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1. A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Author

Denomme-Pichon A. -S., Bruel A. -L., Duffourd Y., Safraou H., Thauvin-Robinet C., Tran Mau-Them F., Philippe C., Vitobello A., Jean-Marcais N., Moutton S., Thevenon J., Faivre L., Matalonga L., de Boer E., Gilissen C., Hoischen A., Kleefstra T., Pfundt R., de Vries B. B. A., Willemsen M. H., Vissers L. E. L. M., Jackson A., Banka S., Clayton-Smith J., Benetti E., Fallerini C., Renieri A., Ciolfi A., Dallapiccola B., Pizzi S., Radio F. C., Tartaglia M., Ellwanger K., Graessner H., Haack T. B., Zurek B., Havlovicova M., Macek M., Ryba L., Schwarz M., Votypka P., Lopez-Martin E., Posada M., Mencarelli M. A., Rooryck C., Trimouille A., Verloes A., Abbott K. M., Kerstjens M., Martin E. L., Maystadt I., Morleo M., Nigro V., Pinelli M., Riess O., Agathe J. -M. D. S., Santen G. W. E., Thauvin C., Torella A., Vissers L., Zguro K., Boer E. D., Cohen E., Danis D., Gao F., Horvath R., Johari M., Johanson L., Li S., Morsy H., Nelson I., Paramonov I., te Paske I. B. A. W., Robinson P., Savarese M., Steyaert W., Topf A., van der Velde J. K., Vandrovcova J., Ossowski S., Demidov G., Sturm M., Schulze-Hentrich J. M., Schule R., Xu J., Kessler C., Wayand M., Synofzik M., Wilke C., Traschutz A., Schols L., Hengel H., Lerche H., Kegele J., Heutink P., Brunner H., Scheffer H., Hoogerbrugge N., 't Hoen P. A. C., Sablauskas K., de Voer R. M., Kamsteeg E. -J., van de Warrenburg B., van Os N., Paske I. T., Janssen E., Steehouwer M., Yaldiz B., Brookes A. J., Veal C., Gibson S., Maddi V., Mehtarizadeh M., Riaz U., Warren G., Dizjikan F. Y., Shorter T., Straub V., Bettolo C. M., Manera J. D., Hambleton S., Engelhardt K., Alexander E., Peyron C., Pelissier A., Beltran S., Gut I. G., Laurie S., Piscia D., Papakonstantinou A., Bullich G., Corvo A., Fernandez-Callejo M., Hernandez C., Pico D., Lochmuller H., Gumus G., Bros-Facer V., Rath A., Hanauer M., Lagorce D., Hongnat O., Chahdil M., Lebreton E., Stevanin G., Durr A., Davoine C. -S., Guillot-Noel L., Heinzmann A., Coarelli G., Bonne G., Evangelista T., Allamand V., Ben Yaou R., Metay C., Eymard B., Atalaia A., Stojkovic T., Turnovec M., Thomasova D., Kremlikova R. P., Frankova V., Liskova P., Dolezalova P., Parkinson H., Keane T., Freeberg M., Thomas C., Spalding D., Robert G., Costa A., Patch C., Hanna M., Houlden H., Reilly M., Efthymiou S., Cali E., Magrinelli F., Sisodiya S. M., Rohrer J., Muntoni F., Zaharieva I., Sarkozy A., Timmerman V., Baets J., de Vries G., De Winter J., Beijer D., de Jonghe P., Van de Vondel L., De Ridder W., Weckhuysen S., Mutarelli M., Varavallo A., Banfi S., Musacchia F., Piluso G., Ferlini A., Selvatici R., Gualandi F., Bigoni S., Rossi R., Neri M., Aretz S., Spier I., Sommer A. K., Peters S., Oliveira C., Pelaez J. G., Matos A. R., Jose C. S., Ferreira M., Gullo I., Fernandes S., Garrido L., Ferreira P., Carneiro F., Swertz M. A., Johansson L., van der Vries G., Neerincx P. B., Ruvolo D., Kerstjens Frederikse W. S., Zonneveld-Huijssoon E., Roelofs-Prins D., van Gijn M., Kohler S., Metcalfe A., Drunat S., Heron D., Mignot C., Keren B., Lacombe D., Capella G., Valle L., Holinski-Feder E., Laner A., Steinke-Lange V., Cilio M. -R., Carpancea E., Depondt C., Lederer D., Sznajer Y., Duerinckx S., Mary S., Macaya A., Cazurro-Gutierrez A., Perez-Duenas B., Munell F., Jarava C. F., Maso L. B., Marce-Grau A., Colobran R., Hackman P., Udd B., Hemelsoet D., Dermaut B., Schuermans N., Poppe B., Verdin H., Osorio A. N., Depienne C., Roos A., Cordts I., Deschauer M., Striano P., Zara F., Riva A., Iacomino M., Uva P., Scala M., Scudieri P., Basak A. N., Claeys K., Boztug K., Haimel M., W. E G., Ruivenkamp C. A. L., Natera de Benito D., Thompson R., Polavarapu K., Grimbacher B., Zaganas I., Kokosali E., Lambros M., Evangeliou A., Spilioti M., Kapaki E., Bourbouli M., Balicza P., Molnar M. J., De la Paz M. P., Sanchez E. B., Delgado B. M., Alonso Garcia de la Rosa F. J., Schrock E., Rump A., Mei D., Vetro A., Balestrini S., Guerrini R., Chinnery P. F., Ratnaike T., Schon K., Maver A., Peterlin B., Munchau A., Lohmann K., Herzog R., Pauly M., May P., Beeson D., Cossins J., Furini S., Afenjar A., Goldenberg A., Masurel A., Phan A., Dieux-Coeslier A., Fargeot A., Guerrot A. -M., Toutain A., Molin A., Sorlin A., Putoux A., Jouret B., Laudier B., Demeer B., Doray B., Bonniaud B., Isidor B., Gilbert-Dussardier B., Leheup B., Reversade B., Paul C., Vincent-Delorme C., Neiva C., Poirsier C., Quelin C., Chiaverini C., Coubes C., Francannet C., Colson C., Desplantes C., Wells C., Goizet C., Sanlaville D., Amram D., Lehalle D., Genevieve D., Gaillard D., Zivi E., Sarrazin E., Steichen E., Schaefer E., Lacaze E., Jacquemin E., Bongers E., Kilic E., Colin E., Giuliano F., Prieur F., Laffargue F., Morice-Picard F., Petit F., Cartault F., Feillet F., Baujat G., Morin G., Diene G., Journel H., Perthus I., Lespinasse J., Alessandri J. -L., Amiel J., Martinovic J., Delanne J., Albuisson J., Lambert L., Perrin L., Ousager L. B., Van Maldergem L., Pinson L., Ruaud L., Samimi M., Bournez M., Bonnet-Dupeyron M. N., Vincent M., Jacquemont M. -L., Cordier-Alex M. -P., Gerard-Blanluet M., Willems M., Spodenkiewicz M., Doco-Fenzy M., Rossi M., Renaud M., Fradin M., Mathieu M., Holder-Espinasse M. H., Houcinat N., Hanna N., Leperrier N., Chassaing N., Philip N., Boute O., Van Kien P. K., Parent P., Bitoun P., Sarda P., Vabres P., Jouk P. -S., Touraine R., El Chehadeh S., Whalen S., Marlin S., Passemard S., Grotto S., Bellanger S. A., Blesson S., Nambot S., Naudion S., Lyonnet S., Odent S., Attie-Bitach T., Busa T., Drouin-Garraud V., Layet V., Bizaoui V., Cusin V., Capri Y., Alembik Y., Unión Europea. Comisión Europea. H2020, Unión Europea. Comisión Europea. 7 Programa Marco, Instituto de Salud Carlos III, Instituto Nacional de Bioinformatica (España), Ministry of Health (República Checa), Ministry of Education, Youth and Sports (República Checa), Denomme-Pichon, A. -S., Bruel, A. -L., Duffourd, Y., Safraou, H., Thauvin-Robinet, C., Tran Mau-Them, F., Philippe, C., Vitobello, A., Jean-Marcais, N., Moutton, S., Thevenon, J., Faivre, L., Matalonga, L., de Boer, E., Gilissen, C., Hoischen, A., Kleefstra, T., Pfundt, R., de Vries, B. B. A., Willemsen, M. H., Vissers, L. E. L. M., Jackson, A., Banka, S., Clayton-Smith, J., Benetti, E., Fallerini, C., Renieri, A., Ciolfi, A., Dallapiccola, B., Pizzi, S., Radio, F. C., Tartaglia, M., Ellwanger, K., Graessner, H., Haack, T. B., Zurek, B., Havlovicova, M., Macek, M., Ryba, L., Schwarz, M., Votypka, P., Lopez-Martin, E., Posada, M., Mencarelli, M. A., Rooryck, C., Trimouille, A., Verloes, A., Abbott, K. M., Kerstjens, M., Martin, E. L., Maystadt, I., Morleo, M., Nigro, V., Pinelli, M., Riess, O., Agathe, J. -M. D. S., Santen, G. W. E., Thauvin, C., Torella, A., Vissers, L., Zguro, K., Boer, E. D., Cohen, E., Danis, D., Gao, F., Horvath, R., Johari, M., Johanson, L., Li, S., Morsy, H., Nelson, I., Paramonov, I., te Paske, I. B. A. W., Robinson, P., Savarese, M., Steyaert, W., Topf, A., van der Velde, J. K., Vandrovcova, J., Ossowski, S., Demidov, G., Sturm, M., Schulze-Hentrich, J. M., Schule, R., Xu, J., Kessler, C., Wayand, M., Synofzik, M., Wilke, C., Traschutz, A., Schols, L., Hengel, H., Lerche, H., Kegele, J., Heutink, P., Brunner, H., Scheffer, H., Hoogerbrugge, N., 't Hoen, P. A. C., Sablauskas, K., de Voer, R. M., Kamsteeg, E. -J., van de Warrenburg, B., van Os, N., Paske, I. T., Janssen, E., Steehouwer, M., Yaldiz, B., Brookes, A. J., Veal, C., Gibson, S., Maddi, V., Mehtarizadeh, M., Riaz, U., Warren, G., Dizjikan, F. Y., Shorter, T., Straub, V., Bettolo, C. M., Manera, J. D., Hambleton, S., Engelhardt, K., Alexander, E., Peyron, C., Pelissier, A., Beltran, S., Gut, I. G., Laurie, S., Piscia, D., Papakonstantinou, A., Bullich, G., Corvo, A., Fernandez-Callejo, M., Hernandez, C., Pico, D., Lochmuller, H., Gumus, G., Bros-Facer, V., Rath, A., Hanauer, M., Lagorce, D., Hongnat, O., Chahdil, M., Lebreton, E., Stevanin, G., Durr, A., Davoine, C. -S., Guillot-Noel, L., Heinzmann, A., Coarelli, G., Bonne, G., Evangelista, T., Allamand, V., Ben Yaou, R., Metay, C., Eymard, B., Atalaia, A., Stojkovic, T., Turnovec, M., Thomasova, D., Kremlikova, R. P., Frankova, V., Liskova, P., Dolezalova, P., Parkinson, H., Keane, T., Freeberg, M., Thomas, C., Spalding, D., Robert, G., Costa, A., Patch, C., Hanna, M., Houlden, H., Reilly, M., Efthymiou, S., Cali, E., Magrinelli, F., Sisodiya, S. M., Rohrer, J., Muntoni, F., Zaharieva, I., Sarkozy, A., Timmerman, V., Baets, J., de Vries, G., De Winter, J., Beijer, D., de Jonghe, P., Van de Vondel, L., De Ridder, W., Weckhuysen, S., Mutarelli, M., Varavallo, A., Banfi, S., Musacchia, F., Piluso, G., Ferlini, A., Selvatici, R., Gualandi, F., Bigoni, S., Rossi, R., Neri, M., Aretz, S., Spier, I., Sommer, A. K., Peters, S., Oliveira, C., Pelaez, J. G., Matos, A. R., Jose, C. S., Ferreira, M., Gullo, I., Fernandes, S., Garrido, L., Ferreira, P., Carneiro, F., Swertz, M. A., Johansson, L., van der Vries, G., Neerincx, P. B., Ruvolo, D., Kerstjens Frederikse, W. S., Zonneveld-Huijssoon, E., Roelofs-Prins, D., van Gijn, M., Kohler, S., Metcalfe, A., Drunat, S., Heron, D., Mignot, C., Keren, B., Lacombe, D., Capella, G., Valle, L., Holinski-Feder, E., Laner, A., Steinke-Lange, V., Cilio, M. -R., Carpancea, E., Depondt, C., Lederer, D., Sznajer, Y., Duerinckx, S., Mary, S., Macaya, A., Cazurro-Gutierrez, A., Perez-Duenas, B., Munell, F., Jarava, C. F., Maso, L. B., Marce-Grau, A., Colobran, R., Hackman, P., Udd, B., Hemelsoet, D., Dermaut, B., Schuermans, N., Poppe, B., Verdin, H., Osorio, A. N., Depienne, C., Roos, A., Cordts, I., Deschauer, M., Striano, P., Zara, F., Riva, A., Iacomino, M., Uva, P., Scala, M., Scudieri, P., Basak, A. N., Claeys, K., Boztug, K., Haimel, M., W. E, G., Ruivenkamp, C. A. L., Natera de Benito, D., Thompson, R., Polavarapu, K., Grimbacher, B., Zaganas, I., Kokosali, E., Lambros, M., Evangeliou, A., Spilioti, M., Kapaki, E., Bourbouli, M., Balicza, P., Molnar, M. J., De la Paz, M. P., Sanchez, E. B., Delgado, B. M., Alonso Garcia de la Rosa, F. J., Schrock, E., Rump, A., Mei, D., Vetro, A., Balestrini, S., Guerrini, R., Chinnery, P. F., Ratnaike, T., Schon, K., Maver, A., Peterlin, B., Munchau, A., Lohmann, K., Herzog, R., Pauly, M., May, P., Beeson, D., Cossins, J., Furini, S., Afenjar, A., Goldenberg, A., Masurel, A., Phan, A., Dieux-Coeslier, A., Fargeot, A., Guerrot, A. -M., Toutain, A., Molin, A., Sorlin, A., Putoux, A., Jouret, B., Laudier, B., Demeer, B., Doray, B., Bonniaud, B., Isidor, B., Gilbert-Dussardier, B., Leheup, B., Reversade, B., Paul, C., Vincent-Delorme, C., Neiva, C., Poirsier, C., Quelin, C., Chiaverini, C., Coubes, C., Francannet, C., Colson, C., Desplantes, C., Wells, C., Goizet, C., Sanlaville, D., Amram, D., Lehalle, D., Genevieve, D., Gaillard, D., Zivi, E., Sarrazin, E., Steichen, E., Schaefer, E., Lacaze, E., Jacquemin, E., Bongers, E., Kilic, E., Colin, E., Giuliano, F., Prieur, F., Laffargue, F., Morice-Picard, F., Petit, F., Cartault, F., Feillet, F., Baujat, G., Morin, G., Diene, G., Journel, H., Perthus, I., Lespinasse, J., Alessandri, J. -L., Amiel, J., Martinovic, J., Delanne, J., Albuisson, J., Lambert, L., Perrin, L., Ousager, L. B., Van Maldergem, L., Pinson, L., Ruaud, L., Samimi, M., Bournez, M., Bonnet-Dupeyron, M. N., Vincent, M., Jacquemont, M. -L., Cordier-Alex, M. -P., Gerard-Blanluet, M., Willems, M., Spodenkiewicz, M., Doco-Fenzy, M., Rossi, M., Renaud, M., Fradin, M., Mathieu, M., Holder-Espinasse, M. H., Houcinat, N., Hanna, N., Leperrier, N., Chassaing, N., Philip, N., Boute, O., Van Kien, P. K., Parent, P., Bitoun, P., Sarda, P., Vabres, P., Jouk, P. -S., Touraine, R., El Chehadeh, S., Whalen, S., Marlin, S., Passemard, S., Grotto, S., Bellanger, S. A., Blesson, S., Nambot, S., Naudion, S., Lyonnet, S., Odent, S., Attie-Bitach, T., Busa, T., Drouin-Garraud, V., Layet, V., Bizaoui, V., Cusin, V., Capri, Y., Alembik, Y., and Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center]

Subjects
Exome reanalysis, Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7], Multidisciplinaire, généralités & autres [D99] [Sciences de la santé humaine], Developmental disorder, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Biology and Life Sciences, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], ClinVar, Rare diseases, All institutes and research themes of the Radboud University Medical Center, Medicine and Health Sciences, Genetics & genetic processes [F10] [Life sciences], Génétique & processus génétiques [F10] [Sciences du vivant], Multidisciplinary, general & others [D99] [Human health sciences], Exome reanalysi, Genetics (clinical)
Abstract

Purpose: Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the "ClinVar low-hanging fruit" reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods: Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results: We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion: The "ClinVar low-hanging fruit" analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock. The Solve-RD project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement number 779257. Data were analyzed using the RD-Connect Genome-Phenome Analysis Platform, which received funding from the EU projects RD-Connect, Solve-RD, and European Joint Programme on Rare Diseases (grant numbers FP7 305444, H2020 779257, H2020 825575), Instituto de Salud Carlos III (grant numbers PT13/0001/0044, PT17/0009/0019; Instituto Nacional de Bioinformática), and ELIXIR Implementation Studies. The collaborations in this study were facilitated by the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies, one of the 24 European Reference Networks approved by the European Reference Network Board of Member States, cofunded by the European Commission. This project was supported by the Czech Ministry of Health (number 00064203) and by the Czech Ministry of Education, Youth and Sports (number - LM2018132) to M.M. Sí

Published
2023

3. Progressive myoclonic epilepsy as an adult-onset manifestation of Leigh syndrome due to m.14487T>C

Author

Dermaut, B., Seneca, S., Dom, L., Smets, K., Ceulemans, L., Smet, J., De Paepe, B., Tousseyn, S., Weckhuysen, S., Gewillig, M., Pals, P., Parizel, P., De Bleecker, J.L., Boon, P., De Meirleir, L., De Jonghe, P., Van Coster, R., Van Paesschen, W., and Santens, P.

Subjects
Leigh disease -- Genetic aspects, Leigh disease -- Research, Myoclonic epilepsy -- Genetic aspects, Myoclonic epilepsy -- Research, Mitochondrial DNA -- Research, Gene mutations -- Research, Health, Psychology and mental health
Published
2010

5. Contribution of homozygous and compound heterozygous missense mutations in VWA2 to Alzheimer’s disease

Author

Hoogmartens, Julie, primary, Hens, Elisabeth, additional, Engelborghs, Sebastiaan, additional, Vandenberghe, Rik, additional, De Deyn, Peter-P., additional, Cacace, Rita, additional, Van Broeckhoven, Christine, additional, Cras, P., additional, Goeman, J., additional, Crols, R., additional, De Bleecker, J.L., additional, Van Langenhove, T., additional, Sieben, A., additional, Dermaut, B., additional, Deryck, O., additional, Bergmans, B., additional, and Versijpt, J., additional

Published
2021
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6. Octapeptide repeat insertions in the prion protein gene and early onset dementia

Author

Croes, E.A., Theuns, J., Houwing-Duistermat, J.J., Dermaut, B., Sleegers, K., Roks, G., Van den Broeck, M., van Harten, B., van Swieten, J.C., Cruts, M., Van Broeckhoven, C., and van Duijn, C.M.

Subjects
Dementia -- Research, Dementia -- Genetic aspects, Prions -- Genetic aspects, Prions -- Research, Health, Psychology and mental health
Published
2004

7. Increased expression of BIN1 mediates Alzheimer genetic risk by modulating tau pathology

Author

Chapuis, J, Hansmannel, F, Gistelinck, M, Mounier, A, Van Cauwenberghe, C, Kolen, K V, Geller, F, Sottejeau, Y, Harold, D, Dourlen, P, Grenier-Boley, B, Kamatani, Y, Delepine, B, Demiautte, F, Zelenika, D, Zommer, N, Hamdane, M, Bellenguez, C, Dartigues, J-F, Hauw, J-J, Letronne, F, Ayral, A-M, Sleegers, K, Schellens, A, Broeck, L V, Engelborghs, S, De Deyn, P P, Vandenberghe, R, OʼDonovan, M, Owen, M, Epelbaum, J, Mercken, M, Karran, E, Bantscheff, M, Drewes, G, Joberty, G, Campion, D, Octave, J-N, Berr, C, Lathrop, M, Callaerts, P, Mann, D, Williams, J, Buée, L, Dewachter, I, Van Broeckhoven, C, Amouyel, P, Moechars, D, Dermaut, B, and Lambert, J-C

Published
2013
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9. Prospective Belgian study of neurodegenerative and vascular dementia: APOE genotype effects

Author

Engelborghs, S, Dermaut, B, Goeman, J, Saerens, J, Marien, P, Pickut, BA, Van den Broeck, M, Serneels, S, Cruts, M, Van Broeckhoven, C, and De Deyn, PP

Subjects
Dementia -- Health aspects -- Genetic aspects -- Diagnosis -- Research -- Care and treatment, Patients -- Care and treatment -- Health aspects -- Genetic aspects -- Physiological aspects -- Research, Nervous system -- Degeneration, Vascular dementia -- Health aspects -- Genetic aspects -- Diagnosis -- Care and treatment -- Research, Genotype -- Physiological aspects -- Health aspects -- Research -- Genetic aspects, Apolipoproteins -- Physiological aspects -- Genetic aspects -- Health aspects -- Research, Alzheimer's disease -- Health aspects -- Diagnosis -- Genetic aspects -- Care and treatment -- Research, Clinical neuropsychology -- Research -- Health aspects -- Physiological aspects, Binswanger's disease -- Health aspects -- Genetic aspects -- Diagnosis -- Care and treatment -- Research, Health, Psychology and mental health, Diagnosis, Care and treatment, Physiological aspects, Genetic aspects, Research, Health aspects
Abstract

Objective: The authors conducted a prospective study of neurodegenerative and vascular dementia in Belgium. Strict diagnostic inclusion criteria were used to include well defined patients and controls. The results of [...]

Published
2003

11. Male-specific epistasis between WWC1 and TLN2 genes is associated with Alzheimer's disease

Author

Gusareva, E, Twizere, J, Sleegers, K, Dourlen, P, Abisambra, J, Meier, S, Cloyd, R, Weiss, B, Dermaut, B, Bessonov, K, Van Der Lee, S, Carrasquillo, M, Katsumata, Y, Cherkaoui, M, Asselbergh, B, Ikram, M, Mayeux, R, Farrer, L, Haines, J, Pericak-Vance, M, Schellenberg, G, (GERAD1), Genetic And Environmental Risk In Alzheimer'S Disease 1 Consortium, (ADGC), Alzheimer'S Disease Genetics Consortium, Consortium), European Alzheimer Disease Initiative Investigators (EADI1, Sims, R, Williams, J, Amouyel, P, Van Duijn, C, Ertekin-Taner, N, Van Broeckhoven, C, Dequiedt, F, Fardo, D, Lambert, J, Van Steen, K, Epidemiology, Neurology, Radiology & Nuclear Medicine, Amsterdam Neuroscience - Neurodegeneration, Genetic Environmental Risk, Alzheimers Dis Genetics Consortium, and European Alzheimer Dis Initiative

Subjects
0301 basic medicine, Male, Talin, Aging, Single-nucleotide polymorphism, Genome-wide association study, Biology, Article, Cohort Studies, 03 medical and health sciences, Sex Factors, Meta-Analysis as Topic, Alzheimer Disease, Humans, Gene, Temporal cortex, Genetics, Sex Characteristics, General Neuroscience, HEK 293 cells, Intracellular Signaling Peptides and Proteins, Epistasis, Genetic, Phosphoproteins, 030104 developmental biology, Cell culture, TLN2, Epistasis, Female, Human medicine, Neurology (clinical), Geriatrics and Gerontology, Developmental Biology
Abstract

Systematic epistasis analyses in multifactorial disorders are an important step to better characterize complex genetic risk structures. We conducted a hypothesis-free sex-stratified genome-wide screening for epistasis contributing to Alzheimer's disease (AD) susceptibility. We identified a statistical epistasis signal between the single nucleotide polymorphisms rs3733980 and rs7175766 that was associated with AD in males (genome-wide significant p(Bonferroni-corrected) = 0.0165). This signal pointed toward the genes WW and C2 domain containing 1, aka KIBRA; 5q34 and TLN2 (talin 2; 15q22.2). Gene-based meta-analysis in 3 independent consortium data sets confirmed the identified interaction: the most significant (metaBonferroni- corrected = 9.02*10(-3)) was for the single nucleotide polymorphism pair rs1477307 and rs4077746. In functional studies, WWand C2 domain containing 1, aka KIBRA and TLN2 coexpressed in the temporal cortex brain tissue of AD subjects (beta = 0.17, 95% CI 0.04 to 0.30, p = 0.01); modulated Tau toxicity in Drosophila eye experiments; colocalized in brain tissue cells, N2a neuroblastoma, and HeLa cell lines; and coimmunoprecipitated both in brain tissue and HEK293 cells. Our finding points toward new AD-related pathways and provides clues toward novel medical targets for the cure of AD. (C) 2018 Elsevier Inc. All rights reserved.

Published
2018

18. Chromosome 17 linked dementia in the absence of tau mutations

Author

Rademakers, R., Cruts, M., Dermaut, B., Roks, G., Van den Broeck, M., Van Duijn, C.M., and Van Broeckhoven, C.

Subjects
Human genetics -- Research, Genetic disorders -- Research, Dementia -- Genetic aspects, Biological sciences
Published
2001

19. Functional screening of Alzheimer risk loci identifies PTK2B as an in vivo modulator and early marker of Tau pathology

Author

Dourlen, P, primary, Fernandez-Gomez, F J, additional, Dupont, C, additional, Grenier-Boley, B, additional, Bellenguez, C, additional, Obriot, H, additional, Caillierez, R, additional, Sottejeau, Y, additional, Chapuis, J, additional, Bretteville, A, additional, Abdelfettah, F, additional, Delay, C, additional, Malmanche, N, additional, Soininen, H, additional, Hiltunen, M, additional, Galas, M-C, additional, Amouyel, P, additional, Sergeant, N, additional, Buée, L, additional, Lambert, J-C, additional, and Dermaut, B, additional

Published
2016
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29. Increased expression of BIN1 mediates Alzheimer genetic risk by modulating tau pathology.

Author

UCL - SSS/IONS/CEMO - Pôle Cellulaire et moléculaire, Chapuis, J, Hansmannel, F, Gistelinck, M, Mounier, A, Van Cauwenberghe, C, Kolen, K V, Geller, F, Sottejeau, Y, Harold, D, Dourlen, P, Grenier-Boley, B, Kamatani, Y, Delepine, B, Demiautte, F, Zelenika, D, Zommer, N, Hamdane, M, Bellenguez, C, Dartigues, J-F, Hauw, J-J, Letronne, F, Ayral, A-M, Sleegers, K, Schellens, A, Broeck, L V, Engelborghs, S, De Deyn, P P, Vandenberghe, R, O'Donovan, M, Owen, M, Epelbaum, J, Mercken, M, Karran, E, Bantscheff, M, Drewes, G, Joberty, G, Campion, D, Octave, Jean-Noël, Berr, C, Lathrop, M, Callaerts, P, Mann, D, Williams, J, Buée, L, Dewachter, Ilse, Van Broeckhoven, C, Amouyel, P, Moechars, D, Dermaut, B, Lambert, J-C, GERAD consortium, UCL - SSS/IONS/CEMO - Pôle Cellulaire et moléculaire, Chapuis, J, Hansmannel, F, Gistelinck, M, Mounier, A, Van Cauwenberghe, C, Kolen, K V, Geller, F, Sottejeau, Y, Harold, D, Dourlen, P, Grenier-Boley, B, Kamatani, Y, Delepine, B, Demiautte, F, Zelenika, D, Zommer, N, Hamdane, M, Bellenguez, C, Dartigues, J-F, Hauw, J-J, Letronne, F, Ayral, A-M, Sleegers, K, Schellens, A, Broeck, L V, Engelborghs, S, De Deyn, P P, Vandenberghe, R, O'Donovan, M, Owen, M, Epelbaum, J, Mercken, M, Karran, E, Bantscheff, M, Drewes, G, Joberty, G, Campion, D, Octave, Jean-Noël, Berr, C, Lathrop, M, Callaerts, P, Mann, D, Williams, J, Buée, L, Dewachter, Ilse, Van Broeckhoven, C, Amouyel, P, Moechars, D, Dermaut, B, Lambert, J-C, and GERAD consortium

Abstract

Genome-wide association studies (GWAS) have identified a region upstream the BIN1 gene as the most important genetic susceptibility locus in Alzheimer's disease (AD) after APOE. We report that BIN1 transcript levels were increased in AD brains and identified a novel 3 bp insertion allele ∼28 kb upstream of BIN1, which increased (i) transcriptional activity in vitro, (ii) BIN1 expression levels in human brain and (iii) AD risk in three independent case-control cohorts (Meta-analysed Odds ratio of 1.20 (1.14-1.26) (P=3.8 × 10(-11))). Interestingly, decreased expression of the Drosophila BIN1 ortholog Amph suppressed Tau-mediated neurotoxicity in three different assays. Accordingly, Tau and BIN1 colocalized and interacted in human neuroblastoma cells and in mouse brain. Finally, the 3 bp insertion was associated with Tau but not Amyloid loads in AD brains. We propose that BIN1 mediates AD risk by modulating Tau pathology.

Published
2013

33. Linkage and association studies identify a novel locus for Alzheimer disease at 7q36 in a Dutch population-based sample

Author

Rijk, P. (Peter) de, Cruts, M. (Marc), Sleegers, K. (Kristel), Dermaut, B. (Bart), Theuns, J. (Jessie), Weckx, S., Duijn, C.M. (Cornelia) van, Pooter, T., Corsmit, E., Del-Favero, J. (Jurgen), Swieten, J.C. (John) van, Aulchenko, Y.S. (Yurii), Rademakers, R. (Rosa), Broeck, M. (Marleen) van den, Broeckhoven, C. (Christine) van, Rijk, P. (Peter) de, Cruts, M. (Marc), Sleegers, K. (Kristel), Dermaut, B. (Bart), Theuns, J. (Jessie), Weckx, S., Duijn, C.M. (Cornelia) van, Pooter, T., Corsmit, E., Del-Favero, J. (Jurgen), Swieten, J.C. (John) van, Aulchenko, Y.S. (Yurii), Rademakers, R. (Rosa), Broeck, M. (Marleen) van den, and Broeckhoven, C. (Christine) van

Abstract

We obtained conclusive linkage of Alzheimer disease (AD) with a candidate region of 19.7 cM at 7q36 in an extended multiplex family, family 1270, ascertained in a population-based study of early-onset AD in the northern Netherlands. Single-nucleotide polymorphism and haplotype association analyses of a Dutch patient-control sample further supported the linkage at 7q36. In addition, we identified a shared haplotype at 7q36 between family 1270 and three of six multiplex AD-affected families from the same geographical region, which is indicative of a founder effect and defines a priority region of 9.3 cM. Mutation analysis of coding exons of 29 candidate genes identified one linked synonymous mutation, g.38030G-->C in exon 10, that affected codon 626 of the PAX transactivation domain interacting protein gene (PAXIP1). It remains to be determined whether PAXIP1 has a functional role in the expression of AD in family 1270 or whether another mutation at this locus explains the observed linkage and sharing. Together, our linkage data from the informative family 1270 and the association data in the population-based early-onset AD patient-control sample strongly support the identification of a novel AD locus at 7q36 and re-emphasize the genetic heterogeneity of AD.

Published
2005

34. Linkage and association studies identify a novel locus for Alzheimer disease at 7q36 in a Dutch population-based sample

Author

Rademakers, R, Cruts, M, Sleegers, K (Kristel), Dermaut, B, Theuns, J, Aulchenko, Yuriy, Weckx, S, De Pooter, T, van den Broeck, M, Corsmit, E, De Rijk, P, Del-Favero, J, van Swieten, J.C., Duijn, Cornelia, van Broeckhoven, C, Rademakers, R, Cruts, M, Sleegers, K (Kristel), Dermaut, B, Theuns, J, Aulchenko, Yuriy, Weckx, S, De Pooter, T, van den Broeck, M, Corsmit, E, De Rijk, P, Del-Favero, J, van Swieten, J.C., Duijn, Cornelia, and van Broeckhoven, C

Published
2005

35. Octapeptide repeat insertions in the prion protein gene and early onset dementia

Author

Croes, E.A. (Esther), Theuns, J. (Jessie), Houwing-Duistermaat, J.J. (Jeanine), Dermaut, B. (Bart), Sleegers, K. (Kristel), Roks, C.M.A.A. (Gerwin), Broeckhoven, C. (Christine) van, Harten, B. van, Swieten, J.C. (John) van, Cruts, M. (Marc), Duijn, C.M. (Cornelia) van, Croes, E.A. (Esther), Theuns, J. (Jessie), Houwing-Duistermaat, J.J. (Jeanine), Dermaut, B. (Bart), Sleegers, K. (Kristel), Roks, C.M.A.A. (Gerwin), Broeckhoven, C. (Christine) van, Harten, B. van, Swieten, J.C. (John) van, Cruts, M. (Marc), and Duijn, C.M. (Cornelia) van

Abstract

Objectives: The most common familial early onset dementia mutations are found in the genes involved in Alzheimer's disease; the amyloid precursor protein (APP) and the presenilin 1 and 2 (PSEN1 and 2) genes; the prion protein gene (PRNP) may be involved. Methods: Following identification of a two-octapeptide repeat insertion in PRNP, we conducted a meta-analysis to investigate the relation of number of PRNP octapeptide repeats with age at disease onset and duration of illness; identifying 55 patients with PRNP octapeptide repeat insertions. We used a linear mixed effects model to assess the relation of number of repeats with age at disease onset, and studied the effect of the number of inserted octapeptide repeats on disease duration with a Cox proportional hazards regression analysis. Results: We found an increasing number of repeats associated with younger age at onset (p<0.001). Duration of the disease decreased significantly with the length of the octapeptide repeat (p<0,001) when adjusting for age at onset. Conclusions: Our findings show significant inverse associations of the length of the PRNP octapeptide repeat with age at disease onset and disease duration in the spongiform encephalopathies.

Published
2004
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36. Polymorphisms in the prion protein gene and in the doppel gene increase susceptibility for Creutzfeldt-Jakob disease

Author

Croes, E.A. (Esther), Alizadeh, B.Z. (Behrooz), Bertoli Avella, A.M. (Aida), Rademaker, T.A.M. (Tessa), Vergeer-Drop, J. (Jeannette), Dermaut, B. (Bart), Houwing-Duistermaat, J.J. (Jeanine), Wientjens, D.P.W.M. (Dorothee), Hofman, A. (Albert), Broeckhoven, C. (Christine) van, Duijn, C.M. (Cornelia) van, Croes, E.A. (Esther), Alizadeh, B.Z. (Behrooz), Bertoli Avella, A.M. (Aida), Rademaker, T.A.M. (Tessa), Vergeer-Drop, J. (Jeannette), Dermaut, B. (Bart), Houwing-Duistermaat, J.J. (Jeanine), Wientjens, D.P.W.M. (Dorothee), Hofman, A. (Albert), Broeckhoven, C. (Christine) van, and Duijn, C.M. (Cornelia) van

Abstract

The prion protein gene (PRNP) plays a central role in the origin of Creutzfeldt-Jakob disease (CJD), but there is growing interest in other polymorphisms that may be involved in CJD. Polymorphisms upstream of PRNP that may modulate the prion protein production as well as polymorphisms in the prion-like doppel gene (PRND) have been studied, with inconsistent findings. We investigated the role of a single-nucleotide polymorphism (SNP 1368) located upstream of PRNP and three polymorphisms in PRND (T26M, P56L and T174M) in CJD. The study included a population-based sample of 52 patients with sporadic CJD and 250 controls. We analysed our data as single markers and haplotypes. Further, we conducted a meta-analysis on PRND T174M comparing the data of the four studies conducted to date. For SNP 1368 and PRNP M129V, we found significant evidence for linkage disequilibrium. No evidence was found for a relation of SNP 1368 to CJD independent of PRNP M129V. We further found a significant increased prevalence of M homozygotes at PRND T174M among sporadic CJD patients, when adjusting the analyses for the other genotypes. In the haplotype analyses, the association was strongest for persons homozygous for PRNP 129M and PRND 174M (odds ratio 4.35, 95% confidence interval 1.05-8.09; P=0.04). The meta-analysis on the PRND T174M polymorphism did not show a consistent effect across studies, raising the question as to whether PRND 174M is causally related to CJD, or whether the PRND allele is in linkage disequilibrium with another polymorphism related to CJD.

Published
2004
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37. Octapeptide repeat insertions in the prion protein gene and early onset dementia

Author

Croes, EA (Esther), Theuns, J, Houwing-Duistermaat, JJ, Dermaut, B, Sleegers, K (Kristel), Roks, CMAA (Gerwin), van den Broeck, M, van Harten, B, van Swieten, J.C., Cruts, M, van Broeckhoven, C, Duijn, Cornelia, Croes, EA (Esther), Theuns, J, Houwing-Duistermaat, JJ, Dermaut, B, Sleegers, K (Kristel), Roks, CMAA (Gerwin), van den Broeck, M, van Harten, B, van Swieten, J.C., Cruts, M, van Broeckhoven, C, and Duijn, Cornelia

Published
2004

38. Functional screening of Alzheimer risk loci identifies PTK2B as an in vivo modulator and early marker of Tau pathology

Author

Dourlen, P, Fernandez-Gomez, F J, Dupont, C, Grenier-Boley, B, Bellenguez, C, Obriot, H, Caillierez, R, Sottejeau, Y, Chapuis, J, Bretteville, A, Abdelfettah, F, Delay, C, Malmanche, N, Soininen, H, Hiltunen, M, Galas, M-C, Amouyel, P, Sergeant, N, Buée, L, Lambert, J-C, and Dermaut, B

Abstract

A recent genome-wide association meta-analysis for Alzheimer’s disease (AD) identified 19 risk loci (in addition to APOE) in which the functional genes are unknown. Using Drosophila, we screened 296 constructs targeting orthologs of 54 candidate risk genes within these loci for their ability to modify Tau neurotoxicity by quantifying the size of >6000 eyes. Besides Drosophila Amph (ortholog of BIN1), which we previously implicated in Tau pathology, we identified p130CAS (CASS4), Eph (EPHA1), Fak (PTK2B) and Rab3-GEF (MADD) as Tau toxicity modulators. Of these, the focal adhesion kinase Fak behaved as a strong Tau toxicity suppressor in both the eye and an independent focal adhesion-related wing blister assay. Accordingly, the human Tau and PTK2B proteins biochemically interacted in vitro and PTK2B co-localized with hyperphosphorylated and oligomeric Tau in progressive pathological stages in the brains of AD patients and transgenic Tau mice. These data indicate that PTK2B acts as an early marker and in vivo modulator of Tau toxicity.

Published
2017
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39. Early cognitive decline is associated with prion protein codon 129 polymorphism

Author

Croes, E.A. (Esther), Dermaut, B. (Bart), Houwing-Duistermaat, J.J. (Jeanine), Broeck, M. (Marleen) van den, Cruts, M. (Marc), Breteler, M.M.B. (Monique), Hofman, A. (Albert), Broeckhoven, C. (Christine) van, Duijn, C.M. (Cornelia) van, Croes, E.A. (Esther), Dermaut, B. (Bart), Houwing-Duistermaat, J.J. (Jeanine), Broeck, M. (Marleen) van den, Cruts, M. (Marc), Breteler, M.M.B. (Monique), Hofman, A. (Albert), Broeckhoven, C. (Christine) van, and Duijn, C.M. (Cornelia) van

Published
2003
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40. Progressive myoclonic epilepsy as an adult-onset manifestation of Leigh syndrome due to m.14487T>C

Author

Dermaut, B, primary, Seneca, S, additional, Dom, L, additional, Smets, K, additional, Ceulemans, L, additional, Smet, J, additional, De Paepe, B, additional, Tousseyn, S, additional, Weckhuysen, S, additional, Gewillig, M, additional, Pals, P, additional, Parizel, P, additional, De Bleecker, J L, additional, Boon, P, additional, De Meirleir, L, additional, De Jonghe, P, additional, Van Coster, R, additional, Van Paesschen, W, additional, and Santens, P, additional

Published
2009
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41. Genetic variability in the regulatory region of presenilin 1 associated with risk for Alzheimer's disease and variable

Author

Theuns, J. (Jessie), Del-Favero, J. (Jurgen), Dermaut, B. (Bart), Duijn, C.M. (Cornelia) van, Serneels, S. (Sally), Corsmit, E., Cruts, M. (Marc), Backhovens, H. (Hubert), Broeck, M. (Marleen) van den, Broeckhoven, C. (Christine) van, Theuns, J. (Jessie), Del-Favero, J. (Jurgen), Dermaut, B. (Bart), Duijn, C.M. (Cornelia) van, Serneels, S. (Sally), Corsmit, E., Cruts, M. (Marc), Backhovens, H. (Hubert), Broeck, M. (Marleen) van den, and Broeckhoven, C. (Christine) van

Abstract

Mutations in the presenilin 1 ( PSEN1 ) gene have been implicated in 18-50% of autosomal dominant cases with early-onset Alzheimer's disease (EOAD). Also, PSEN1 has been suggested as a potential risk gene in late-onset AD cases. We recently showed genetic association in a population-based study of EOAD, pointing to the 5' regulatory region of PSEN1. In this study we systematically screened 3.5 kb of the PSEN1 upstream region and found four novel polymorphisms. Genetic analysis confirmed association of two polymorphisms with increased risk for EOAD. In addition, we detected two different mutations in EOAD cases at-280 and-2818 relative to the transcription initiation site in exon 1A of PSEN1. Analysis of the mutant and wild-type-280 variants using luciferase reporter gene expression in transiently transfected neuroblastoma cells showed a 30% decrease in transcriptional activity for the mutant-280G PSEN1 promoter variant compared with the wild-type variant-280C. Our data suggest that the increased risk for EOAD associated with PSEN1 may result from genetic variations in the regulatory region leading to altered expression levels of the PSEN1 protein.

Published
2000

43. The Glu318Gly substitution in presenilin 1 is not causally related to Alzheimer disease

Author

Dermaut, B. (Bart), Cruts, M. (Marc), Slooter, A.J.C. (Arjen), Gestel, S. van, Jonghe, C. (Chris) de, Vanderstichele, H.M.J. (Hugo), Vanmechelen, E. (Eugeen), Breteler, M.M.B. (Monique), Duijn, C.M. (Cornelia) van, Broeckhoven, C. (Christine) van, Hofman, A. (Albert), Dermaut, B. (Bart), Cruts, M. (Marc), Slooter, A.J.C. (Arjen), Gestel, S. van, Jonghe, C. (Chris) de, Vanderstichele, H.M.J. (Hugo), Vanmechelen, E. (Eugeen), Breteler, M.M.B. (Monique), Duijn, C.M. (Cornelia) van, Broeckhoven, C. (Christine) van, and Hofman, A. (Albert)

Published
1999

47. Recessive POLG mutations presenting with sensory and ataxic neuropathy in compound heterozygote patients with progressive external ophthalmoplegia

Author

Van Goethem, G, primary, Martin, J.J, additional, Dermaut, B, additional, Löfgren, A, additional, Wibail, A, additional, Ververken, D, additional, Tack, P, additional, Dehaene, I, additional, Van Zandijcke, M, additional, Moonen, M, additional, Ceuterick, C, additional, De Jonghe, P, additional, and Van Broeckhoven, C, additional

Published
2003
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