Common genetic variants influence human subcortical brain structures
Open accessAbstract
The highly complex structure of the human brain is strongly shaped by genetic influences. Subcortical brain regions form circuits with cortical areas to coordinate movement, learning, memory and motivation, and altered circuits can lead to abnormal behaviour and disease. To investigate how common genetic variants affect the structure of these brain regions, here we conduct genome-wide association studies of the volumes of seven subcortical regions and the intracranial volume derived from magnetic resonance images of 30,717 individuals from 50 cohorts. We identify five novel genetic variants influencing the volumes of the putamen and caudate nucleus. We also find stronger evidence for three loci with previously established influences on hippocampal volume and intracranial volume. These variants show specific volumetric effects on brain structures rather than global effects across structures. The strongest effects were found for the putamen, where a novel intergenic locus with replicable influence on volume (rs945270; P = 1.08 × 10(-33); 0.52% variance explained) showed evidence of altering the expression of the KTN1 gene in both brain and blood tissue. Variants influencing putamen volume clustered near developmental genes that regulate apoptosis, axon guidance and vesicle transport. Identification of these genetic variants provides insight into the causes of variability in human brain development, and may help to determine mechanisms of neuropsychiatric dysfunction.
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Effect sizes of individual SNPs were small but detectable due to inclusion of cohorts comprising thousands of individuals.
“As expected for a genetically complex neuroanatomical phenotype [22], effect sizes of individual SNPs were small (Figure 3C) but detectable here due to inclusion of cohorts comprising thousands of individuals.”
From Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity (2019) · cites this paper as [22]
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- Authors
- Initiative, T. A. D. N., Hibar, D. P., The CHARGE Consortium, EPIGEN, IMAGEN, SYS, Stein, J. L., Renteria, M. E., Arias-Vasquez, A., Desrivières, S., Jahanshad, N., Toro, R., Wittfeld, K., Abramovic, L., Andersson, M., Aribisala, B. S., Armstrong, N. J., Bernard, M., Bohlken, M. M., Boks, M. P., Bralten, J., Brown, A. A., Mallar Chakravarty, M., Chen, Q., Ching, C. R. K., Cuellar-Partida, G., den Braber, A., Giddaluru, S., Goldman, A. L., Grimm, O., Guadalupe, T., Hass, J., Woldehawariat, G., Holmes, A. J., Hoogman, M., Janowitz, D., Jia, T., Kim, S., Klein, M., Kraemer, B., Lee, P. H., Olde Loohuis, L. M., Luciano, M., Macare, C., Mather, K. A., Mattheisen, M., Milaneschi, Y., Nho, K., Papmeyer, M., Ramasamy, A., Risacher, S. L., Roiz-Santiañez, R., Rose, E. J., Salami, A., Sämann, P. G., Schmaal, L., Schork, A. J., Shin, J., Strike, L. T., Teumer, A., van Donkelaar, M. M. J., van Eijk, K. R., Walters, R. K., Westlye, L. T., Whelan, C. D., Winkler, A. M., Zwiers, M. P., Alhusaini, S., Athanasiu, L., Ehrlich, S., Hakobjan, M. M. H., Hartberg, C. B., Haukvik, U. K., Heister, A. J. G. A. M., Hoehn, D., Kasperaviciute, D., Liewald, D. C. M., Lopez, L. M., Makkinje, R. R. R., Matarin, M., Naber, M. A. M., Reese McKay, D., Needham, M., Nugent, A. C., Pütz, B., Royle, N. A., Shen, L., Sprooten, E., Trabzuni, D., van der Marel, S. S. L., van Hulzen, K. J. E., Walton, E., Wolf, C., Almasy, L., Ames, D., Arepalli, S., Assareh, A. A., Bastin, M. E., Brodaty, H., Bulayeva, K. B., Carless, M. A., Cichon, S., Corvin, A., Curran, J. E., Czisch, M., de Zubicaray, G. I., Dillman, A., Duggirala, R., Dyer, T. D., Erk, S., Fedko, I. O., Ferrucci, L., Foroud, T. M., Fox, P. T., Fukunaga, M., Raphael Gibbs, J., Göring, H. H. H., Green, R. C., Guelfi, S., Hansell, N. K., Hartman, C. A., Hegenscheid, K., Heinz, A., Hernandez, D. G., Heslenfeld, D. J., Hoekstra, P. J., Holsboer, F., Homuth, G., Hottenga, J.-J., Ikeda, M., Jack, C. R., Jenkinson, M., Johnson, R., Kanai, R., Keil, M., Kent, J. W., Kochunov, P., Kwok, J. B., Lawrie, S. M., Liu, X., Longo, D. L., McMahon, K. L., Meisenzahl, E., Melle, I., Mohnke, S., Montgomery, G. W., Mostert, J. C., Mühleisen, T. W., Nalls, M. A., Nichols, T. E., Nilsson, L. G., Nöthen, M. M., Ohi, K., Olvera, R. L., Perez-Iglesias, R., Bruce Pike, G., Potkin, S. G., Reinvang, I., Reppermund, S., Rietschel, M., Romanczuk-Seiferth, N., Rosen, G. D., Rujescu, D., Schnell, K., Schofield, P. R., Smith, C., Steen, V. M., Sussmann, J. E., Thalamuthu, A., Toga, A. W., Traynor, B. J., Troncoso, J., Turner, J. A., Valdés Hernández, M. C., van 't Ent, D., van der Brug, M., van der Wee, N. J. A., van Tol, M.-J., Veltman, D. J., Wassink, T. H., Westman, E., Zielke, R. H., Zonderman, A. B., Ashbrook, D. G., Hager, R., Lu, L., McMahon, F. J., Morris, D. W., Williams, R. W., Brunner, H. G., Buckner, R. L., Buitelaar, J. K., Cahn, W., Calhoun, V. D., Cavalleri, G. L., Crespo-Facorro, B., Dale, A. M., Davies, G. E., Delanty, N., Depondt, C., Djurovic, S., Drevets, W. C., Espeseth, T., Gollub, R. L., Ho, B.-C., Hoffmann, W., Hosten, N., Kahn, R. S., Le Hellard, S., Meyer-Lindenberg, A., Müller-Myhsok, B., Nauck, M., Nyberg, L., Pandolfo, M., Penninx, B. W. J. H., Roffman, J. L., Sisodiya, S. M., Smoller, J. W., van Bokhoven, H., van Haren, N. E. M., Völzke, H., Walter, H., Weiner, M. W., Wen, W., White, T., Agartz, I., Andreassen, O. A., Blangero, J., Boomsma, D. I., Brouwer, R. M., Cannon, D. M., Cookson, M. R., de Geus, E. J. C., Deary, I. J., Donohoe, G., Fernández, G., Fisher, S. E., Francks, C., Glahn, D. C., Grabe, H. J., Gruber, O., Hardy, J., Hashimoto, R., Hulshoff Pol, H. E., Jönsson, E. G., Kloszewska, I., Lovestone, S., Mattay, V. S., Mecocci, P., McDonald, C., McIntosh, A. M., Ophoff, R. A., Paus, T., Pausova, Z., Ryten, M., Sachdev, P. S., Saykin, A. J., Simmons, A., Singleton, A., Soininen, H., Wardlaw, J. M., Weale, M. E., Weinberger, D. R., Adams, H. H. H., Launer, L. J., Seiler, S., Schmidt, R., Chauhan, G., Satizabal, C. L., Becker, J. T., Yanek, L., van der Lee, S. J., Ebling, M., Fischl, B., Longstreth, W. T., Greve, D., Schmidt, H., Nyquist, P., Vinke, L. N., van Duijn, C. M., Xue, L., Mazoyer, B., Bis, J. C., Gudnason, V., Seshadri, S., Ikram, M. A., Martin, N. G., Wright, M. J., Schumann, G., Franke, B., Thompson, P. M., & Medland, S. E.
- Affiliations
- University of Southern California (US)
- QIMR Berghofer Medical Research Institute (AU)
- Radboud University Medical Center (NL)
- King's College London (GB)
- Centre National de la Recherche Scientifique (FR)
- Universitätsmedizin Greifswald (DE)
- University of Toronto (CA)
- University Medical Center Utrecht (NL)
- Lagos State University (NG)
- The University of Sydney (AU)
- University of Oslo (NO)
- Douglas Mental Health University Institute (CA)
- Oslo University Hospital (NO)
- Lieber Institute for Brain Development (US)
- Haukeland University Hospital (NO)
- Heidelberg University (DE)
- Radboud University Nijmegen (NL)
- Yale University (US)
- University of California, Los Angeles (US)
- Broad Institute (US)
- Royal Edinburgh Hospital (GB)
- Amsterdam Neuroscience (NL)
- Universidad de Cantabria (ES)
- Trinity College Dublin (IE)
- Max Planck Institute of Psychiatry (DE)
- University of Maryland, Baltimore (US)
- Stockholm University (SE)
- The University of Queensland (AU)
- Montreal Neurological Institute and Hospital (CA)
- Hartford Hospital (US)
- King Faisal Specialist Hospital & Research Centre (SA)
- National Institutes of Health (US)
- UNSW Sydney (AU)
- Texas Biomedical Research Institute (US)
- The Royal Melbourne Hospital (AU)
- University of Basel (CH)
- University of Bonn (DE)
- The University of Texas at San Antonio Health Science Center (US)
- National Institute on Aging (US)
- Brigham and Women's Hospital (US)
- UCL Queen Square Institute of Neurology (GB)
- University Medical Center Groningen (NL)
- The University of Melbourne (AU)
- Mayo Clinic (US)
- Fujita Health University (JP)
- University of Warwick (GB)
- Centro de Investigación Biomédica en Red de Salud Mental (ES)
- University of California, Irvine (US)
- Beth Israel Deaconess Medical Center (US)
- Johns Hopkins University (US)
- Georgia State University (US)
- University of Iowa (US)
- Karolinska Institutet (SE)
- University of Tennessee Health Science Center (US)
- Massachusetts General Hospital (US)
- Mind Research Network (US)
- Harvard University (US)
- National Institute of Mental Health (US)
- Royal College of Surgeons in Ireland (IE)
- Université Libre de Bruxelles (BE)
- Diakonhjemmet Hospital (NO)
- Erasmus MC (NL)
- Ollscoil na Gaillimhe – University of Galway (IE)
- Max Planck Institute for Psycholinguistics (NL)
- Medical University of Lodz (PL)
- University of Oxford (GB)
- University of Eastern Finland (FI)
- Indiana University Indianapolis (US)
- Université de Bordeaux (FR)
- Boston University (US)
- University of Pittsburgh (US)
- University of Washington (US)
- Corresponding author
- Thompson, Paul M.
- Medland, Sarah E.
- ORCID
- Stein, Jason L.
- Desrivières, Sylvane
- Jahanshad, Neda
- Toro, Roberto
- Wittfeld, Katharina
- Abramovic, Lucija
- Andersson, Micael
- Aribisala, Benjamin S.
- Armstrong, Nicola J.
- Bernard, Manon
- Boks, Marco P.
- Bralten, Janita
- Brown, Andrew A.
- Chen, Qiang
- Ching, Christopher R. K.
- Goldman, Aaron L.
- Holmes, Avram J.
- Hoogman, Martine
- Janowitz, Deborah
- Jia, Tianye
- Kim, Sungeun
- Klein, Marieke
- Lee, Phil H.
- Mather, Karen A.
- Mattheisen, Manuel
- Milaneschi, Yuri
- Nho, Kwangsik
- Ramasamy, Adaikalavan
- Risacher, Shannon L.
- Rose, Emma J.
- Salami, Alireza
- Sämann, Philipp G.
- Schmaal, Lianne
- Schork, Andrew J.
- Shin, Jean
- Strike, Lachlan T.
- Teumer, Alexander
- Walters, Raymond K.
- Westlye, Lars T.
- Whelan, Christopher D.
- Winkler, Anderson M.
- Zwiers, Marcel P.
- Alhusaini, Saud
- Athanasiu, Lavinia
- Ehrlich, Stefan
- Hartberg, Cecilie B.
- Haukvik, Unn K.
- Hoehn, David
- Liewald, David C. M.
- Lopez, Lorna M.
- Nugent, Allison C.
- Pütz, Benno
- Shen, Li
- Sprooten, Emma
- Trabzuni, Daniah
- Walton, Esther
- Wolf, Christiane
- Almasy, Laura
- Bastin, Mark E.
- Brodaty, Henry
- Bulayeva, Kazima B.
- Carless, Melanie A.
- Cichon, Sven
- Corvin, Aiden
- Curran, Joanne E.
- Czisch, Michael
- Dillman, Allissa
- Dyer, Thomas D.
- Erk, Susanne
- Fedko, Iryna O.
- Ferrucci, Luigi
- Foroud, Tatiana M.
- Fox, Peter T.
- Fukunaga, Masaki
- Göring, Harald H. H.
- Green, Robert C.
- Guelfi, Sebastian
- Hansell, Narelle K.
- Hartman, Catharina A.
- Hegenscheid, Katrin
- Heinz, Andreas
- Hernandez, Dena G.
- Hoekstra, Pieter J.
- Homuth, Georg
- Hottenga, Jouke-Jan
- Ikeda, Masashi
- Jack, Clifford R.
- Jenkinson, Mark
- Keil, Maria
- Kent, Jack W.
- Kochunov, Peter
- Kwok, John B.
- Lawrie, Stephen M.
- Liu, Xinmin
- McMahon, Katie L.
- Meisenzahl, Eva
- Melle, Ingrid
- Mohnke, Sebastian
- Montgomery, Grant W.
- Mostert, Jeanette C.
- Mühleisen, Thomas W.
- Nichols, Thomas E.
- Nöthen, Markus M.
- Ohi, Kazutaka
- Olvera, Rene L.
- Potkin, Steven G.
- Reppermund, Simone
- Rietschel, Marcella
- Rosen, Glenn D.
- Rujescu, Dan
- Schnell, Knut
- Schofield, Peter R.
- Smith, Colin
- Steen, Vidar M.
- Thalamuthu, Anbupalam
- Toga, Arthur W.
- Traynor, Bryan J.
- Troncoso, Juan
- Turner, Jessica A.
- Veltman, Dick J.
- Wassink, Thomas H.
- Westman, Eric
- Zonderman, Alan B.
- Ashbrook, David G.
- Hager, Reinmar
- Lu, Lu
- McMahon, Francis J.
- Morris, Derek W.
- Williams, Robert W.
- Brunner, Han G.
- Buckner, Randy L.
- Buitelaar, Jan K.
- Cahn, Wiepke
- Calhoun, Vince D.
- Cavalleri, Gianpiero L.
- Dale, Anders M.
- Delanty, Norman
- Depondt, Chantal
- Djurovic, Srdjan
- Drevets, Wayne C.
- Espeseth, Thomas
- Gollub, Randy L.
- Ho, Beng-Choon
- Hoffmann, Wolfgang
- Hosten, Norbert
- Kahn, René S.
- Nauck, Matthias
- Nyberg, Lars
- Pandolfo, Massimo
- Penninx, Brenda W. J. H.
- Roffman, Joshua L.
- Sisodiya, Sanjay M.
- Smoller, Jordan W.
- Völzke, Henry
- Walter, Henrik
- Weiner, Michael W.
- Wen, Wei
- White, Tonya
- Agartz, Ingrid
- Andreassen, Ole A.
- Blangero, John
- Boomsma, Dorret I.
- Brouwer, Rachel M.
- Cannon, Dara M.
- Cookson, Mark R.
- Deary, Ian J.
- Donohoe, Gary
- Fernández, Guillén
- Fisher, Simon E.
- Francks, Clyde
- Glahn, David C.
- Grabe, Hans J.
- Gruber, Oliver
- Hardy, John
- Hashimoto, Ryota
- Jönsson, Erik G.
- Lovestone, Simon
- Mattay, Venkata S.
- Mecocci, Patrizia
- McDonald, Colm
- McIntosh, Andrew M.
- Ophoff, Roel A.
- Ryten, Mina
- Sachdev, Perminder S.
- Saykin, Andrew J.
- Singleton, Andrew
- Soininen, Hilkka
- Wardlaw, Joanna M.
- Weale, Michael E.
- Weinberger, Daniel R.
- Adams, Hieab H. H.
- Launer, Lenore J.
- Seiler, Stephan
- Schmidt, Reinhold
- Chauhan, Ganesh
- Becker, James T.
- Yanek, Lisa
- Fischl, Bruce
- Greve, Douglas
- Schmidt, Helena
- Nyquist, Paul
- Vinke, Louis N.
- Xue, Luting
- Mazoyer, Bernard
- Bis, Joshua C.
- Gudnason, Vilmundur
- Seshadri, Sudha
- Ikram, M. Arfan
- Martin, Nicholas G.
- Wright, Margaret J.
- Franke, Barbara
- Thompson, Paul M.
- Medland, Sarah E.
- Venue
- Nature
- Published
- 2015-01-21
- Volume
- 520
- Issue
- 7546
- Pages
- 224-229
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4393366
- OpenAlex
- W2140054173
- Cited by
- 858
- References
- 63
- Citations by year
- 2026: 35 · 2025: 42 · 2024: 61 · 2023: 53 · 2022: 42 · 2021: 63 · 2020: 102 · 2019: 105 · 2018: 91 · 2017: 107 · 2016: 95 · 2015: 59 · 2014: 1 · 2012: 1
- FWCI
- 80.18
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
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- MPG.PuRe (Max Planck Society) (submittedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- RePub (Erasmus University Rotterdam) (submittedVersion)
- University of Galway Research Repository (submittedVersion, cc-by-nc)
- IUScholarWorks (Indiana University) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
- Research Publications (Maastricht University) (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion)
- Research Repository UCD (University College Dublin) (cc-by-nc)
- Funders
- Wellcome Trust (104036, 100309/A/12/Z, 100309)
- National Institute for Health and Care Research (NF-SI-0512-10053, ACF-2012-17-017)
- Lundbeckfonden (R155-2014-1724)
- Medical Research Council (MR/K026992/1, MR/L016400/1, MR/N000390/1)
- Biotechnology and Biological Sciences Research Council (1088088, BB/F019394/1)
- Japan Society for the Promotion of Science (26293266, 221S0003, 26670541, 25293250)
- National Institute of Mental Health (K99MH101367)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neurotransmitter Receptor Influence on Behavior
- Keywords
- subcortical structures, brain volume, genetic variants, putamen, caudate nucleus, hippocampal volume, intracranial volume, head size, brain development, neuropsychiatric dysfunction, novel genetic loci, intergenic variants
- MeSH terms
- Adolescent, Adult, Aged, Aged, 80 and over, Aging, Brain, Caudate Nucleus, Child, Female, Hippocampus, Humans, Magnetic Resonance Imaging, Male, Membrane Proteins, Middle Aged, Organ Size, Putamen, Sex Characteristics, Skull, Genetic Variation, Apoptosis, Gene Expression Regulation, Developmental, Genome-Wide Association Study, Young Adult, Genetic Loci
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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