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. 2017 Nov 28;21(9):2597-2613.
doi: 10.1016/j.celrep.2017.11.028.

Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets

Max Lam  1 Joey W Trampush  2 Jin Yu  3 Emma Knowles  4 Gail Davies  5 David C Liewald  6 John M Starr  7 Srdjan Djurovic  8 Ingrid Melle  9 Kjetil Sundet  10 Andrea Christoforou  11 Ivar Reinvang  12 Pamela DeRosse  3 Astri J Lundervold  13 Vidar M Steen  14 Thomas Espeseth  10 Katri Räikkönen  15 Elisabeth Widen  16 Aarno Palotie  17 Johan G Eriksson  18 Ina Giegling  19 Bettina Konte  19 Panos Roussos  20 Stella Giakoumaki  21 Katherine E Burdick  22 Antony Payton  23 William Ollier  24 Ornit Chiba-Falek  25 Deborah K Attix  26 Anna C Need  27 Elizabeth T Cirulli  28 Aristotle N Voineskos  29 Nikos C Stefanis  30 Dimitrios Avramopoulos  31 Alex Hatzimanolis  30 Dan E Arking  32 Nikolaos Smyrnis  33 Robert M Bilder  34 Nelson A Freimer  34 Tyrone D Cannon  35 Edythe London  34 Russell A Poldrack  36 Fred W Sabb  37 Eliza Congdon  34 Emily Drabant Conley  38 Matthew A Scult  39 Dwight Dickinson  40 Richard E Straub  41 Gary Donohoe  42 Derek Morris  42 Aiden Corvin  43 Michael Gill  43 Ahmad R Hariri  39 Daniel R Weinberger  41 Neil Pendleton  44 Panos Bitsios  45 Dan Rujescu  19 Jari Lahti  46 Stephanie Le Hellard  14 Matthew C Keller  47 Ole A Andreassen  48 Ian J Deary  5 David C Glahn  4 Anil K Malhotra  49 Todd Lencz  50
Affiliations

Large-Scale Cognitive GWAS Meta-Analysis Reveals Tissue-Specific Neural Expression and Potential Nootropic Drug Targets

Max Lam et al. Cell Rep. .

Abstract

Here, we present a large (n = 107,207) genome-wide association study (GWAS) of general cognitive ability ("g"), further enhanced by combining results with a large-scale GWAS of educational attainment. We identified 70 independent genomic loci associated with general cognitive ability. Results showed significant enrichment for genes causing Mendelian disorders with an intellectual disability phenotype. Competitive pathway analysis implicated the biological processes of neurogenesis and synaptic regulation, as well as the gene targets of two pharmacologic agents: cinnarizine, a T-type calcium channel blocker, and LY97241, a potassium channel inhibitor. Transcriptome-wide and epigenome-wide analysis revealed that the implicated loci were enriched for genes expressed across all brain regions (most strongly in the cerebellum). Enrichment was exclusive to genes expressed in neurons but not oligodendrocytes or astrocytes. Finally, we report genetic correlations between cognitive ability and disparate phenotypes including psychiatric disorders, several autoimmune disorders, longevity, and maternal age at first birth.

Keywords: GWAS; calcium channel; cerebellum; gene expression; general cognitive ability; neurodevelopment; nootropics; potassium channel; synapse.

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Conflict of interest statement

Conflict of Interest

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
a) Manhattan plot depicting results of GWAS meta-analysis of cognitive performance. Dotted red line indicates threshold for genome-wide significance (P<5E-08). b) Manhattan plot depicting results of MTAG of cognitive performance with educational attainment. Dotted red line indicates threshold for genome-wide significance (P<5E-08).
Figure 2
Figure 2
Venn diagram depicting overlap and independence of genome-wide significant SNP loci observed in three studies: the MTAG analysis of the present report; the cognitive performance GWAS reported by Sniekers et al. (2017); and the educational attainment GWAS of Okbay et al. (2016).
Figure 3
Figure 3
a) Polygenic risk score prediction for MTAG results against held-out ASPIS cohort. b) Comparison of MTAG, cognitive (IQ) GWAS (Sniekers et al. 2017), and educational attainment (EDU) GWAS (Okbay et al. 2016) as source of weights for polygenic risk score prediction against held-out ASPIS cohort. c) Polygenic risk score prediction for MTAG results against held-out GCAP cohort. d) Comparison of MTAG, cognitive (IQ) GWAS (Sniekers et al. 2017), and educational attainment (EDU) GWAS (Okbay et al. 2016) as source of weights for polygenic risk score prediction against held-out GCAP cohort.
Figure 4
Figure 4
a) Tissue expression profile analysis for genome-wide significant genes (as defined by MAGMA) emerging from the MTAG analysis. Gene results were significantly enriched for expression in nearly all central nervous system tissues (except for substantia nigra and spinal cord), but no tissues outside the CNS. b) Circular Manhattan Plot for MetaXcan results based on MTAG of cognitive performance with educational attainment. From inner circle out, GTEX tissue order is as follows: ACC: Anterior Cingulate Cortex; CDBG: Caudate – Basal Ganglia; CRBHM: Cerebellar Hemisphere; CRBLM: Cerebellum; CRTX: Cortex; FCTX: Frontal Cortex; HIPP: Hippocampus; HYPO: Hypothalamus; NACMB: Nucleus Accumbens; PUTM: Putamen. GWAS threshold is set at Bonferroni-corrected P < 0.05.
Figure 5
Figure 5
Genetic correlations (rg) between cognitive phenotypes and other publicly available GWAS results, based on LD score regression. The first and second columns (labelled METAL and MTAG, respectively) refer to results of the cognitive meta-analyses in the present report. The third column displays correlations for the educational attainment GWAS of Okbay et al. (2016).

Comment in

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