exceptions to every rule: CNVs >400 kb or even >1 Mb are found in control populations at frequencies of 11% and 2% (3); however, detailed phenotyping is not usually performed to determine whether there is a previously unappreciated or unreported clinical phenotype.

While some CNVs are always associated with an abnormal and often recognizable phenotype, others are associated with more variable outcomes. Many of these are recurrent CNVs—those that occur in regions of the genome that are susceptible to deletion or duplication. Examples that are important for epilepsy include recurrent deletions of 15q13, 16q13, and 15q11 (4). Deletions at each of these regions increase the risk of epilepsy as well as autism, intellectual disability (ID), and schizophrenia. Other examples of recurrent CNVs with variable outcomes include deletions and duplications of 16p11.2 that are associated with autism, developmental delay, and overweight or underweight, respectively (5, 6). While previous studies in healthy controls confirm that some of these recurrent CNVs are present at a very low frequency in the population, the clinical effect in individuals who have not come to medical attention (if any) is not clear.

In a recent study, Mannik and colleagues test individuals from a population databank who were not selected for intellectual ability, health status, or other features. The investigators performed CNV testing in the population samples with the goal of identifying recurrent CNVs and rare, intermediate-size CNVs (250–500 kb) to assess the effect on ID and educational attainment in an unselected population. The authors randomly sampled ~7,000 of 52,000 participants who were collected from across Estonia. Each participant filled out a standardized questionnaire at enrollment, and their physician provided information about known medical conditions. A subset of individuals who were identified through the study to carry a CNV underwent additional phenotyping.

They first looked for 57 recurrent or disease-associated CNVs that are known to be associated with an abnormal phenotype and found that 0.7% of their cohort carried one. Of note, those CNVs known to be associated with more severe phenotypes were less frequent in their cohort than expected, which is not surprising. Most individuals were not aware that they were carriers of a disease-associated CNV, even though, upon review, they clearly had findings associated with the CNV. Individuals who had a disease-associated CNV had a higher prevalence of ID compared to controls (8.9% compared to 1.7%).

They also looked at all rare CNVs >250 kb in their population, regardless of whether the CNV had a known disease association. They found that 3% of the cohort carried a rare deletion and 7% carried a rare duplication. Again, there was an enrichment among the CNV carriers for ID (3.2% versus 1.7%), greatest when considering deletion carriers only (5.1%). Their results also demonstrated that the frequency of ID increased with CNV size, though the difference in frequency of ID for duplication carriers compared to controls was only significant for duplications >1 Mb. Similar trends were seen when considering levels of educational attainment instead of ID in the same population. Importantly, these findings were consistent across several replication cohorts using different measures for intellect and education level.

An intriguing result of this study was an excess of females among the rare deletion carriers (female:male ratio 1.28:1) and that the reduction in mean educational attainment was greater for the female carriers (−0.42) than for male carriers (−0.02). Several recent studies suggest that females can tolerate a higher mutational burden than can males (7) and are therefore protected from neurodevelopmental disorders. This may, in part, explain the gender difference in disorders such as autism where the male:female ratio is 4:1.

This large study of individuals from a population-based cohort suggests that the role of intermediate-size and large CNVs in cognitive abilities and educational attainment may be underappreciated. Specific CNVs conferring risk were not identified in this study. Much larger cohorts will be required to pinpoint specific genomic regions as risk factors (especially for nonrecurrent CNVs) before this type of genomic information can be applied in clinical practice.