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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

2. Correction: Solving unsolved rare neurological diseases—a Solve-RD viewpoint (European Journal of Human Genetics, (2021), 29, 9, (1332-1336), 10.1038/s41431-021-00901-1)

Author

Schule R., Timmann D., Erasmus C. E., Reichbauer J., Wayand M., Baets J., Balicza P., Chinnery P., Durr A., Haack T., Hengel H., Horvath R., Houlden H., Kamsteeg E. -J., Kamsteeg C., Lohmann K., Macaya A., Marce-Grau A., Maver A., Molnar J., Munchau A., Peterlin B., Riess O., Schols L., Stevanin G., Synofzik M., Timmerman V., van de Warrenburg B., van Os N., Vandrovcova J., Wilke C., Bevot A., Zuchner S., Beltran S., Laurie S., Matalonga L., Graessner H., Zurek B., Ellwanger K., Ossowski S., Demidov G., Sturm M., Schulze-Hentrich J. M., Heutink P., Brunner H., Scheffer H., Hoogerbrugge N., Hoischen A., 't Hoen P. A. C., Vissers L. E. L. M., Gilissen C., Steyaert W., Sablauskas K., de Voer R. M., Janssen E., de Boer E., Steehouwer M., Yaldiz B., Kleefstra T., Brookes A. J., Veal C., Gibson S., Wadsley M., Mehtarizadeh M., Riaz U., Warren G., Dizjikan F. Y., Shorter T., Topf A., Straub V., Bettolo C. M., Specht S., Clayton-Smith J., Banka S., Alexander E., Jackson A., Faivre L., Thauvin C., Vitobello A., Denomme-Pichon A. -S., Duffourd Y., Tisserant E., Bruel A. -L., Peyron C., Pelissier A., Gut I. G., Piscia D., Papakonstantinou A., Bullich G., Corvo A., Garcia C., Fernandez-Callejo M., Hernandez C., Pico D., Paramonov I., Lochmuller H., Gumus G., Bros-Facer V., Rath A., Hanauer M., Olry A., Lagorce D., Havrylenko S., Izem K., Rigour F., Davoine C. -S., Guillot-Noel L., Heinzmann A., Coarelli G., Bonne G., Evangelista T., Allamand V., Nelson I., Yaou R. B., Metay C., Eymard B., Cohen E., Atalaia A., Stojkovic T., Macek M., Turnovec M., Thomasova D., Kremlikova R. P., Frankova V., Havlovicova M., Kremlik V., Parkinson H., Keane T., Spalding D., Senf A., Robinson P., Danis D., Robert G., Costa A., Patch C., Hanna M., Reilly M., Muntoni F., Zaharieva I., Sarkozy A., de Jonghe P., Nigro V., Banfi S., Torella A., Musacchia F., Piluso G., Ferlini A., Selvatici R., 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 Velde J. K., van der Vries G., Neerincx P. B., Roelofs-Prins D., Kohler S., Metcalfe A., Verloes A., Drunat S., Rooryck C., Trimouille A., Castello R., Morleo M., Pinelli M., Varavallo A., De la Paz M. P., Sanchez E. B., Martin E. L., Delgado B. M., de la Rosa F. J. A. G., Ciolfi A., Dallapiccola B., Pizzi S., Radio F. C., Tartaglia M., Renieri A., Benetti E., Molnar M. J., Herzog R., Pauly M., Osorio A. N., de Benito D. N., Thompson R., Polavarapu K., Beeson D., Cossins J., Cruz P. M. R., Hackman P., Johari M., Savarese M., Udd B., Capella G., Valle L., Holinski-Feder E., Laner A., Steinke-Lange V., Schrock E., Rump A., Schule, R., Timmann, D., Erasmus, C. E., Reichbauer, J., Wayand, M., Baets, J., Balicza, P., Chinnery, P., Durr, A., Haack, T., Hengel, H., Horvath, R., Houlden, H., Kamsteeg, E. -J., Kamsteeg, C., Lohmann, K., Macaya, A., Marce-Grau, A., Maver, A., Molnar, J., Munchau, A., Peterlin, B., Riess, O., Schols, L., Stevanin, G., Synofzik, M., Timmerman, V., van de Warrenburg, B., van Os, N., Vandrovcova, J., Wilke, C., Bevot, A., Zuchner, S., Beltran, S., Laurie, S., Matalonga, L., Graessner, H., Zurek, B., Ellwanger, K., Ossowski, S., Demidov, G., Sturm, M., Schulze-Hentrich, J. M., Heutink, P., Brunner, H., Scheffer, H., Hoogerbrugge, N., Hoischen, A., 't Hoen, P. A. C., Vissers, L. E. L. M., Gilissen, C., Steyaert, W., Sablauskas, K., de Voer, R. M., Janssen, E., de Boer, E., Steehouwer, M., Yaldiz, B., Kleefstra, T., Brookes, A. J., Veal, C., Gibson, S., Wadsley, M., Mehtarizadeh, M., Riaz, U., Warren, G., Dizjikan, F. Y., Shorter, T., Topf, A., Straub, V., Bettolo, C. M., Specht, S., Clayton-Smith, J., Banka, S., Alexander, E., Jackson, A., Faivre, L., Thauvin, C., Vitobello, A., Denomme-Pichon, A. -S., Duffourd, Y., Tisserant, E., Bruel, A. -L., Peyron, C., Pelissier, A., Gut, I. G., Piscia, D., Papakonstantinou, A., Bullich, G., Corvo, A., Garcia, C., Fernandez-Callejo, M., Hernandez, C., Pico, D., Paramonov, I., Lochmuller, H., Gumus, G., Bros-Facer, V., Rath, A., Hanauer, M., Olry, A., Lagorce, D., Havrylenko, S., Izem, K., Rigour, F., Davoine, C. -S., Guillot-Noel, L., Heinzmann, A., Coarelli, G., Bonne, G., Evangelista, T., Allamand, V., Nelson, I., Yaou, R. B., Metay, C., Eymard, B., Cohen, E., Atalaia, A., Stojkovic, T., Macek, M., Turnovec, M., Thomasova, D., Kremlikova, R. P., Frankova, V., Havlovicova, M., Kremlik, V., Parkinson, H., Keane, T., Spalding, D., Senf, A., Robinson, P., Danis, D., Robert, G., Costa, A., Patch, C., Hanna, M., Reilly, M., Muntoni, F., Zaharieva, I., Sarkozy, A., de Jonghe, P., Nigro, V., Banfi, S., Torella, A., Musacchia, F., Piluso, G., Ferlini, A., Selvatici, R., 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 Velde, J. K., van der Vries, G., Neerincx, P. B., Roelofs-Prins, D., Kohler, S., Metcalfe, A., Verloes, A., Drunat, S., Rooryck, C., Trimouille, A., Castello, R., Morleo, M., Pinelli, M., Varavallo, A., De la Paz, M. P., Sanchez, E. B., Martin, E. L., Delgado, B. M., de la Rosa, F. J. A. G., Ciolfi, A., Dallapiccola, B., Pizzi, S., Radio, F. C., Tartaglia, M., Renieri, A., Benetti, E., Molnar, M. J., Herzog, R., Pauly, M., Osorio, A. N., de Benito, D. N., Thompson, R., Polavarapu, K., Beeson, D., Cossins, J., Cruz, P. M. R., Hackman, P., Johari, M., Savarese, M., Udd, B., Capella, G., Valle, L., Holinski-Feder, E., Laner, A., Steinke-Lange, V., Schrock, E., and Rump, A.

Abstract

In the original publication of the article, consortium author lists were missing in the article. The details are given below

Published
2021

3. GENOTYPE-PHENOTYPE ASSOCIATIONS PROVIDE A RATIONAL TO IDENTIFY POTENTIALLY ACTIONABLE VUS

Author

Pelaez J, Monteiro R, Lobo S, Sousa L, Pinheiro H, Castedo S, Garrido L, Teixeira M, Michils G, Bours V, de Putter R, Golmard L, Blanluet M, Colas C, Benusiglio P, Desseignes C, Florence C, Aretz S, Spier I, Huneburg R, Gieldon L, Schrock E, Holinski-Feder E, Steinke V, Calistri D, Tedaldi G, Ranzani G, Genuardi M, Silveira C, Silva I, Krajc M, Blatnik A, Novacovik S, Patino-Garcia A, Soto J, Lazaro C, Capella G, Brunet-Vidal J, Balmana J, Dominguez-Garrido E, Ligtenberg M, Fewings E, Fitzgerald R, Woodward E, Evans G, Hanson H, Lagerstedt-Robinson K, Bajalica-Lagercrantz S, Egas C, Tejada M, Dahan K, Feret D, Hoogerbrugge N, Tischkowitz M, and Oliveira C

Published
2021

4. Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression

Author

Carvalho, B., Postma, C., Mongera, S., Hopmans, E., Diskin, S., van de Wiel, M.A., van Criekinge, W., Thas, O., Matthai, A., Cuesta, M.A., Terhaar sive Droste, J.S., Craanen, M., Schrock, E., Yistra, B., and Meijer, G.A.

Subjects
Colorectal cancer -- Genetic aspects, Colorectal cancer -- Development and progression, Colorectal cancer -- Research, Adenoma -- Genetic aspects, Adenoma -- Development and progression, Adenoma -- Research, Genetic markers -- Research, Health
Published
2009

8. Clinical management of an atypical dental invagination

Author

Badran, Zahi, Lopez-Cazaux, Serena, Crauste, Eleonore, Bray, Estelle, Soueidan, Assem, Armengol, Valérie, Di Donato, N., Isidor, B., Lopez Cazaux, S., Le Caignec, C., Klink, B., Kraus, C., Schrock, E., Hackmann, K., Regenerative Medicine and Skeleton research lab (RMeS), Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), Université de Nantes (UN)-Université de Nantes (UN), Service d’Odontologie Conservatrice et Pédiatrique [CHU Nantes], Centre hospitalier universitaire de Nantes (CHU Nantes)-Centre de compétences Malformations orales et dentaires rares [CHU Nantes], Laboratoire d'ingénierie osteo-articulaire et dentaire (LIOAD), Université de Nantes (UN)-IFR26-Institut National de la Santé et de la Recherche Médicale (INSERM), Département de Dentisterie Conservatrice et d'Endodontie [Hôtel Dieu, Nantes], Hôtel-Dieu de Nantes, Service de génétique médicale - Unité de génétique clinique [Nantes], Université de Nantes (UN)-Centre hospitalier universitaire de Nantes (CHU Nantes), Jehan, Frederic, Regenerative Medicine and Skeleton (RMeS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre hospitalier universitaire de Nantes (CHU Nantes)-Université de Nantes - UFR de Médecine et des Techniques Médicales (UFR MEDECINE), and Université de Nantes (UN)-Université de Nantes (UN)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)

Subjects
[SDV]Life Sciences [q-bio], Dentistry, Case Report, TOOTH MALFORMATION, Oral hygiene, 030207 dermatology & venereal diseases, 03 medical and health sciences, Dens invaginatus, 0302 clinical medicine, Incisor, stomatognathic system, medicine, General Dentistry, Attachment loss, ComputingMilieux_MISCELLANEOUS, Permanent teeth, Orthodontics, [SDV.MHEP.RSOA] Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, [SDV.MHEP.GEG] Life Sciences [q-bio]/Human health and pathology/Geriatry and gerontology, business.industry, dental invagination, [SDV.MHEP.GEG]Life Sciences [q-bio]/Human health and pathology/Geriatry and gerontology, Invagination, 030206 dentistry, medicine.disease, stomatognathic diseases, malformation, medicine.anatomical_structure, Clinical attachment loss, [SDV.MHEP.RSOA]Life Sciences [q-bio]/Human health and pathology/Rhumatology and musculoskeletal system, Etiology, business
Abstract

Dental invagination (DI) is a tooth malformation that usually affects permanent teeth. Its precise etiology is still controversial and represents a clinical challenge as it can favor the development of carious lesion or periodontal inflammation. This paper presents a case of a 23-year-old Caucasian male, where an atypical buccal DI could not be completely diagnosed in the dens invaginatus category. Furthermore, other differential diagnoses could not be confirmed. The dental malformation was seen on a permanent maxillary first incisor and was associated with periodontal inflammation and attachment loss. Successful clinical management of this case consisted of surgical restorative treatment and regular follow-up, accompanied by thorough oral hygiene procedures.

Published
2019

9. Boosting care and knowledge about hereditary cancer: European Reference Network on Genetic Tumour Risk Syndromes

Author

Vos, JR, Giepmans, L, Rohl, C, Geverink, N, Hoogerbrugge, N, Ligtenberg, M, Kets, M, Sijmons, R, Evans, G, Woodward, E, Tischkowitz, M, Maher, E, Steinke-Lange, V, Holinski-Feder, E, Frebourg, T, Houdayer, C, Ferner, RE, Lubinski, J, Ertmanska, K, Lagercrantz, SB, Tham, E, Guillermo, IB, Capella, G, Vidal, JB, Lazaro, C (Conxi), Balmana, J, Bours, V, Legius, E, Wolkenstein, P, Melegh, B, Oliveira, C, Teixeira, M, Poppe, B, Claes, K, Hernandez, HS, Aretz, AWM, Spier, I, Oostenbrink, Rianne, Krajc, M, Blatnik, A, Schrock, E, Peltonen, S, Hietala, M, Ern, G, Guided Treatment in Optimal Selected Cancer Patients (GUTS), Erasmus School of Health Policy & Management, Pediatrics, and Legius, Eric

Subjects
0301 basic medicine, Cancer Research, Pediatrics, Databases, Factual, Colorectal cancer, International Cooperation, 030105 genetics & heredity, Medical Oncology, GUIDELINES, COLORECTAL-CANCER, Tumours of the digestive tract Radboud Institute for Health Sciences [Radboudumc 14], 0302 clinical medicine, Epidemiology, Medicine and Health Sciences, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], Registries, Genetics (clinical), Syndrome, Quality Improvement, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], Rare diseases, Europe, Oncology, 030220 oncology & carcinogenesis, Clinical Competence, Hereditary diffuse gastric cancer, medicine.medical_specialty, Short Communication, European Reference Network, behavioral disciplines and activities, Time-to-Treatment, 03 medical and health sciences, All institutes and research themes of the Radboud University Medical Center, Cross border health care, SDG 3 - Good Health and Well-being, Genetic, Neoplastic Syndromes, Hereditary, Genetics, medicine, Genetic predisposition, Humans, Genetic Predisposition to Disease, Genetic Testing, Neurofibromatosis, Information Services, business.industry, Information Dissemination, Remote Consultation, Cancer, medicine.disease, PREVENTION, Hereditary cancer, Li–Fraumeni syndrome, business, Rare disease
Abstract

Approximately 27-36 million patients in Europe have one of the ~ 5.000-8.000 known rare diseases. These patients often do not receive the care they need or they have a substantial delay from diagnosis to treatment. In March 2017, twenty-four European Reference Networks (ERNs) were launched with the aim to improve the care for these patients through cross border healthcare, in a way that the medical knowledge and expertise travels across the borders, rather than the patients. It is expected that through the ERNs, European patients with a rare disease get access to expert care more often and more quickly, and that research and guideline development will be accelerated resulting in improved diagnostics and therapies. The ERN on Genetic Tumour Risk Syndromes (ERN GENTURIS) aims to improve the identification, genetic diagnostics, prevention of cancer, and treatment of European patients with a genetic predisposition for cancer. The ERN GENTURIS focuses on syndromes such as hereditary breast cancer, hereditary colorectal cancer and polyposis, neurofibromatosis and more rare syndromes e.g. PTEN Hamartoma Tumour Syndrome, Li Fraumeni Syndrome and hereditary diffuse gastric cancer. ispartof: Familial Cancer vol:18 issue:2 pages:281-284 ispartof: location:Netherlands status: published

Published
2019

10. Mutant IDH1 Differently Affects Redox State and Metabolism in Glial Cells of Normal and Tumor Origin

Author

Biedermann, J., Preussler, M., Conde, M., Peitzsch, M., Richter, S., Wiedemuth, R., Abou-El-Ardat, K., Kruger, A., Meinhardt, M., Schackert, G., Leenders, W.P.J., Herold-Mende, C., Niclou, S.P., Bjerkvig, R., Eisenhofer, G., Temme, A., Seifert, M., Kunz-Schughart, L.A., Schrock, E., and Klink, B.

Subjects
Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19]
Abstract

Contains fulltext : 215221.pdf (Publisher’s version ) (Open Access) IDH1(R132H) (isocitrate dehydrogenase 1) mutations play a key role in the development of low-grade gliomas. IDH1(wt) converts isocitrate to alpha-ketoglutarate while reducing nicotinamide adenine dinucleotide phosphate (NADP(+)), whereas IDH1(R132H) uses alpha-ketoglutarate and NADPH to generate the oncometabolite 2-hydroxyglutarate (2-HG). While the effects of 2-HG have been the subject of intense research, the 2-HG independent effects of IDH1(R132H) are still ambiguous. The present study demonstrates that IDH1(R132H) expression but not 2-HG alone leads to significantly decreased tricarboxylic acid (TCA) cycle metabolites, reduced proliferation, and enhanced sensitivity to irradiation in both glioblastoma cells and astrocytes in vitro. Glioblastoma cells, but not astrocytes, showed decreased NADPH and NAD(+) levels upon IDH1(R132H) transduction. However, in astrocytes IDH1(R132H) led to elevated expression of the NAD-synthesizing enzyme nicotinamide phosphoribosyltransferase (NAMPT). These effects were not 2-HG mediated. This suggests that IDH1(R132H) cells utilize NAD(+) to restore NADP pools, which only astrocytes could compensate via induction of NAMPT. We found that the expression of NAMPT is lower in patient-derived IDH1-mutant glioma cells and xenografts compared to IDH1-wildtype models. The Cancer Genome Atlas (TCGA) data analysis confirmed lower NAMPT expression in IDH1-mutant versus IDH1-wildtype gliomas. We show that the IDH1 mutation directly affects the energy homeostasis and redox state in a cell-type dependent manner. Targeting the impairments in metabolism and redox state might open up new avenues for treating IDH1-mutant gliomas.

Published
2019

13. Multicolor spectral karyotyping of human chromosomes

Author

Schrock, E., Du Manoir, S., Veldman, T., Schoell, B., Wienberg, J., Ferguson-Smith, M.A., Ning, Y., Ledbetter, D.H., Bar-Am, I., Soenksen, D., Garini, Y., and Ried, T.

Subjects
Human chromosomes -- Models -- Methods -- Usage, Spectrum analysis -- Usage -- Methods -- Models, Karyotypes -- Methods -- Usage -- Models, Science and technology, Usage, Models, Methods
Abstract

The simultaneous and unequivocal discernment of all human chromosomes in different colors would be of significant clinical and biologic importance. Whole-genome scanning by spectral karyotyping allowed instantaneous visualization of defined emission spectra for each human chromosome after fluorescence in situ hybridization. By means of computer separation (classification) of spectra, spectrally overlapping chromosome-specific DNA probes could be resolved, and all human chromosomes were simultaneous identified., Cytogenetic analysis of numerical and structural chromosomal aberrations in pre- and postnatal diagnostics and cancer cytogenetics is an integral part of clinical care ( 1). Fluorescence in situ hybridization (FISH) [...]

Published
1996

15. Optimizing Genetic Workup in Pheochromocytoma and Paraganglioma by Integrating Diagnostic and Research Approaches

Author

Gieldon, L., William, D., Hackmann, K., Jahn, W., Jahn, A., Wagner, J., Rump, A., Bechmann, N., Nolting, S., Knosel, T., Gudziol, V., Constantinescu, G., Masjkur, J., Beuschlein, F., Timmers, H.J.L.M., Canu, L., Pacak, K., Robledo, M., Aust, D., Schrock, E., Eisenhofer, G., Richter, S., Klink, B., Gieldon, L., William, D., Hackmann, K., Jahn, W., Jahn, A., Wagner, J., Rump, A., Bechmann, N., Nolting, S., Knosel, T., Gudziol, V., Constantinescu, G., Masjkur, J., Beuschlein, F., Timmers, H.J.L.M., Canu, L., Pacak, K., Robledo, M., Aust, D., Schrock, E., Eisenhofer, G., Richter, S., and Klink, B.

Abstract

Contains fulltext : 206791.pdf (publisher's version ) (Open Access), Pheochromocytomas and paragangliomas (PPGL) are rare neuroendocrine tumors with a strong hereditary background and a large genetic heterogeneity. Identification of the underlying genetic cause is crucial for the management of patients and their families as it aids differentiation between hereditary and sporadic cases. To improve diagnostics and clinical management we tailored an enrichment based comprehensive multi-gene next generation sequencing panel applicable to both analyses of tumor tissue and blood samples. We applied this panel to tumor samples and compared its performance to our current routine diagnostic approach. Routine diagnostic sequencing of 11 PPGL susceptibility genes was applied to blood samples of 65 unselected PPGL patients at a single center in Dresden, Germany. Predisposing germline mutations were identified in 19 (29.2%) patients. Analyses of 28 PPGL tumor tissues using the dedicated PPGL panel revealed pathogenic or likely pathogenic variants in known PPGL susceptibility genes in 21 (75%) cases, including mutations in IDH2, ATRX and HRAS. These mutations suggest sporadic tumor development. Our results imply a diagnostic benefit from extended molecular tumor testing of PPGLs and consequent improvement of patient management. The approach is promising for determination of prognostic biomarkers that support therapeutic decision-making.

Published
2019

16. Novel BRCA1 Large Genomic Rearrangements in Italian Breast/Ovarian Cancer Patients

Author

Rizza, R, Hackmann, K, Paris, I, Minucci, A, De Leo, R, Schrock, E, Urbani, A, Capoluongo, E, Gelli, G, Concolino, P, Urbani, A (ORCID:0000-0001-9168-3174), Capoluongo, E (ORCID:0000-0001-9872-0572), Rizza, R, Hackmann, K, Paris, I, Minucci, A, De Leo, R, Schrock, E, Urbani, A, Capoluongo, E, Gelli, G, Concolino, P, Urbani, A (ORCID:0000-0001-9168-3174), and Capoluongo, E (ORCID:0000-0001-9872-0572)

Abstract

Background In recent years, the number of patients being offered BRCA1/2 testing has changed dramatically. Advances in high-throughput sequencing technology have led many diagnostic laboratories to test next-generation sequencing (NGS)-based platforms as the main technology for clinical testing. As a consequence, the proportion of novel BRCA1/2 variants detected has greatly increased. Here, we describe two novel BRCA1 large deletions detected in Italian patients affected by hereditary breast and ovarian cancer syndrome (HBOC). Methods We applied an NGS pipeline with a reliable copy number variation (CNV) prediction algorithm. Successively, samples were investigated using the Multiplex Amplicon Quantification (MAQ) assay and array comparative genomic hybridization (CGH). In a single case, long-range polymerase chain reaction (PCR) was employed for careful detection of the breakpoint region, while the RepeatMasker program was used to identify Alu sequences at the junction point. Results A 137.8 kb deletion, involving the first six exons of BRCA1 and the full NBR2, BRCA1P1, NBR1, and TMEM106a genes, was detected in an Italian woman diagnosed with high-grade serous ovarian carcinoma. A second rearrangement, involving the deletion of BRCA1 11-14 exons, was detected in a breast cancer patient and was fully characterized and reported according to recommended Human Genome Variation Society (HGVS) nomenclature: NG_005905.2: g.125038_143266del; NM_007294.3: c.2817_4716del; NP_009225: p.Lys862Metfs? Conclusion Although it was not possible to perform a familial segregation analysis and more direct evidence of the relationship between genotype and phenotype is necessary, both of the novel reported rearrangements cause the loss of crucial functional domains of the BRCA1 protein and this event supports their pathogenicity.

Published
2019

19. Integrative genomic and transcriptomic analysis of leiomyosarcoma

Author

Chudasama, P, Mughal, SS, Sanders, Mathijs, Hubschmann, D, Chung, I, Deeg, KI, Wong, SH, Rabe, S, Hlevnjak, M, Zapatka, M, Ernst, A, Kleinheinz, K, Schlesner, M, Sieverling, L, van Klink, B, Schrock, E, Hoogenboezem, Remco, Kasper, B, Heilig, CE, Egerer, G, Wolf, S, von Kalle, C, Eils, R, Stenzinger, A, Weichert, W, Glimm, H, Groschel, S, Kopp, HG, Omlor, G, Lehner, B, Bauer, S, Schimmack, S, Ulrich, A, Mechtersheimer, G, Rippe, K, Brors, B, Hutter, B, Renner, M, Hohenberger, P, Scholl, C, Frohling, S, Chudasama, P, Mughal, SS, Sanders, Mathijs, Hubschmann, D, Chung, I, Deeg, KI, Wong, SH, Rabe, S, Hlevnjak, M, Zapatka, M, Ernst, A, Kleinheinz, K, Schlesner, M, Sieverling, L, van Klink, B, Schrock, E, Hoogenboezem, Remco, Kasper, B, Heilig, CE, Egerer, G, Wolf, S, von Kalle, C, Eils, R, Stenzinger, A, Weichert, W, Glimm, H, Groschel, S, Kopp, HG, Omlor, G, Lehner, B, Bauer, S, Schimmack, S, Ulrich, A, Mechtersheimer, G, Rippe, K, Brors, B, Hutter, B, Renner, M, Hohenberger, P, Scholl, C, and Frohling, S

Published
2018

21. Characterization of a new BRCA1 rearrangement in an Italian woman with hereditary breast and ovarian cancer syndrome

Author

Concolino, P, Rizza, Roberta, Hackmann, K, Paris, Ida, Minucci, Angelo, De Paolis, Elisa, Scambia, Giovanni, Zuppi, Cecilia, Schrock, E, Capoluongo, Ettore Domenico, Rizza, R, Paris, I, Minucci, A, De Paolis, E, Scambia, G (ORCID:0000-0003-2758-1063), Zuppi, C (ORCID:0000-0003-4710-4934), Capoluongo, E. (ORCID:0000-0001-9872-0572), Concolino, P, Rizza, Roberta, Hackmann, K, Paris, Ida, Minucci, Angelo, De Paolis, Elisa, Scambia, Giovanni, Zuppi, Cecilia, Schrock, E, Capoluongo, Ettore Domenico, Rizza, R, Paris, I, Minucci, A, De Paolis, E, Scambia, G (ORCID:0000-0003-2758-1063), Zuppi, C (ORCID:0000-0003-4710-4934), and Capoluongo, E. (ORCID:0000-0001-9872-0572)

Abstract

We report a novel BRCA1 LGR, involving the complete duplication of exon 3, in an Italian patient with a strong family history of breast and ovarian cancer. Our purpose is to provide an effective characterization of this LGR using a combination of different methods able to establish the exact breakpoints of the duplication. MAQ assay was used as primary screening method in LGRs detection. Array CGH, RT-PCR, and Long-PCR were used for a careful characterization of rearrangement and breakpoint regions. The Repeat Masker program was employed to identify Alu sequences at breakpoint junctions. RNA analysis showed that this in tandem duplication of exon 3 causes an in frame insertion of 18 amino acids within the protein. Array CGH and Long-PCR strategies revealed that the duplication (g.100411_102863dup) involves exactly 2.452 nucleotides between intron 2 and intron 3 of the gene. In addition, while an Alu Sx sequence was identified at upstream breakpoint, no Alu repeats were found at downstream junction. This supports the hypothesis that the new duplication was the result of a non-homologous recombination event between Alu and Non-Alu sequences. Our strategy, which combines a comprehensive set of methodologies, has been able to characterize the new BRCA1 duplication confirming, as previously reported, that MAQ assay represents a reliable and effective method for a primary screening of BRCA rearrangements. We underline the relevance of incorporating quantitative methods for BRCA genes dosage testing into routine diagnostic practice.

Published
2017

22. Identification and Characterization of a New BRCA2 Rearrangement in an Italian Family with Hereditary Breast and Ovarian Cancer Syndrome

Author

Concolino, P, Rizza, R, Hackmann, K, Minucci, A, Scaglione, Gl, De Bonis, M, Costella, A, Zuppi, C, Schrock, E, Capoluongo, E., Scaglione, GL, Zuppi, C (ORCID:0000-0003-4710-4934), Capoluongo, E. (ORCID:0000-0001-9872-0572), Concolino, P, Rizza, R, Hackmann, K, Minucci, A, Scaglione, Gl, De Bonis, M, Costella, A, Zuppi, C, Schrock, E, Capoluongo, E., Scaglione, GL, Zuppi, C (ORCID:0000-0003-4710-4934), and Capoluongo, E. (ORCID:0000-0001-9872-0572)

Abstract

Background: Epithelial ovarian cancer (EOC) is a spectrum of different diseases, which makes their treatment a challenge. Forkhead box M1 (FOXM1) is an oncogene aberrantly expressed in many solid cancers including serous EOC, but its role in non-serous EOCs remains undefined. We examined FOXM1 expression and its correlation to prognosis across the three major EOC subtypes, and its role in tumorigenesis and chemo-resistance in vitro. Methods: Gene signatures were generated by microarray for 14 clear-cell and 26 endometrioid EOCs, and 15 normal endometrium snap-frozen biopsies. Validation of FOXM1 expression was performed by RT-qPCR and immunohistochemistry in the same samples and additionally in 50 high-grade serous EOCs and in their most adequate normal controls (10 luminal fallopian tube and 20 ovarian surface epithelial brushings). Correlations of FOXM1 expression to clinic-pathological parameters and patients' prognosis were evaluated by Kaplan-Meier and Cox proportional-hazards analyses. OVCAR-3 and two novel deeply characterized EOC cell lines (EOC-CC1 and OSPC2, with clear-cell and serous subtype, respectively) were employed for in vitro studies. Effects of FOXM1 inhibition by transient siRNA transfection were evaluated on cell-proliferation, cell-cycle, colony formation, invasion, and response to conventional first-and second-line anticancer agents, and to the PARP-inhibitor olaparib. Gene signatures of FOXM1-silenced cell lines were generated by microarray and confirmed by RT-qPCR. Results: A significant FOXM1 mRNA up-regulation was found in EOCs compared to normal controls. FOXM1 protein overexpression significantly correlated to serous histology (p = 0.001) and advanced FIGO stage (p = 0.004). Multivariate analyses confirmed FOXM1 protein overexpression as an independent indicator of worse disease specific survival in non-serous EOCs, and of shorter time to progression in platinum-resistant cases. FOXM1 downregulation in EOC cell lines inhibited cell growt

Published
2017

25. The NCI and NCBI SKY/CGH Interactive Online Database

Author

Knutsen, T., Augustus, M., Gobu, V., Padilla-Nash, H., Schrock, E., Shenmen, C., Plotkin, J., Greenhut, S., Kriebel, J., Sirotkin, K., and Ried, T.

Subjects
Human genetics -- Research, Karyotypes -- Research, Cancer -- Genetic aspects, Genetic disorders -- Research, Karyotyping, Biological sciences
Published
2001

27. Molecular cytogenetic analysis of the bladder carcinoma cell line BK-10 by spectral karyotyping

Author

Padilla-Nash, H.M., Nash, W.G., Padilla, G.M., Roberson, K.M., Robertson, C., Macville, M.V.E., Schrock, E., and Ried, T.

Subjects
Molecular screening to improve cytopathological diagnosis of cervical premalignancies, Moleculaire screening ter verbetering van cytopathologische diagnose van cervicale premaligniteiten
Abstract

Item does not contain fulltext

Published
1999

29. Characterization of genetic changes in oligodendroglial tumors including glioblastomas with oligodendroglial component

Author

Klink, B, Gerlach, EM, Hackmann, K, Patt, S, Schrock, E, and Krex, D

Subjects
ddc: 610, 610 Medical sciences, Medicine, neoplasms, nervous system diseases
Abstract

Objective: In contrast to astrocytic tumors including glioblastomas (GBM), oligodendrogliomas (O) have a better prognosis and increased responsiveness to chemotherapy. Interestingly, a small subgroup of glioblastomas contains areas with histological features of oligodendroglial differentiation. In the[for full text, please go to the a.m. URL], 61. Jahrestagung der Deutschen Gesellschaft für Neurochirurgie (DGNC) im Rahmen der Neurowoche 2010

Published
2010
Full Text
View/download PDF

31. Jumping translocations are common in solid tumor cell lines and result in recurrent fusions of whole chromosome arms

Author

Padilla-Nash, H.M., Heselmeyer-Haddad, K., Wangsa, D., Zhang, H., Ghadimi, B.M., Macville, M.V.E., Augustus, M., Schrock, E., Hilgenfeld, E., and Ried, T.

Subjects
Tumor pathology, Tumor pathologie
Abstract

Item does not contain fulltext Jumping translocations (JTs) and segmental jumping translocations (SJTs) are unbalanced translocations involving a donor chromosome arm or chromosome segment that has fused to multiple recipient chromosomes. In leukemia, where JTs have been predominantly observed, the donor segment (usually 1q) preferentially fuses to the telomere regions of recipient chromosomes. In this study, spectral karyotyping (SKY) and FISH analysis revealed 188 JTs and SJTs in 10 cell lines derived from carcinomas of the bladder, prostate, breast, cervix, and pancreas. Multiple JTs and SJTs were detected in each cell line and contributed to recurrent unbalanced whole-arm translocations involving chromosome arms 5p, 14q, 15q, 20q, and 21q. Sixty percent (113/188) of JT breakpoints occurred within centromere or pericentromeric regions of the recipient chromosomes, whereas only 12% of the breakpoints were located in the telomere regions. JT breakpoints of both donor and recipient chromosomes coincided with numerous fragile sites as well as viral integration sites for human DNA viruses. The JTs within each tumor cell line promoted clonal progression, leading to the acquisition of extra copies of the donated chromosome segments that often contained oncogenes (MYC, ABL, HER2/NEU, etc.), consequently resulting in tumor-specific genomic imbalances. Published 2001 Wiley-Liss, Inc.

Published
2001

32. Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study

Author

Rauch, A., Wieczorek, D., Graf, E., Wieland, T., Endele, S., Schwarzmayr, T., Albrecht, B., Bartholdi, D., Beygo, J., Di Donato, N., Dufke, A., Cremer, K., Hempel, M., Horn, D., Hoyer, J., Joset, P., Ropke, A., Moog, U., Riess, A., Thiel, C.T., Tzschach, A., Wiesener, A., Wohlleber, E., Zweier, C., Ekici, A.B., Zink, A.M., Rump, A., Meisinger, C., Grallert, H., Sticht, H., Schenck, A., Engels, H., Rappold, G., Schrock, E., Wieacker, P., Riess, O., Meitinger, T., Reis, A., Strom, T.M., Rauch, A., Wieczorek, D., Graf, E., Wieland, T., Endele, S., Schwarzmayr, T., Albrecht, B., Bartholdi, D., Beygo, J., Di Donato, N., Dufke, A., Cremer, K., Hempel, M., Horn, D., Hoyer, J., Joset, P., Ropke, A., Moog, U., Riess, A., Thiel, C.T., Tzschach, A., Wiesener, A., Wohlleber, E., Zweier, C., Ekici, A.B., Zink, A.M., Rump, A., Meisinger, C., Grallert, H., Sticht, H., Schenck, A., Engels, H., Rappold, G., Schrock, E., Wieacker, P., Riess, O., Meitinger, T., Reis, A., and Strom, T.M.

Abstract

Item does not contain fulltext, BACKGROUND: The genetic cause of intellectual disability in most patients is unclear because of the absence of morphological clues, information about the position of such genes, and suitable screening methods. Our aim was to identify de-novo variants in individuals with sporadic non-syndromic intellectual disability. METHODS: In this study, we enrolled children with intellectual disability and their parents from ten centres in Germany and Switzerland. We compared exome sequences between patients and their parents to identify de-novo variants. 20 children and their parents from the KORA Augsburg Diabetes Family Study were investigated as controls. FINDINGS: We enrolled 51 participants from the German Mental Retardation Network. 45 (88%) participants in the case group and 14 (70%) in the control group had de-novo variants. We identified 87 de-novo variants in the case group, with an exomic mutation rate of 1.71 per individual per generation. In the control group we identified 24 de-novo variants, which is 1.2 events per individual per generation. More participants in the case group had loss-of-function variants than in the control group (20/51 vs 2/20; p=0.022), suggesting their contribution to disease development. 16 patients carried de-novo variants in known intellectual disability genes with three recurrently mutated genes (STXBP1, SYNGAP1, and SCN2A). We deemed at least six loss-of-function mutations in six novel genes to be disease causing. We also identified several missense alterations with potential pathogenicity. INTERPRETATION: After exclusion of copy-number variants, de-novo point mutations and small indels are associated with severe, sporadic non-syndromic intellectual disability, accounting for 45-55% of patients with high locus heterogeneity. Autosomal recessive inheritance seems to contribute little in the outbred population investigated. The large number of de-novo variants in known intellectual disability genes is only partially attributable to known

Published
2012

37. Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression

Author

Carvalho, B, primary, Postma, C, additional, Mongera, S, additional, Hopmans, E, additional, Diskin, S, additional, van de Wiel, M A, additional, van Criekinge, W, additional, Thas, O, additional, Matthai, A, additional, Cuesta, M A, additional, Terhaar sive Droste, J S, additional, Craanen, M, additional, Schrock, E, additional, Ylstra, B, additional, and Meijer, G A, additional

Published
2008
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40. Cytogenetic and molecular characterization of random chromosomal rearrangements activating the drug resistance gene, MDR 1/P-glycoprotein, in drug-selected cell lines and patients with drug refractory ALL

Author

Knutsen, T., Mickley, L.A., Ried, T., Green, E.D., Manoir, S. du, Schrock, E., Macville, M.V.E., Ning, Y., Robey, R., Polymeropoulos, M., Torres, R., Fojo, T., Knutsen, T., Mickley, L.A., Ried, T., Green, E.D., Manoir, S. du, Schrock, E., Macville, M.V.E., Ning, Y., Robey, R., Polymeropoulos, M., Torres, R., and Fojo, T.

Abstract

Item does not contain fulltext

Published
1998

42. Severe forms of Baraitser-Winter syndrome are caused by ACTB mutations rather than ACTG1 mutations.

Author

Di Donato, N, Rump, A, Koenig, R, Der Kaloustian, V M, Halal, F, Sonntag, K, Krause, C, Hackmann, K, Hahn, G, Schrock, E, and Verloes, A

Subjects
HUMAN abnormalities, ACTIN, PROTEIN genetics, GENETIC mutation, BLEPHAROPTOSIS, CONGENITAL disorders
Abstract

ACTB and ACTG1 mutations have recently been reported to cause Baraitser-Winter syndrome (BRWS) - a rare condition characterized by ptosis, colobomata, neuronal migration disorder, distinct facial anomalies and intellectual disability. One of the patients carrying an ACTB mutation was previously diagnosed with Fryns-Aftimos syndrome (FAS), which is a rare and severe, multiple congenital anomaly (MCA) syndrome whose symptoms partially overlap with that of BRWS. However, several patients with Fryns-Aftimos were considered not to fit into the ACTB and ACTG1 spectrum because of their severe impairment and additional malformations. We report on three patients who had been diagnosed with FAS. All three patients carry a mutation in the ACTB gene. On the basis of the ACTB mutations and analysis of the clinical findings, we reclassify the diagnosis of these patients as severe BRWS. We suggest that mutations in ACTB cause a distinctly more severe phenotype than ACTG1 mutations, despite the structural similarity of beta- and gamma-actins and their overlapping expression pattern. We expand the spectrum of BRWS and confirm that FAS is not a separate entity but an early and severe manifestation of BRWS. [ABSTRACT FROM AUTHOR]

Published
2014
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47. Effect of a PlateletActivating Factor Antagonist on Pancreas Perfusion After 24 h of Ischemia

Author

Leonhardt, U., Exner, B., Schrock, E., Ritzel, U., Nebendahl, K., and Stöckmann, F.

Abstract

Platelet-activating factor (PAF) is a strong mediator of inflammation that is present in many mammalian tissues and cell types. In the pancreas, PAF can be synthesized in acinar cells after stimulation with secretagogues. The present study uses a perfused porcine pancreas model to investigate the role of PAF in pancreatic ischemia and the effect of the PAF antagonist bepafant on pancreas preservation. Pancreata were preserved with or without bepafant, stored for 24 h at 4°C, and then reperfused at 37°C in a perfusion chamber. Reperfusions were significantly improved by the addition of bepafant. This was indicated by a significantly increased arteriovenous volume flow (16.54±1.88 ml/min versus controls 8.54±1.31 mumin; p0.0068; bepafant, n7; controls, n12) and a reduced vascular resistance (p0.0068; bepafant, 1.95±0.22 mm Hg min/ml versus controls 4.08±0.56 mm Hg min/ml). Radioimmunological quantification of PAF in pancreatic tissue revealed that PAF levels remain unchanged during storage in a cold protective solution at 4°C but increase significantly during surgical pancreas preparation under general anesthesia (from 142.1±21.2 to 368.8±52.5 pg/g; n 15; p0.0007). The present study shows that bepafant improves pancreas preservation after cold ischemia. The beneficial effect might be explained by antagonizing inflammatory and vasoconstrictory responses to PAF synthesized during surgical pancreas preparation.

Published
1995

50. Germline truncating-mutations in BRCA1 and MSH6 in a patient with early onset endometrial cancer

Author

Kast Karin, Neuhann Teresa M, Görgens Heike, Becker Kerstin, Keller Katja, Klink Barbara, Aust Daniela, Distler Wolfgang, Schröck Evelin, and Schackert Hans K

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background Hereditary Breast and Ovarian Cancer Syndrome (HBOCS) and Hereditary Non-Polyposis Colorectal Cancer Syndrome (HNPCC, Lynch Syndrome) are two tumor predisposition syndromes responsible for the majority of hereditary breast and colorectal cancers. Carriers of both germline mutations in breast cancer genes BRCA1 or BRCA2 and in mismatch repair (MMR) genes MLH1, MSH2, MSH6 or PMS2 are very rare. Case presentation We identified germline mutations in BRCA1 and in MSH6 in a patient with increased risk for HBOC diagnosed with endometrial cancer at the age of 46 years. Conclusions Although carriers of mutations in both MMR and BRCA genes are rare in Caucasian populations and anamnestical and histopathological findings may guide clinicians to identify these families, both syndromes can only be diagnosed through a complete gene analysis of the respective genes.

Published
2012
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