Genome-wide analysis of gene dosage in 24,092 individuals estimates that 10,000 genes modulate cognitive ability.

TitleGenome-wide analysis of gene dosage in 24,092 individuals estimates that 10,000 genes modulate cognitive ability.
Publication TypeJournal Article
Year of Publication2021
AuthorsHuguet G, Schramm C, Douard E, Tamer P, Main A, Monin P, England J, Jizi K, Renne T, Poirier M, Nowak S, Martin C-O, Younis N, Knoth ISophia, Jean-Louis M, Saci Z, Auger M, Tihy F, Mathonnet G, Maftei C, Léveillé F, Porteous D, Davies G, Redmond P, Harris SE, W Hill D, Lemyre E, Schumann G, Bourgeron T, Pausova Z, Paus T, Karama S, Lippe S, Deary IJ, Almasy L, Labbe A, Glahn D, Greenwood CMT, Jacquemont S
JournalMol Psychiatry
Date Published2021 06
KeywordsCognition, DNA Copy Number Variations, Gene Dosage, Genome, Humans, Intelligence Tests

Genomic copy number variants (CNVs) are routinely identified and reported back to patients with neuropsychiatric disorders, but their quantitative effects on essential traits such as cognitive ability are poorly documented. We have recently shown that the effect size of deletions on cognitive ability can be statistically predicted using measures of intolerance to haploinsufficiency. However, the effect sizes of duplications remain unknown. It is also unknown if the effect of multigenic CNVs are driven by a few genes intolerant to haploinsufficiency or distributed across tolerant genes as well. Here, we identified all CNVs > 50 kilobases in 24,092 individuals from unselected and autism cohorts with assessments of general intelligence. Statistical models used measures of intolerance to haploinsufficiency of genes included in CNVs to predict their effect size on intelligence. Intolerant genes decrease general intelligence by 0.8 and 2.6 points of intelligence quotient when duplicated or deleted, respectively. Effect sizes showed no heterogeneity across cohorts. Validation analyses demonstrated that models could predict CNV effect sizes with 78% accuracy. Data on the inheritance of 27,766 CNVs showed that deletions and duplications with the same effect size on intelligence occur de novo at the same frequency. We estimated that around 10,000 intolerant and tolerant genes negatively affect intelligence when deleted, and less than 2% have large effect sizes. Genes encompassed in CNVs were not enriched in any GOterms but gene regulation and brain expression were GOterms overrepresented in the intolerant subgroup. Such pervasive effects on cognition may be related to emergent properties of the genome not restricted to a limited number of biological pathways.

Alternate JournalMol Psychiatry
PubMed ID33414497
Grant ListU01 MH119690 / MH / NIMH NIH HHS / United States
159734 / / CIHR / Canada
/ WT_ / Wellcome Trust / United Kingdom
U01 MH119739 / MH / NIMH NIH HHS / United States