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Raveane A, Aneli S, Montinaro F, Athanasiadis G, Barlera S, Birolo G, Boncoraglio G, Di Blasio AM, Di Gaetano C, Pagani L, Parolo S, Paschou P, Piazza A, Stamatoyannopoulos G, Angius A, Brucato N, Cucca F, Hellenthal G, Mulas A, Peyret-Guzzon M, Zoledziewska M, Baali A, Bycroft C, Cherkaoui M, Chiaroni J, Di Cristofaro J, Dina C, Dugoujon JM, Galan P, Giemza J, Kivisild T, Mazieres S, Melhaoui M, Metspalu M, Myers S, Pereira L, Ricaut FX, Brisighelli F, Cardinali I, Grugni V, Lancioni H, Pascali VL, Torroni A, Semino O, Matullo G, Achilli A, Olivieri A, Capelli C. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe. Sci Adv 2019; 5:eaaw3492. [PMID: 31517044 PMCID: PMC6726452 DOI: 10.1126/sciadv.aaw3492] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/10/2019] [Accepted: 08/06/2019] [Indexed: 05/10/2023]
Abstract
European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.
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Affiliation(s)
- A. Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- Department of Zoology, University of Oxford, Oxford, UK
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - S. Aneli
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - F. Montinaro
- Department of Zoology, University of Oxford, Oxford, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
| | - G. Athanasiadis
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - S. Barlera
- Department of Cardiovascular Research, Istituto di Ricovero e Cura a Carattere Scientifico–Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - G. Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - G. Boncoraglio
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
- PhD Program in Neuroscience, University Milano-Bicocca, Monza, Italy
| | - A. M. Di Blasio
- Istituto Auxologico Italiano, IRCCS, Centro di Ricerche e Tecnologie Biomediche, Milano, Italy
| | - C. Di Gaetano
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - L. Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- APE lab, Department of Biology, University of Padua, Padua, Italy
| | - S. Parolo
- Computational Biology Unit, Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - P. Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - A. Piazza
- Department of Medical Sciences, University of Turin, Turin, Italy
- Academy of Sciences, Turin, Italy
| | - G. Stamatoyannopoulos
- Department of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA
| | - A. Angius
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - N. Brucato
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - G. Hellenthal
- University College London Genetics Institute (UGI), University College London, London, UK
| | - A. Mulas
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Lanusei, Italy
| | - M. Peyret-Guzzon
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - A. Baali
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - C. Bycroft
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Cherkaoui
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - J. Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - J. Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - C. Dina
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - J. M. Dugoujon
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - P. Galan
- Equipe de Recherche en Epidémiologie Nutritionnelle (EREN), Centre de Recherche en Epidémiologie et Statistiques, Université Paris 13/Inserm U1153/Inra U1125/ Cnam, COMUE Sorbonne Paris Cité, F-93017 Bobigny, France
| | - J. Giemza
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - T. Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Herestraat 49, box 604, Leuven 3000, Belgium
| | - S. Mazieres
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - M. Melhaoui
- Faculté des Sciences, Université Mohammed Premier, Oujda, Morocco
| | - M. Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - S. Myers
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - L. Pereira
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - F. X. Ricaut
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Brisighelli
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - I. Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - H. Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. L. Pascali
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - A. Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - O. Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - G. Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - A. Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - A. Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - C. Capelli
- Department of Zoology, University of Oxford, Oxford, UK
- Corresponding author. (A.R.); (S.A.); (F.M.); (C.C.)
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Le Guennec K, Quenez O, Nicolas G, Wallon D, Rousseau S, Richard AC, Alexander J, Paschou P, Charbonnier C, Bellenguez C, Grenier-Boley B, Lechner D, Bihoreau MT, Olaso R, Boland A, Meyer V, Deleuze JF, Amouyel P, Munter HM, Bourque G, Lathrop M, Frebourg T, Redon R, Letenneur L, Dartigues JF, Martinaud O, Kalev O, Mehrabian S, Traykov L, Ströbel T, Le Ber I, Caroppo P, Epelbaum S, Jonveaux T, Pasquier F, Rollin-Sillaire A, Génin E, Guyant-Maréchal L, Kovacs GG, Lambert JC, Hannequin D, Campion D, Rovelet-Lecrux A, Rovelet-Lecrux A. 17q21.31 duplication causes prominent tau-related dementia with increased MAPT expression. Mol Psychiatry 2017; 22:1119-1125. [PMID: 27956742 DOI: 10.1038/mp.2016.226] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/26/2016] [Accepted: 10/27/2016] [Indexed: 01/07/2023]
Abstract
To assess the role of rare copy number variations in Alzheimer's disease (AD), we conducted a case-control study using whole-exome sequencing data from 522 early-onset cases and 584 controls. The most recurrent rearrangement was a 17q21.31 microduplication, overlapping the CRHR1, MAPT, STH and KANSL1 genes that was found in four cases, including one de novo rearrangement, and was absent in controls. The increased MAPT gene dosage led to a 1.6-1.9-fold expression of the MAPT messenger RNA. Clinical signs, neuroimaging and cerebrospinal fluid biomarker profiles were consistent with an AD diagnosis in MAPT duplication carriers. However, amyloid positon emission tomography (PET) imaging, performed in three patients, was negative. Analysis of an additional case with neuropathological examination confirmed that the MAPT duplication causes a complex tauopathy, including prominent neurofibrillary tangle pathology in the medial temporal lobe without amyloid-β deposits. 17q21.31 duplication is the genetic basis of a novel entity marked by prominent tauopathy, leading to early-onset dementia with an AD clinical phenotype. This entity could account for a proportion of probable AD cases with negative amyloid PET imaging recently identified in large clinical series.
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Affiliation(s)
- K Le Guennec
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France
| | - O Quenez
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - G Nicolas
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - D Wallon
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
| | - S Rousseau
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - A-C Richard
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - J Alexander
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupoli, Greece
| | - P Paschou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupoli, Greece
| | - C Charbonnier
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - C Bellenguez
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - B Grenier-Boley
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - D Lechner
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - M-T Bihoreau
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - R Olaso
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - A Boland
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - V Meyer
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - J-F Deleuze
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France.,Fondation Jean Dausset, Centre d'études du Polymorphisme Humain, Paris, France
| | - P Amouyel
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - H M Munter
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - G Bourque
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - M Lathrop
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - T Frebourg
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - R Redon
- Inserm, UMR 1087, l'institut du thorax, CHU Nantes, Nantes, France.,CNRS, UMR 6291, Université de Nantes, Nantes, France
| | - L Letenneur
- INSERM, U1219, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - J-F Dartigues
- INSERM, U1219, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - O Martinaud
- CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
| | - O Kalev
- Institute of Pathology and Neuropathology, Kepler University Hospital, Linz, Austria
| | - S Mehrabian
- Department of Neurology, Alexandrovska University Hospital, Medical University-Sofia, Sofia, Bulgaria
| | - L Traykov
- Department of Neurology, Alexandrovska University Hospital, Medical University-Sofia, Sofia, Bulgaria
| | - T Ströbel
- Institute of Neurology, Medical University Vienna, Vienna, Austria
| | - I Le Ber
- Sorbonne Universités, Inserm, CNRS, UPMC Univ Paris 06, UMR S 1127, Paris, France.,CNR-MAJ, IMMA, département des maladies du système nerveux, Hôpital Pitié-Salpêtrière, Paris, France
| | - P Caroppo
- Sorbonne Universités, Inserm, CNRS, UPMC Univ Paris 06, UMR S 1127, Paris, France.,CNR-MAJ, IMMA, département des maladies du système nerveux, Hôpital Pitié-Salpêtrière, Paris, France
| | - S Epelbaum
- Sorbonne Universités, Inserm, CNRS, UPMC Univ Paris 06, UMR S 1127, Paris, France.,CNR-MAJ, IMMA, département des maladies du système nerveux, Hôpital Pitié-Salpêtrière, Paris, France
| | - T Jonveaux
- Centre Mémoire de Ressources et de Recherche de Lorraine, CHRU Nancy Service de Gériatrie, Hôpital de Brabois, Vandoeuvre les Nancy, France.,Laboratoire INTERPSY, EA 4432, Groupe de recherche sur les Communications (GRC), Université de Lorraine, Psychologie, Nancy, France
| | - F Pasquier
- CNR-MAJ Inserm U1171, Univ Lille, CHU, Lille, France
| | | | - E Génin
- Inserm, UMR1078, CHU Brest, Université Bretagne Occidentale, Brest, France
| | - L Guyant-Maréchal
- Department of Neurology, Rouen University Hospital, Rouen, France.,Department of Neurophysiology, Rouen University Hospital, Rouen, France
| | - G G Kovacs
- Institute of Neurology, Medical University Vienna, Vienna, Austria
| | - J-C Lambert
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - D Hannequin
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
| | - D Campion
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Research, Rouvray Psychiatric Hospital, Sotteville-lès-Rouen, France
| | - A Rovelet-Lecrux
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
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