Effects of copy number variations on brain structure and risk for psychiatric illness: large-scale studies from the ENIGMA working groups on CNVs

The Enhancing NeuroImaging Genetics through Meta-Analysis copy number variant (ENIGMA-CNV) and 22q11.2 Deletion Syndrome Working Groups (22q-ENIGMA WGs) were created to gain insight into the involvement of genetic factors in human brain development and related cognitive, psychiatric and behavioral manifestations. To that end, the ENIGMA-CNV WG has collated CNV and magnetic resonance imaging (MRI) data from ~49,000 individuals across 38 global research sites, yielding one of the largest studies to date on the effects of CNVs on brain structures in the general population. The 22q-ENIGMA WG includes 12 international research centers that assessed over 533 individuals with a confirmed 22q11.2 deletion syndrome, 40 with 22q11.2 duplications, and 333 typically developing controls, creating the largest-ever 22q11.2 CNV neuroimaging data set. In this review, we outline the ENIGMA infrastructure and procedures for multi-site analysis of CNVs and MRI data. So far, ENIGMA has identified effects of the 22q11.2, 16p11.2 distal, 15q11.2, and 1q21.1 distal CNVs on subcortical and cortical brain structures. Each CNV is associated with differences in cognitive, neurodevelopmental and neuropsychiatric traits, with characteristic patterns of brain structural abnormalities. Evidence of gene-dosage effects on distinct brain regions also emerged, providing further insight into genotype-phenotype relationships. Taken together, these results offer a more comprehensive picture of molecular mechanisms involved in typical and atypical brain development. This "genotype-first" approach also contributes to our understanding of the etiopathogenesis of brain disorders. Finally, we outline future directions to better understand effects of CNVs on brain structure and behavior.Funding information: European Union's Horizon2020 Research and Innovation Programme, Grant/Award Number: CoMorMent project; Grant #847776; KG Jebsen Stiftelsen; National Institutes of Health, Grant/Award Number: U54 EB020403; Norges Forskningsråd, Grant/Award Number: #223273; South-Eastern Norway Regional Health Authority, Grant/Award Number: #2020060ACKNOWLEDGMENTS: The ENIGMA Consortium is supported by the NIH Big Data to Knowledge (BD2K) program under consortium grant number U54 EB020403 (PI: Thompson). OAA is supported by the Research Council of Norway, South East Norway Health Authority, KG Jebsen Stiftelsen, EU H2020. C. A. has been funded by the Spanish Ministry of Science and Innovation; Instituto de Salud Carlos III (SAM16PE07CP1, PI16/02012, PI19/ 024), co-financed by ERDF Funds from the European Commission, “A way of making Europe”, CIBERSAM; Madrid Regional Government (B2017/BMD-3740 AGES-CM-2), European Union Structural Funds; European Union Seventh Framework Program under grant agreements FP7-4-HEALTH-2009-2.2.1-2-241,909 (Project EU-GEI), FP7- HEALTH-2013-2.2.1-2-603,196 (Project PSYSCAN) and FP7- HEALTH-2013- 2.2.1-2-602,478 (Project METSY); and European Union H2020 Program under the Innovative Medicines Initiative two Joint Undertaking (grant agreement No 115916, Project PRISM, and grant agreement No 777394, Project AIMS-2-TRIALS), Fundación Familia Alonso and Fundación Alicia Koplowitz. R. A-A is funded by a Miguel Servet contract from the Carlos III Health Institute (CP18/00003). G. B. is supported by the Dutch Organization for Health Research and Development ZonMw (grants 91112002 & 91712394). A. S. B. is supported by the Dalglish Family Chair in 22q11.2 Deletion Syndrome, Canadian Institutes of Health Research (CIHR) grants MOP-79518, MOP89066, MOP-97800 and MOP-111238, and NIMH grant number U01 MH101723–01(3/5). C. E. B. is also supported by the National Institute of Mental Health: RO1 MH085953, R01 MH100900 and 1U01MH119736. N. E. B. is granted the KNAW Academy Professor Award (PAH/6635). V. D. C. is supported by NIH R01 MH094524. S. C. is supported by the European Union's Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3); Helmholtz Initiative and Networking Fund. C. R. K. C. is supported by NIA T32AG058507. E. W. C. C. is supported by the Canadian Institutes of Health Research, Ontario Mental Health Foundation grant MOP-74631 and NIMH grant U01MH101723–01(3/5). S. Ci. has received funding from the European Union's Horizon 2020 Framework Programme for Research and Innovation under the Specific Grant Agreement No. 945539 (Human Brain Project SGA3). M. C. C. is supported by the Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London. N. A. C. is supported by Agencia Nacional de Investigación y Desarrollo (ANID Chile) PIA ACT192064. GId. Z. is supported by the NHMRC. J. L. D. and D. E. J. L. are supported by the Wellcome Trust. T. B. C. is supported by NICHD grant PO1-HD070454, NIH grant UO1-MH191719, and NIMH grant R01 MH087636-01A1. AMD is supported by U24DA041147. B. D. is supported by the Swiss National Science Foundation (NCCR Synapsy, project grant numbers 32003B_135679, 32003B_159780, 324730_192755 and CRSK3_190185), the Leenaards Foundation and the Roger De Spoelberch Foundation. SE is supported by the NARSAD-Young Investigator Grant “Epigenetic Regulation of Intermediate Phenotypes in Schizophrenia”. B. E. S. is supported by the NIH (NIMH). D. C. G. is supported by NIH grant numbers MH078143, MH083824, AG058464. W. R. K. is supported by NIH/MH R0106824. R. E. G. is supported by NIH/NIMH grant numbers MH087626, MH119737. DMMcD-McG is supported by National Institutes of Mental Health (NIMH), grant numbers MH119737-02; MH191719; and MH087636-01A1. S. E. M. is supported by NHMRC grants APP1103623; APP1158127; APP1172917. TM is supported by Research Council of Norway - grant number 273345. D. G. M. is supported by the National Institute for Health Research Mental Health Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London and S (European Autism Interventions)/EU AIMS-2-TRIALS, a European Innovative Medicines Initiative Joint Undertaking under grant agreements 115300 and 777394. T. N. was supported by Stiftelsen KG Jebsen under grant number SKGJ-MED-021. R. A. O. is supported by NIMH R01 MH090553. S. Y. S. has been funded by the Canadain Institutes of Health Research. M. J. O. is supported by MRC Centre grant MR/L010305/1 and Wellcome Trust grant 100,202/Z/12/Z; Dr. Owen has received research support from Takeda. Z. P. is supported by CIHR, CFI, HSFC. B. G. P. is supported by CIHR FDN 143290 and CAIP Chair. G. M. R. is supported by Fondecyt-Chile #1171014 and ANID-Chile ACT192064. A. Re. was supported by a grant from the Swiss National Science Foundation (31003A_182632). DRR is supported by R01 MH120174 (PI: Roalf). This report represents independent research funded by the National Institute for Health Research (NIHR) Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London (to J. J. R). PSS is supported by NHMRC (Australia) program grant 1093083. J. E. S. is supported by NIH K01-ES026840. S. M. S. is supported by the Epilepsy Society. T. J. S. is supported by NIH grants R01MH107108, R01HD042794, and HDU54079125. I. E. S. is supported by South-Eastern Norway Regional Health Authority (#2020060), European Union's Horizon2020 Research and Innovation Programme (CoMorMent project; grant #847776) and the KG Jebsen Foundation (SKGJ-MED-021). V. M. S. is supported by Research Council of Norway (CoE funding scheme, grant number 223273). D. J. S. is supported by the SA MRC. C. K. T. is supported by Research Council of Norway (#230345, #288083, #223273) and South-Eastern Norway Regional Health Authority (#2019069, #2021070, #500189). D. T.-G. was supported by the Instituto de Salud Carlos III (PI14/00639 and PI14/00918) and Fundación Instituto de Investigación Marqués de Valdecilla (NCT0235832 and NCT02534363). Dvd. M. is supported by Research Council of Norway #276082. F. V. R. is supported by the Michael Smith Foundation for Health Research Scholar Award. deCODE genetics has received support from the Innovative Medicines Initiative Joint Undertaking under grant agreements' no. 115008 (NEWMEDS) and no. 115300 (EUAIMS), of which resources are composed of EFPIA in-kind contribution and financial contribution from the European Union's Seventh Framework Programme (EU-FP7/ 2007–2013). L. T. W. is supported by Research Council of Norway, European Research Council. The IDIVAL neuroimage unit is supported by Instituto de Salud Carlos III PI020499, research funding SCIII-INT13/0014, MICINN research funding SAF2010-20840-C02- 02, SAF2013-46292-R. The TOP/NORMENT study are supported by the Research Council of Norway (#223273). The GOBS study data collection was supported in part by the National Institutes of Health (NIH) grants: R01 MH078143, R01 MH078111, and R01 MH083824 with work conducted in part in facilities constructed under the support of NIH grant number C06 RR020547. The Sydney Memory and Ageing Study has been funded by three National Health & Medical Research Council (NHMRC) Program Grants (ID No. ID350833, ID568969, and APP1093083). We thank the participants and their informants for their time and generosity in contributing to this research. We also acknowledge the MAS research team: https://cheba.unsw.edu.au/researchprojects/sydney-memory-and-ageing-study. We acknowledge the contribution of the OATS research team (https://cheba.unsw.edu.au/ project/older-australian-twins-study) to this study. The OATS study has been funded by a National Health & Medical Research Council (NHMRC) and Australian Research Council (ARC) Strategic Award Grant of the Aging Well, Aging Productively Program (ID No. 401162); NHMRC Project (seed) Grants (ID No. 1024224 and 1025243); NHMRC Project Grants (ID No. 1045325 and 1085606); and NHMRC Program Grants (ID No. 568969 and 1093083). We thank the participants for their time and generosity in contributing to this research. This research was facilitated through access to Twins Research Australia, a national resource supported by a Centre of Research Excellence Grant (ID No. 1079102) from the National Health and Medical Research Council. The NCNG sample collection was supported by grants from the Bergen Research Foundation and the University of Bergen, the Dr Einar Martens Fund, the KG Jebsen Foundation, the Research Council of Norway, to S. L. H., V. M. S., A. J. L., and T. E. The authors thank Dr. Eike Wehling for recruiting participants in Bergen, and Professor Jonn-Terje Geitung and Haraldplass Deaconess Hospital for access to the MRI facility. Additional support by RCN grants 177458/V50 and 231286/F20. The Betula study was supported by a Wallenberg Scholar Grant (KAW). The HUNT Study is a collaboration between HUNT Research Centre (Faculty of Medicine and Health Sciences, NTNU—Norwegian University of Science and Technology), Nord-Trøndelag County Council, Central Norway Health Authority, and the Norwegian Institute of Public Health. HUNT-MRI was funded by the Liaison Committee between the Central Norway Regional Health Authority and the Norwegian University of Science and Technology, and the Norwegian National Advisory Unit for functional MRI. Research for the GAP cohort was supported by the Department of Health via the National Institute for Health Research (NIHR) Specialist Biomedical Research Center for Mental Health award to South London and Maudsley NHS Foundation Trust (SLaM) and the Institute of Psychiatry at King's College London, London. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health. S.J. is supported by Calcul Quebec (http:// www.calculquebec.ca), Compute Canada (http://www.computecanada. ca), the Brain Canada Multi investigator research initiative (MIRI), the Institute of Data Valorization (Canada First Research Excellence Fund), CHIR, Canada Research Chairs and the Jeanne et Jean Louis Levesque Foundation. The NTR cohort was supported by the Netherlands Organization for Scientific Research (NWO), MW904-61-193 (de Geus & Boomsma), MaGWnr: 400-07-080 (van 't Ent), MagW 480-04-004 (Boomsma), NWO/SPI 56-464-14,192 (Boomsma), the European Research Council, ERC-230374 (Boomsma), and Amsterdam Neuroscience. Funding for genotyping was obtained from the National Institutes of Health (NIMH U24 MH068457-06; Grand Opportunity grants 1RC2 MH089951, and 1RC2 MH089995); the Avera Institute for Human Genetics, Sioux Falls, South Dakota (USA). Part of the genotyping and analyses were funded by the Genetic Association Information Network (GAIN) of the Foundation for the National Institutes of Health. The Brainscale study was supported by the Netherlands Organization for Scientific Research MagW 480-04-004 (Boomsma), 51.02.060 (Hilleke Hulshoff Pol), 668.772 (Boomsma & Hulshoff Pol); NWO/SPI 56-464-14192 (Boomsma), the European Research Council (ERC230374) (Boomsma), High Potential Grant Utrecht University (Hulshoff Pol), NWO Brain and Cognition 433-09-220 (Hulshoff Pol). SHIP is part of the Community Medicine Research net of the University of Greifswald, Germany, which is funded by the Federal Ministry of Education and Research (grants no. 01ZZ9603, 01ZZ0103, and 01ZZ0403), the Ministry of Cultural Affairs and the Social Ministry of the Federal State of Mecklenburg-West Pomerania. Genome-wide SNP typing in SHIP and MRI scans in SHIP and SHIP-TREND have been supported by a joint grant from Siemens Healthcare, Erlangen, Germany and the Federal State of Mecklenburg-West Pomerania. The ENIGMA-22q11.2 Deletion Syndrome Working Group wishes to acknowledge our dear colleague Dr. Clodagh Murphy, who sadly passed away in April 2020. Open access funding enabled and organized by Projekt DEAL

Dose response of the 16p11.2 distal copy number variant on intracranial volume and basal ganglia.

Carriers of large recurrent copy number variants (CNVs) have a higher risk of developing neurodevelopmental disorders. The 16p11.2 distal CNV predisposes carriers to e.g., autism spectrum disorder and schizophrenia. We compared subcortical brain volumes of 12 16p11.2 distal deletion and 12 duplication carriers to 6882 non-carriers from the large-scale brain Magnetic Resonance Imaging collaboration, ENIGMA-CNV. After stringent CNV calling procedures, and standardized FreeSurfer image analysis, we found negative dose-response associations with copy number on intracranial volume and on regional caudate, pallidum and putamen volumes (β = -0.71 to -1.37; P < 0.0005). In an independent sample, consistent results were obtained, with significant effects in the pallidum (β = -0.95, P = 0.0042). The two data sets combined showed significant negative dose-response for the accumbens, caudate, pallidum, putamen and ICV (P = 0.0032, 8.9 × 10-6, 1.7 × 10-9, 3.5 × 10-12 and 1.0 × 10-4, respectively). Full scale IQ was lower in both deletion and duplication carriers compared to non-carriers. This is the first brain MRI study of the impact of the 16p11.2 distal CNV, and we demonstrate a specific effect on subcortical brain structures, suggesting a neuropathological pattern underlying the neurodevelopmental syndromes

ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries.

This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of "big data" (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA's activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors

Genome-wide association study of 23,500 individuals identifies 7 loci associated with brain ventricular volume

The volume of the lateral ventricles (LV) increases with age and their abnormal enlargement is a key feature of several neurological and psychiatric diseases. Although lateral ventricular volume is heritable, a comprehensive investigation of its genetic determinants is lacking. In this meta-analysis of genome-wide association studies of 23,533 healthy middle-aged to elderly individuals from 26 population-based cohorts, we identify 7 genetic loci associated with LV volume. These loci map to chromosomes 3q28, 7p22.3, 10p12.31, 11q23.1, 12q23.3, 16q24.2, and 22q13.1 and implicate pathways related to tau pathology, S1P signaling, and cytoskeleton organization. We also report a significant genetic overlap between the thalamus and LV volumes (ρgenetic = -0.59, p-value = 3.14 × 10-6), suggesting that these brain structures may share a common biology. These genetic associations of LV volume provide insights into brain morphology

Genetic correlations and genome-wide associations of cortical structure in general population samples of 22824 adults

Cortical thickness, surface area and volumes vary with age and cognitive function, and in neurological and psychiatric diseases. Here we report heritability, genetic correlations and genome-wide associations of these cortical measures across the whole cortex, and in 34 anatomically predefined regions. Our discovery sample comprises 22,824 individuals from 20 cohorts within the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and the UK Biobank. We identify genetic heterogeneity between cortical measures and brain regions, and 160 genome-wide significant associations pointing to wnt/β-catenin, TGF-β and sonic hedgehog pathways. There is enrichment for genes involved in anthropometric traits, hindbrain development, vascular and neurodegenerative disease and psychiatric conditions. These data are a rich resource for studies of the biological mechanisms behind cortical development and aging

Cerebral small vessel disease genomics and its implications across the lifespan

White matter hyperintensities (WMH) are the most common brain-imaging feature of cerebral small vessel disease (SVD), hypertension being the main known risk factor. Here, we identify 27 genome-wide loci for WMH-volume in a cohort of 50,970 older individuals, accounting for modification/confounding by hypertension. Aggregated WMH risk variants were associated with altered white matter integrity (p = 2.5×10-7) in brain images from 1,738 young healthy adults, providing insight into the lifetime impact of SVD genetic risk. Mendelian randomization suggested causal association of increasing WMH-volume with stroke, Alzheimer-type dementia, and of increasing blood pressure (BP) with larger WMH-volume, notably also in persons without clinical hypertension. Transcriptome-wide colocalization analyses showed association of WMH-volume with expression of 39 genes, of which four encode known drug targets. Finally, we provide insight into BP-independent biological pathways underlying SVD and suggest potential for genetic stratification of high-risk individuals and for genetically-informed prioritization of drug targets for prevention trials.Peer reviewe

ENIGMA and global neuroscience: A decade of large-scale studies of the brain in health and disease across more than 40 countries

This review summarizes the last decade of work by the ENIGMA (Enhancing NeuroImaging Genetics through Meta Analysis) Consortium, a global alliance of over 1400 scientists across 43 countries, studying the human brain in health and disease. Building on large-scale genetic studies that discovered the first robustly replicated genetic loci associated with brain metrics, ENIGMA has diversified into over 50 working groups (WGs), pooling worldwide data and expertise to answer fundamental questions in neuroscience, psychiatry, neurology, and genetics. Most ENIGMA WGs focus on specific psychiatric and neurological conditions, other WGs study normal variation due to sex and gender differences, or development and aging; still other WGs develop methodological pipelines and tools to facilitate harmonized analyses of "big data" (i.e., genetic and epigenetic data, multimodal MRI, and electroencephalography data). These international efforts have yielded the largest neuroimaging studies to date in schizophrenia, bipolar disorder, major depressive disorder, post-traumatic stress disorder, substance use disorders, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, autism spectrum disorders, epilepsy, and 22q11.2 deletion syndrome. More recent ENIGMA WGs have formed to study anxiety disorders, suicidal thoughts and behavior, sleep and insomnia, eating disorders, irritability, brain injury, antisocial personality and conduct disorder, and dissociative identity disorder. Here, we summarize the first decade of ENIGMA's activities and ongoing projects, and describe the successes and challenges encountered along the way. We highlight the advantages of collaborative large-scale coordinated data analyses for testing reproducibility and robustness of findings, offering the opportunity to identify brain systems involved in clinical syndromes across diverse samples and associated genetic, environmental, demographic, cognitive, and psychosocial factors

The genetic architecture of the human cerebral cortex

The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder

Reproducibility in the absence of selective reporting: An illustration from large‐scale brain asymmetry research

The problem of poor reproducibility of scientific findings has received much attention over recent years, in a variety of fields including psychology and neuroscience. The problem has been partly attributed to publication bias and unwanted practices such as p‐hacking. Low statistical power in individual studies is also understood to be an important factor. In a recent multisite collaborative study, we mapped brain anatomical left–right asymmetries for regional measures of surface area and cortical thickness, in 99 MRI datasets from around the world, for a total of over 17,000 participants. In the present study, we revisited these hemispheric effects from the perspective of reproducibility. Within each dataset, we considered that an effect had been reproduced when it matched the meta‐analytic effect from the 98 other datasets, in terms of effect direction and significance threshold. In this sense, the results within each dataset were viewed as coming from separate studies in an “ideal publishing environment,” that is, free from selective reporting and p hacking. We found an average reproducibility rate of 63.2% (SD = 22.9%, min = 22.2%, max = 97.0%). As expected, reproducibility was higher for larger effects and in larger datasets. Reproducibility was not obviously related to the age of participants, scanner field strength, FreeSurfer software version, cortical regional measurement reliability, or regional size. These findings constitute an empirical illustration of reproducibility in the absence of publication bias or p hacking, when assessing realistic biological effects in heterogeneous neuroscience data, and given typically‐used sample sizes

Gene-mapping study of extremes of cerebral small vessel disease reveals TRIM47 as a strong candidate

Funding Information: This project is an EU Joint Programme Neurodegenerative Disease Research (JPND) project. The project is supported through the following funding organisations under the aegis of JPND www.jpnd. eu: Australia, National Health and Medical Research Council, Austria, Federal Ministry of Science, Research and Economy; Canada, Canadian Institutes of Health Research; France, French National Research Agency; Germany, Federal Ministry of Education and Research; Netherlands, The Netherlands Organization for Health Research and Development; United Kingdom, Medical Research Council. This project has received funding from the European Union s Horizon 2020 research and innovation programme under grant agreement No 643417. This project has also received funding from the European Research Council (ERC) under the European Union s Horizon 2020 research and innovation programme under grant agreement No. 640643 and from the European Union s Horizon 2020 research and innovation programme under grant agreements Nos. 667375 and 754517. This work was also supported by a grant overseen by the French National Research Agency (ANR) as part of ANR-14-CE12-60016 and the Investment for the Future Programme ANR-18-RHUS-0002. Part of the computations were performed at the Bordeaux Bioinformatics Centre (CBiB), University of Bordeaux and at the CREDIM (Centre de Ressource et Dffeveloppement en Informatique Medicale) at University of Bordeaux, on a server infrastructure supported by the Fondation Claude Pompidou. The neurology Working Group in the CHARGE Consortium is partly funded by the CHARGE infrastructure grant R01HL105756 and grants from the National Institute on Aging, AG033193, AG049505, AG052409 and AG059421. P.M.M. acknowledges personal support from the Edmond J Safra Foundation and Lily Safra and an NIHR Senior Investigator Award and research support from the UK Dementia Research Institute and NIHR Imperial College Healthcare Trust Biomedical Research Centre. Study-specific funding information is provided in the Supplementary material. Publisher Copyright: © 2022 The Author(s) (2022). Published by Oxford University Press on behalf of the Guarantors of Brain.Cerebral small vessel disease is a leading cause of stroke and a major contributor to cognitive decline and dementia, but our understanding of specific genes underlying the cause of sporadic cerebral small vessel disease is limited. We report a genome-wide association study and a whole-exome association study on a composite extreme phenotype of cerebral small vessel disease derived from its most common MRI features: white matter hyperintensities and lacunes. Seventeen population-based cohorts of older persons with MRI measurements and genome-wide genotyping (n = 41326), whole-exome sequencing (n = 15965), or exome chip (n = 5249) data contributed 13776 and 7079 extreme small vessel disease samples for the genome-wide association study and whole-exome association study, respectively. The genome-wide association study identified significant association of common variants in 11 loci with extreme small vessel disease, of which the chr12q24.11 locus was not previously reported to be associated with any MRI marker of cerebral small vessel disease. The whole-exome association study identified significant associations of extreme small vessel disease with common variants in the 5′ UTR region of EFEMP1 (chr2p16.1) and one probably damaging common missense variant in TRIM47 (chr17q25.1). Mendelian randomization supports the causal association of extensive small vessel disease severity with increased risk of stroke and Alzheimer's disease. Combined evidence from summary-based Mendelian randomization studies and profiling of human loss-of-function allele carriers showed an inverse relation between TRIM47 expression in the brain and blood vessels and extensive small vessel disease severity. We observed significant enrichment of Trim47 in isolated brain vessel preparations compared to total brain fraction in mice, in line with the literature showing Trim47 enrichment in brain endothelial cells at single cell level. Functional evaluation of TRIM47 by small interfering RNAs-mediated knockdown in human brain endothelial cells showed increased endothelial permeability, an important hallmark of cerebral small vessel disease pathology. Overall, our comprehensive gene-mapping study and preliminary functional evaluation suggests a putative role of TRIM47 in the pathophysiology of cerebral small vessel disease, making it an important candidate for extensive in vivo explorations and future translational work.Peer reviewe