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6 results on '"Lopez-Bigas, N."'

1. Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

Author

Rheinbay E., Nielsen M. M., Abascal F., Wala J. A., Shapira O., Tiao G., Hornshoj H., Hess J. M., Juul R. I., Lin Z., Feuerbach L., Sabarinathan R., Madsen T., Kim J., Mularoni L., Shuai S., Lanzos A., Herrmann C., Maruvka Y. E., Shen C., Amin S. B., Bandopadhayay P., Bertl J., Boroevich K. A., Busanovich J., Carlevaro-Fita J., Chakravarty D., Chan C. W. Y., Craft D., Dhingra P., Diamanti K., Fonseca N. A., Gonzalez-Perez A., Guo Q., Hamilton M. P., Haradhvala N. J., Hong C., Isaev K., Johnson T. A., Juul M., Kahles A., Kahraman A., Kim Y., Komorowski J., Kumar K., Kumar S., Lee D., Lehmann K. -V., Li Y., Liu E. M., Lochovsky L., Park K., Pich O., Roberts N. D., Saksena G., Schumacher S. E., Sidiropoulos N., Sieverling L., Sinnott-Armstrong N., Stewart C., Tamborero D., Tubio J. M. C., Umer H. M., Uuskula-Reimand L., Wadelius C., Wadi L., Yao X., Zhang C. -Z., Zhang J., Haber J. E., Hobolth A., Imielinski M., Kellis M., Lawrence M. S., von Mering C., Nakagawa H., Raphael B. J., Rubin M. A., Sander C., Stein L. D., Stuart J. M., Tsunoda T., Wheeler D. A., Johnson R., Reimand J., Gerstein M., Khurana E., Campbell P. J., Lopez-Bigas N., Bader G. D., Barenboim J., Beroukhim R., Brunak S., Chen K., Choi J. K., Deu-Pons J., Fink J. L., Frigola J., Gambacorti Passerini C., Garsed D. W., Getz G., Gut I. G., Haan D., Harmanci A. O., Helmy M., Hodzic E., Izarzugaza J. M. G., Kim J. K., Korbel J. O., Larsson E., Li S., Li X., Lou S., Marchal K., Martincorena I., Martinez-Fundichely A., McGillivray P. D., Meyerson W., Muinos F., Paczkowska M., Pedersen J. S., Pons T., Pulido-Tamayo S., Reyes-Salazar I., Reyna M. A., Rubio-Perez C., Sahinalp S. C., Salichos L., Shackleton M., Shrestha R., Valencia A., Vazquez M., Verbeke L. P. C., Wang J., Warrell J., Waszak S. M., Weischenfeldt J., Wu G., Yu J., Zhang X., Zhang Y., Zhao Z., Zou L., Akdemir K. C., Alvarez E. G., Baez-Ortega A., Boutros P. C., Bowtell D. D. L., Brors B., Burns K. H., Chan K., Cortes-Ciriano I., Dueso-Barroso A., Dunford A. J., Edwards P. A., Estivill X., Etemadmoghadam D., Frenkel-Morgenstern M., Gordenin D. A., Hutter B., Jones D. T. W., Ju Y. S., Kazanov M. D., Klimczak L. J., Koh Y., Lee E. A., Lee J. J. -K., Lynch A. G., Macintyre G., Markowetz F., Meyerson M., Miyano S., Navarro F. C. P., Ossowski S., Park P. J., Pearson J. V., Puiggros M., Rippe K., Roberts S. A., Rodriguez-Martin B., Scully R., Torrents D., Villasante I., Waddell N., Yang L., Yoon S. -S., Zamora J., Rheinbay, E, Nielsen, M, Abascal, F, Wala, J, Shapira, O, Tiao, G, Hornshoj, H, Hess, J, Juul, R, Lin, Z, Feuerbach, L, Sabarinathan, R, Madsen, T, Kim, J, Mularoni, L, Shuai, S, Lanzos, A, Herrmann, C, Maruvka, Y, Shen, C, Amin, S, Bandopadhayay, P, Bertl, J, Boroevich, K, Busanovich, J, Carlevaro-Fita, J, Chakravarty, D, Chan, C, Craft, D, Dhingra, P, Diamanti, K, Fonseca, N, Gonzalez-Perez, A, Guo, Q, Hamilton, M, Haradhvala, N, Hong, C, Isaev, K, Johnson, T, Juul, M, Kahles, A, Kahraman, A, Kim, Y, Komorowski, J, Kumar, K, Kumar, S, Lee, D, Lehmann, K, Li, Y, Liu, E, Lochovsky, L, Park, K, Pich, O, Roberts, N, Saksena, G, Schumacher, S, Sidiropoulos, N, Sieverling, L, Sinnott-Armstrong, N, Stewart, C, Tamborero, D, Tubio, J, Umer, H, Uuskula-Reimand, L, Wadelius, C, Wadi, L, Yao, X, Zhang, C, Zhang, J, Haber, J, Hobolth, A, Imielinski, M, Kellis, M, Lawrence, M, von Mering, C, Nakagawa, H, Raphael, B, Rubin, M, Sander, C, Stein, L, Stuart, J, Tsunoda, T, Wheeler, D, Johnson, R, Reimand, J, Gerstein, M, Khurana, E, Campbell, P, Lopez-Bigas, N, Bader, G, Barenboim, J, Beroukhim, R, Brunak, S, Chen, K, Choi, J, Deu-Pons, J, Fink, J, Frigola, J, Gambacorti Passerini, C, Garsed, D, Getz, G, Gut, I, Haan, D, Harmanci, A, Helmy, M, Hodzic, E, Izarzugaza, J, Korbel, J, Larsson, E, Li, S, Li, X, Lou, S, Marchal, K, Martincorena, I, Martinez-Fundichely, A, Mcgillivray, P, Meyerson, W, Muinos, F, Paczkowska, M, Pedersen, J, Pons, T, Pulido-Tamayo, S, Reyes-Salazar, I, Reyna, M, Rubio-Perez, C, Sahinalp, S, Salichos, L, Shackleton, M, Shrestha, R, Valencia, A, Vazquez, M, Verbeke, L, Wang, J, Warrell, J, Waszak, S, Weischenfeldt, J, Wu, G, Yu, J, Zhang, X, Zhang, Y, Zhao, Z, Zou, L, Akdemir, K, Alvarez, E, Baez-Ortega, A, Boutros, P, Bowtell, D, Brors, B, Burns, K, Chan, K, Cortes-Ciriano, I, Dueso-Barroso, A, Dunford, A, Edwards, P, Estivill, X, Etemadmoghadam, D, Frenkel-Morgenstern, M, Gordenin, D, Hutter, B, Jones, D, Ju, Y, Kazanov, M, Klimczak, L, Koh, Y, Lee, E, Lee, J, Lynch, A, Macintyre, G, Markowetz, F, Meyerson, M, Miyano, S, Navarro, F, Ossowski, S, Park, P, Pearson, J, Puiggros, M, Rippe, K, Roberts, S, Rodriguez-Martin, B, Scully, R, Torrents, D, Villasante, I, Waddell, N, Yang, L, Yoon, S, Zamora, J, Gonzalez-Perez, Abel [0000-0002-8582-4660], Apollo - University of Cambridge Repository, University of St Andrews. School of Medicine, University of St Andrews. Statistics, University of St Andrews. Sir James Mackenzie Institute for Early Diagnosis, and University of St Andrews. Cellular Medicine Division

Subjects
QA75, EXPRESSION, SELECTION, Untranslated region, medicine.medical_specialty, GENES, QA75 Electronic computers. Computer science, 610 Medicine & health, Genome-wide association study, Tumors -- Genètica, Computational biology, Biology, Genoma humà, ANNOTATION, Genome, Article, RC0254, 03 medical and health sciences, 0302 clinical medicine, SDG 3 - Good Health and Well-being, REGULATORY MUTATIONS, Cancer genomics, Medicine and Health Sciences, medicine, RECURRENT, Gene, 030304 developmental biology, Medicinsk genetik, 0303 health sciences, Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17], Multidisciplinary, LANDSCAPE, RC0254 Neoplasms. Tumors. Oncology (including Cancer), Point mutation, Mutació (Biologia), Biology and Life Sciences, Cancer genomics, Computational biology, bioinformatics, protein-coding genes, cancer, non-coding, 3rd-DAS, Human genetics, Women's cancers Radboud Institute for Health Sciences [Radboudumc 17], Computational biology and bioinformatics, 3. Good health, TERT PROMOTER MUTATIONS, TARGET, DISCOVERY, Medical genetics, Human genome, Medical Genetics, 030217 neurology & neurosurgery
Abstract

The discovery of drivers of cancer has traditionally focused on protein-coding genes1–4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium5 of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). For point mutations, we developed a statistically rigorous strategy for combining significance levels from multiple methods of driver discovery that overcomes the limitations of individual methods. For structural variants, we present two methods of driver discovery, and identify regions that are significantly affected by recurrent breakpoints and recurrent somatic juxtapositions. Our analyses confirm previously reported drivers6,7, raise doubts about others and identify novel candidates, including point mutations in the 5′ region of TP53, in the 3′ untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available., Analyses of 2,658 whole genomes across 38 types of cancer identify the contribution of non-coding point mutations and structural variants to driving cancer.

Published
2020

2. EU Pancreas: An Integrated European Platform for Pancreas Cancer Research - from Basic Science to Clinical and Public Health Interventions for a Rare Disease

Author

Milne, R., La Vecchia, C., Van Steen, K., Hahn, S., Buchholz, M., Costello, E., Esposito, I., Hoheisel, J. D., Lange, B., Lopez-Bigas, N., Michalski, C. W., Real, F. X., Brand, A., Malats, N., LaVecchia, C., Macic, D., Ceric, T., Iovanna, J., Kleeff, J., Gazouli, M., Dervenis, C., Hegyi, P., Ruhl, R., Shafat, A., Sharp, L., Rayan, A., DeCarli, A., Tortora, G., Sileikis, A., Barauskas, G., Eriksson Steigen, S., Ikdahl, T., Malecka-Panas, E., Silva, F. S., Barbu, T. S., Popescu, I., Durisova, M., Majekova, M., Dolzan, V., Genc, L., Yildirim, H., Crnogorac-Jurcevic, T., Bulchholz, M., Greenhalf, B., Campbell, F., Kloeppel, G., De Mesquita, B. B., Hoheisel, J., Brazma, A., Herwig, R., Van Cutsum, E., Goldstein, D., Birney, E., Bassi, C., Biankin, A., Scarpa, A., Michalski, C., Dufresne, M., Chelala, C., Kocher, H., Steyerberg, E., Cecconi, D., Löhr, M., Gutierrez- Ibarluzea, I., Adany, R., Horgan, D., Taruscio, D., Wolff-Boehnisch, B., Dauben, H. -P., Barbardorttir, R. B., Papadopoulos, I., Callens, P., Holcatova, I., Brenner, H., Campa, D., Canzian, F., Rizzato, C., Lüttges, J., Gress, T., Bartch, D., Vlahou, T., Fillat, C., Bayés, M., Gut, I., Gut, M., Gasull, M., Barberá, V., Porta, M., Molero, X., Duell, E., Ález-Couto, E., Carrato, A., Guillén, C., Martinelli, P., Hidalgo, M., Heeschen, C., Valencia, A., Calle, M. L., Guigó, R., Scelo, G., Boffetta, P., Maisonneuve, P., Bosetti, C., Lucenteforte, E., Jeurnink, S., Van Duijnhoven, F., Zatonski, W., Petronijevic, L., Verbeke, C., Neoptolemos, J., Institute for Public Health Genomics, Health Services Research, Genetica & Celbiologie, RS: GROW - School for Oncology and Reproduction, Milne, R., La Vecchia, C., Van Steen, K., Hahn, S., Buchholz, M., Costello, E., Esposito, I., Hoheisel, J.D., Lange, B., Lopez-Bigas, N., Michalski, C.W., Real, F.X., Brand, A., Malats, N., LaVecchia, C., Macic, D., Ceric, T., Iovanna, J., Kleeff, J., Gazouli, M., Dervenis, C., Hegyi, P., Ruhl, R., Shafat, A., Sharp, L., Rayan, A., DeCarli, A., Tortora, G., Sileikis, A., Barauskas, G., Eriksson Steigen, S., Ikdahl, T., Malecka-Panas, E., Silva, F.S., Barbu, T.S., Popescu, I., Durisova, M., Majekova, M., Dolzan, V., Genc, L., Yildirim, H., Crnogorac-Jurcevic, T., Bulchholz, M., Greenhalf, B., Campbell, F., Kloeppel, G., De Mesquita, B.B., Hoheisel, J., Brazma, A., Herwig, R., Van Cutsum, E., Goldstein, D., Birney, E., Bassi, C., Biankin, A., Scarpa, A., Michalski, C., Dufresne, M., Chelala, C., Kocher, H., Steyerberg, E., Cecconi, D., Löhr, M., Gutierrez- Ibarluzea, I., Adany, R., Horgan, D., Taruscio, D., Wolff-Boehnisch, B., Dauben, H.-P., Barbardorttir, R.B., Papadopoulos, I., Callens, P., Holcatova, I., Brenner, H., Campa, D., Canzian, F., Rizzato, C., Lüttges, J., Gress, T., Bartch, D., Vlahou, T., Fillat, C., Bayés, M., Gut, I., Gut, M., Gasull, M., Barberá, V., Porta, M., Molero, X., Duell, E., Ález-Couto, E., Carrato, A., Guillén, C., Martinelli, P., Hidalgo, M., Heeschen, C., Valencia, A., Calle, M.L., Guigó, R., Scelo, G., Boffetta, P., Maisonneuve, P., Bosetti, C., Lucenteforte, E., Jeurnink, S., Van Duijnhoven, F., Zatonski, W., Petronijevic, L., Verbeke, C., and Neoptolemos, J.

Subjects
Biomedical Research, Omics data, International Cooperation, Best practice, Information Dissemination, COST Action BM1204, Context (language use), Translational Research, Biomedical, Rare Diseases, Multidisciplinary approach, Neoplasms, Pancrea, Humans, Medicine, Precision Medicine, Mortality, Pancreas cancer, Genetics (clinical), Public health, Rare disease, Training and mobility, Data integration, Early-stage researchers, Harmonization, Health management system, business.industry, Research, Pancreatic Neoplasm, Public Health, Environmental and Occupational Health, Precision medicine, Research Personnel, ddc, Europe, Pancreatic Neoplasms, Practice Guideline, Action (philosophy), Health, Cancer research, Public Health, Personalized medicine, Therapeutic, business
Abstract

Background: Large-scale international collaboration is essential to decipher relevant information in the context of omics-scale interrogations in cancer research. This is even more important for rare and fatal diseases like pancreas cancer (PC). Methods: The COST Action BM1204 is a unique platform to facilitate the collaboration of a broad range of European and international PC multidisciplinary research groups in order to: (1) integrate knowledge and experience in a multidisciplinary way ‘from cell to society', (2) promote the application of uniform study tools and protocols, (3) foster their optimal use by early-stage researchers, (4) enhance the mobility and training of researchers, and (5) disseminate the results produced to the broader society. Results: This Action will develop novel interdisciplinary tools for collaborative research to improve our understanding of PC and its prevention, diagnosis and treatment. It also aims to answer questions related to the etiology, early detection, evidence-based and personalized treatment, and health management for PC. Furthermore, the Action will contribute to new insights into PC personalized medicine and beyond as well as to the understanding of complex and rare diseases taking PC as a best practice example. The Action aims at attracting young scholars across a range of disciplines in collaboration with more experienced researchers and enhancing active European participation in the international scenario of PC research. Conclusion: The ultimate aim is to foster PC research in Europe and to coordinate this effort with other international initiatives to reduce disease mortality.

Published
2013

3. The whole-genome panorama of cancer drivers

Author

Sabarinathan R, Pich O, Martincorena I, Rubio-Perez C, Juul M, Wala J, Schumacher S, Shapira O, Sidiropoulos N, Waszak S, Tamborero D, Mularoni L, Rheinbay E, Hornshoj H, Deu-Pons J, Muinos F, Bertl J, Guo Q, Weischenfeldt J, Korbel JO, Getz G, Campbell PJ, Pedersen JS, Beroukhim R, Perez-Gonzalez A, Lopez-Bigas N, PCAWG Drivers and Functional Interpretation Group, and ICGC/TCGA Pan-Cancer Analysis of

Subjects
Genetics, 0303 health sciences, Mutation, Somatic cell, Point mutation, Cancer, Genomics, Biology, medicine.disease, medicine.disease_cause, Genome, Germline, 3. Good health, 03 medical and health sciences, 0302 clinical medicine, 030220 oncology & carcinogenesis, medicine, Carcinogenesis, 030304 developmental biology
Abstract

SUMMARYThe advance of personalized cancer medicine requires the accurate identification of the mutations driving each patient’s tumor. However, to date, we have only been able to obtain partial insights into the contribution of genomic events to tumor development. Here, we design a comprehensive approach to identify the driver mutations in each patient’s tumor and obtain a whole-genome panorama of driver events across more than 2,500 tumors from 37 types of cancer. This panorama includes coding and non-coding point mutations, copy number alterations and other genomic rearrangements of somatic origin, and potentially predisposing germline variants. We demonstrate that genomic events are at the root of virtually all tumors, with each carrying on average 4.6 driver events. Most individual tumors harbor a unique combination of drivers, and we uncover the most frequent co-occurring driver events. Half of all cancer genes are affected by several types of driver mutations. In summary, the panorama described here provides answers to fundamental questions in cancer genomics and bridges the gap between cancer genomics and personalized cancer medicine.

Published
2017
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4. Variable interplay of UV-induced DNA damage and repair at transcription factor binding sites

Author

Radhakrishnan Sabarinathan, Abel Gonzalez-Perez, Nuria Lopez-Bigas, Joan Frigola, Institut Català de la Salut, [Frigola J] Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. Thoracic Tumors & Head and Neck Cancer Group, Vall d’Hebron Institute of Oncology (VHIO), Barcelona, Spain. [Sabarinathan R] National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India. [Gonzalez-Perez A] Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. Research Program on Biomedical Informatics, Universitat Pompeu Fabra,Barcelona, Catalonia, Spain. [Lopez-Bigas N] Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain. Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain. Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain, and Vall d'Hebron Barcelona Hospital Campus

Subjects
Mutation rate, Skin Neoplasms, Neoplasms::Neoplasms by Histologic Type::Neoplasms::Neoplasms by Histologic Type::Neoplasms::Neoplasms by Histologic Type::Nevi and Melanomas::Melanoma [DISEASES], DNA Repair, AcademicSubjects/SCI00010, Ultraviolet Rays, DNA repair, DNA damage, Radiació - Efectes fisiològics, Genome Integrity, Repair and Replication, Biology, medicine.disease_cause, Other subheadings::/radiation effects [Other subheadings], 03 medical and health sciences, Genetic Phenomena::DNA Damage [PHENOMENA AND PROCESSES], 0302 clinical medicine, Genetics, medicine, Humans, Binding site, Transcription factor, Melanoma, Otros calificadores::/efectos de la radiación [Otros calificadores], 030304 developmental biology, 0303 health sciences, Mutation, Binding Sites, Whole Genome Sequencing, Mutagenesis, ADN - Dany, Chromosome Mapping, DNA, Neoplasm, fenómenos genéticos::daño del ADN [FENÓMENOS Y PROCESOS], 3. Good health, Cell biology, DNA binding site, Pyrimidine Dimers, neoplasias::neoplasias por tipo histológico::neoplasias::neoplasias por tipo histológico::neoplasias::neoplasias por tipo histológico::nevos y melanomas::melanoma [ENFERMEDADES], 030217 neurology & neurosurgery, DNA Damage, Transcription Factors
Abstract

Llocs d’unió; Dany en l'ADN; Factor de transcripció Sitios de unión; Daño en el ADN; Factor de transcripcion Binding sites; Dna damage; Transcription factor An abnormally high rate of UV-light related mutations appears at transcription factor binding sites (TFBS) across melanomas. The binding of transcription factors (TFs) to the DNA impairs the repair of UV-induced lesions and certain TFs have been shown to increase the rate of generation of these lesions at their binding sites. However, the precise contribution of these two elements to the increase in mutation rate at TFBS in these malignant cells is not understood. Here, exploiting nucleotide-resolution data, we computed the rate of formation and repair of UV-lesions within the binding sites of TFs of different families. We observed, at certain dipyrimidine positions within the binding site of TFs in the Tryptophan Cluster family, an increased rate of formation of UV-induced lesions, corroborating previous studies. Nevertheless, across most families of TFs, the observed increased mutation rate within the entire DNA region covered by the protein results from the decreased repair efficiency. While the rate of mutations across all TFBS does not agree with the amount of UV-induced lesions observed immediately after UV exposure, it strongly agrees with that observed after 48 h. This corroborates the determinant role of the impaired repair in the observed increase of mutation rate. N.L.-B. acknowledges funding from the European Research Council [consolidator grant 682398]; Spanish Ministry of Economy and Competitiveness [SAF2015-66084-R, MINECO/FEDER to U.E.]; IRB Barcelona is a recipient of a Severo Ochoa Centre of Excellence Award from the Spanish Ministry of Economy and Competitiveness (MINECO; Government of Spain) and is supported by CERCA (Generalitat de Catalunya); R.S. acknowledges funding support from the National Centre for Biological Sciences (NCBS-TIFR), Bangalore, India. Funding for open access charge: Spanish Ministry of Economy and Competitiveness.

Published
2020

5. Comprehensive Characterization of Cancer Driver Genes and Mutations

Author

Matthew H. Bailey, Collin Tokheim, Eduard Porta-Pardo, Sohini Sengupta, Denis Bertrand, Amila Weerasinghe, Antonio Colaprico, Michael C. Wendl, Jaegil Kim, Brendan Reardon, Patrick Kwok-Shing Ng, Kang Jin Jeong, Song Cao, Zixing Wang, Jianjiong Gao, Qingsong Gao, Fang Wang, Eric Minwei Liu, Loris Mularoni, Carlota Rubio-Perez, Niranjan Nagarajan, Isidro Cortés-Ciriano, Daniel Cui Zhou, Wen-Wei Liang, Julian M. Hess, Venkata D. Yellapantula, David Tamborero, Abel Gonzalez-Perez, Chayaporn Suphavilai, Jia Yu Ko, Ekta Khurana, Peter J. Park, Eliezer M. Van Allen, Han Liang, Michael S. Lawrence, Adam Godzik, Nuria Lopez-Bigas, Josh Stuart, David Wheeler, Gad Getz, Ken Chen, Alexander J. Lazar, Gordon B. Mills, Rachel Karchin, Li Ding, Samantha J. Caesar-Johnson, John A. Demchok, Ina Felau, Melpomeni Kasapi, Martin L. Ferguson, Carolyn M. Hutter, Heidi J. Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean C. Zenklusen, Jiashan (Julia) Zhang, Sudha Chudamani, Jia Liu, Laxmi Lolla, Rashi Naresh, Todd Pihl, Qiang Sun, Yunhu Wan, Ye Wu, Juok Cho, Timothy DeFreitas, Scott Frazer, Nils Gehlenborg, David I. Heiman, Pei Lin, Sam Meier, Michael S. Noble, Gordon Saksena, Doug Voet, Hailei Zhang, Brady Bernard, Nyasha Chambwe, Varsha Dhankani, Theo Knijnenburg, Roger Kramer, Kalle Leinonen, Yuexin Liu, Michael Miller, Sheila Reynolds, Ilya Shmulevich, Vesteinn Thorsson, Wei Zhang, Rehan Akbani, Bradley M. Broom, Apurva M. Hegde, Zhenlin Ju, Rupa S. Kanchi, Anil Korkut, Jun Li, Shiyun Ling, Wenbin Liu, Yiling Lu, Kwok-Shing Ng, Arvind Rao, Michael Ryan, Jing Wang, John N. Weinstein, Jiexin Zhang, Adam Abeshouse, Joshua Armenia, Debyani Chakravarty, Walid K. Chatila, Ino de Bruijn, Benjamin E. Gross, Zachary J. Heins, Ritika Kundra, Konnor La, Marc Ladanyi, Augustin Luna, Moriah G. Nissan, Angelica Ochoa, Sarah M. Phillips, Ed Reznik, Francisco Sanchez-Vega, Chris Sander, Nikolaus Schultz, Robert Sheridan, S. Onur Sumer, Yichao Sun, Barry S. Taylor, Jioajiao Wang, Hongxin Zhang, Pavana Anur, Myron Peto, Paul Spellman, Christopher Benz, Joshua M. Stuart, Christopher K. Wong, Christina Yau, D. Neil Hayes, Joel S. Parker, Matthew D. Wilkerson, Adrian Ally, Miruna Balasundaram, Reanne Bowlby, Denise Brooks, Rebecca Carlsen, Eric Chuah, Noreen Dhalla, Robert Holt, Steven J.M. Jones, Katayoon Kasaian, Darlene Lee, Yussanne Ma, Marco A. Marra, Michael Mayo, Richard A. Moore, Andrew J. Mungall, Karen Mungall, A. Gordon Robertson, Sara Sadeghi, Jacqueline E. Schein, Payal Sipahimalani, Angela Tam, Nina Thiessen, Kane Tse, Tina Wong, Ashton C. Berger, Rameen Beroukhim, Andrew D. Cherniack, Carrie Cibulskis, Stacey B. Gabriel, Galen F. Gao, Gavin Ha, Matthew Meyerson, Steven E. Schumacher, Juliann Shih, Melanie H. Kucherlapati, Raju S. Kucherlapati, Stephen Baylin, Leslie Cope, Ludmila Danilova, Moiz S. Bootwalla, Phillip H. Lai, Dennis T. Maglinte, David J. Van Den Berg, Daniel J. Weisenberger, J. Todd Auman, Saianand Balu, Tom Bodenheimer, Cheng Fan, Katherine A. Hoadley, Alan P. Hoyle, Stuart R. Jefferys, Corbin D. Jones, Shaowu Meng, Piotr A. Mieczkowski, Lisle E. Mose, Amy H. Perou, Charles M. Perou, Jeffrey Roach, Yan Shi, Janae V. Simons, Tara Skelly, Matthew G. Soloway, Donghui Tan, Umadevi Veluvolu, Huihui Fan, Toshinori Hinoue, Peter W. Laird, Hui Shen, Wanding Zhou, Michelle Bellair, Kyle Chang, Kyle Covington, Chad J. Creighton, Huyen Dinh, HarshaVardhan Doddapaneni, Lawrence A. Donehower, Jennifer Drummond, Richard A. Gibbs, Robert Glenn, Walker Hale, Yi Han, Jianhong Hu, Viktoriya Korchina, Sandra Lee, Lora Lewis, Wei Li, Xiuping Liu, Margaret Morgan, Donna Morton, Donna Muzny, Jireh Santibanez, Margi Sheth, Eve Shinbrot, Linghua Wang, Min Wang, David A. Wheeler, Liu Xi, Fengmei Zhao, Julian Hess, Elizabeth L. Appelbaum, Matthew Bailey, Matthew G. Cordes, Catrina C. Fronick, Lucinda A. Fulton, Robert S. Fulton, Cyriac Kandoth, Elaine R. Mardis, Michael D. McLellan, Christopher A. Miller, Heather K. Schmidt, Richard K. Wilson, Daniel Crain, Erin Curley, Johanna Gardner, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Candace Shelton, Troy Shelton, Mark Sherman, Eric Thompson, Peggy Yena, Jay Bowen, Julie M. Gastier-Foster, Mark Gerken, Kristen M. Leraas, Tara M. Lichtenberg, Nilsa C. Ramirez, Lisa Wise, Erik Zmuda, Niall Corcoran, Tony Costello, Christopher Hovens, Andre L. Carvalho, Ana C. de Carvalho, José H. Fregnani, Adhemar Longatto-Filho, Rui M. Reis, Cristovam Scapulatempo-Neto, Henrique C.S. Silveira, Daniel O. Vidal, Andrew Burnette, Jennifer Eschbacher, Beth Hermes, Ardene Noss, Rosy Singh, Matthew L. Anderson, Patricia D. Castro, Michael Ittmann, David Huntsman, Bernard Kohl, Xuan Le, Richard Thorp, Chris Andry, Elizabeth R. Duffy, Vladimir Lyadov, Oxana Paklina, Galiya Setdikova, Alexey Shabunin, Mikhail Tavobilov, Christopher McPherson, Ronald Warnick, Ross Berkowitz, Daniel Cramer, Colleen Feltmate, Neil Horowitz, Adam Kibel, Michael Muto, Chandrajit P. Raut, Andrei Malykh, Jill S. Barnholtz-Sloan, Wendi Barrett, Karen Devine, Jordonna Fulop, Quinn T. Ostrom, Kristen Shimmel, Yingli Wolinsky, Andrew E. Sloan, Agostino De Rose, Felice Giuliante, Marc Goodman, Beth Y. Karlan, Curt H. Hagedorn, John Eckman, Jodi Harr, Jerome Myers, Kelinda Tucker, Leigh Anne Zach, Brenda Deyarmin, Hai Hu, Leonid Kvecher, Caroline Larson, Richard J. Mural, Stella Somiari, Ales Vicha, Tomas Zelinka, Joseph Bennett, Mary Iacocca, Brenda Rabeno, Patricia Swanson, Mathieu Latour, Louis Lacombe, Bernard Têtu, Alain Bergeron, Mary McGraw, Susan M. Staugaitis, John Chabot, Hanina Hibshoosh, Antonia Sepulveda, Tao Su, Timothy Wang, Olga Potapova, Olga Voronina, Laurence Desjardins, Odette Mariani, Sergio Roman-Roman, Xavier Sastre, Marc-Henri Stern, Feixiong Cheng, Sabina Signoretti, Andrew Berchuck, Darell Bigner, Eric Lipp, Jeffrey Marks, Shannon McCall, Roger McLendon, Angeles Secord, Alexis Sharp, Madhusmita Behera, Daniel J. Brat, Amy Chen, Keith Delman, Seth Force, Fadlo Khuri, Kelly Magliocca, Shishir Maithel, Jeffrey J. Olson, Taofeek Owonikoko, Alan Pickens, Suresh Ramalingam, Dong M. Shin, Gabriel Sica, Erwin G. Van Meir, Hongzheng Zhang, Wil Eijckenboom, Ad Gillis, Esther Korpershoek, Leendert Looijenga, Wolter Oosterhuis, Hans Stoop, Kim E. van Kessel, Ellen C. Zwarthoff, Chiara Calatozzolo, Lucia Cuppini, Stefania Cuzzubbo, Francesco DiMeco, Gaetano Finocchiaro, Luca Mattei, Alessandro Perin, Bianca Pollo, Chu Chen, John Houck, Pawadee Lohavanichbutr, Arndt Hartmann, Christine Stoehr, Robert Stoehr, Helge Taubert, Sven Wach, Bernd Wullich, Witold Kycler, Dawid Murawa, Maciej Wiznerowicz, Ki Chung, W. Jeffrey Edenfield, Julie Martin, Eric Baudin, Glenn Bubley, Raphael Bueno, Assunta De Rienzo, William G. Richards, Steven Kalkanis, Tom Mikkelsen, Houtan Noushmehr, Lisa Scarpace, Nicolas Girard, Marta Aymerich, Elias Campo, Eva Giné, Armando López Guillermo, Nguyen Van Bang, Phan Thi Hanh, Bui Duc Phu, Yufang Tang, Howard Colman, Kimberley Evason, Peter R. Dottino, John A. Martignetti, Hani Gabra, Hartmut Juhl, Teniola Akeredolu, Serghei Stepa, Dave Hoon, Keunsoo Ahn, Koo Jeong Kang, Felix Beuschlein, Anne Breggia, Michael Birrer, Debra Bell, Mitesh Borad, Alan H. Bryce, Erik Castle, Vishal Chandan, John Cheville, John A. Copland, Michael Farnell, Thomas Flotte, Nasra Giama, Thai Ho, Michael Kendrick, Jean-Pierre Kocher, Karla Kopp, Catherine Moser, David Nagorney, Daniel O’Brien, Brian Patrick O’Neill, Tushar Patel, Gloria Petersen, Florencia Que, Michael Rivera, Lewis Roberts, Robert Smallridge, Thomas Smyrk, Melissa Stanton, R. Houston Thompson, Michael Torbenson, Ju Dong Yang, Lizhi Zhang, Fadi Brimo, Jaffer A. Ajani, Ana Maria Angulo Gonzalez, Carmen Behrens, Jolanta Bondaruk, Russell Broaddus, Bogdan Czerniak, Bita Esmaeli, Junya Fujimoto, Jeffrey Gershenwald, Charles Guo, Christopher Logothetis, Funda Meric-Bernstam, Cesar Moran, Lois Ramondetta, David Rice, Anil Sood, Pheroze Tamboli, Timothy Thompson, Patricia Troncoso, Anne Tsao, Ignacio Wistuba, Candace Carter, Lauren Haydu, Peter Hersey, Valerie Jakrot, Hojabr Kakavand, Richard Kefford, Kenneth Lee, Georgina Long, Graham Mann, Michael Quinn, Robyn Saw, Richard Scolyer, Kerwin Shannon, Andrew Spillane, Jonathan Stretch, Maria Synott, John Thompson, James Wilmott, Hikmat Al-Ahmadie, Timothy A. Chan, Ronald Ghossein, Anuradha Gopalan, Douglas A. Levine, Victor Reuter, Samuel Singer, Bhuvanesh Singh, Nguyen Viet Tien, Thomas Broudy, Cyrus Mirsaidi, Praveen Nair, Paul Drwiega, Judy Miller, Jennifer Smith, Howard Zaren, Joong-Won Park, Nguyen Phi Hung, Electron Kebebew, W. Marston Linehan, Adam R. Metwalli, Karel Pacak, Peter A. 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Liptay, Mark Pool, Christopher W. Seder, Kerstin Junker, Larsson Omberg, Mikhail Dinkin, George Manikhas, Domenico Alvaro, Maria Consiglia Bragazzi, Vincenzo Cardinale, Guido Carpino, Eugenio Gaudio, David Chesla, Sandra Cottingham, Michael Dubina, Fedor Moiseenko, Renumathy Dhanasekaran, Karl-Friedrich Becker, Klaus-Peter Janssen, Julia Slotta-Huspenina, Mohamed H. Abdel-Rahman, Dina Aziz, Sue Bell, Colleen M. Cebulla, Amy Davis, Rebecca Duell, J. Bradley Elder, Joe Hilty, Bahavna Kumar, James Lang, Norman L. Lehman, Randy Mandt, Phuong Nguyen, Robert Pilarski, Karan Rai, Lynn Schoenfield, Kelly Senecal, Paul Wakely, Paul Hansen, Ronald Lechan, James Powers, Arthur Tischler, William E. Grizzle, Katherine C. Sexton, Alison Kastl, Joel Henderson, Sima Porten, Jens Waldmann, Martin Fassnacht, Sylvia L. Asa, Dirk Schadendorf, Marta Couce, Markus Graefen, Hartwig Huland, Guido Sauter, Thorsten Schlomm, Ronald Simon, Pierre Tennstedt, Oluwole Olabode, Mark Nelson, Oliver Bathe, Peter R. Carroll, June M. Chan, Philip Disaia, Pat Glenn, Robin K. Kelley, Charles N. Landen, Joanna Phillips, Michael Prados, Jeffry Simko, Karen Smith-McCune, Scott VandenBerg, Kevin Roggin, Ashley Fehrenbach, Ady Kendler, Suzanne Sifri, Ruth Steele, Antonio Jimeno, Francis Carey, Ian Forgie, Massimo Mannelli, Michael Carney, Brenda Hernandez, Benito Campos, Christel Herold-Mende, Christin Jungk, Andreas Unterberg, Andreas von Deimling, Aaron Bossler, Joseph Galbraith, Laura Jacobus, Michael Knudson, Tina Knutson, Deqin Ma, Mohammed Milhem, Rita Sigmund, Andrew K. Godwin, Rashna Madan, Howard G. Rosenthal, Clement Adebamowo, Sally N. Adebamowo, Alex Boussioutas, David Beer, Thomas Giordano, Anne-Marie Mes-Masson, Fred Saad, Therese Bocklage, Lisa Landrum, Robert Mannel, Kathleen Moore, Katherine Moxley, Russel Postier, Joan Walker, Rosemary Zuna, Michael Feldman, Federico Valdivieso, Rajiv Dhir, James Luketich, Edna M. 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Aredes, Armaz Mariamidze, Bailey M.H., Tokheim C., Porta-Pardo E., Sengupta S., Bertrand D., Weerasinghe A., Colaprico A., Wendl M.C., Kim J., Reardon B., Ng P.K.-S., Jeong K.J., Cao S., Wang Z., Gao J., Gao Q., Wang F., Liu E.M., Mularoni L., Rubio-Perez C., Nagarajan N., Cortes-Ciriano I., Zhou D.C., Liang W.-W., Hess J.M., Yellapantula V.D., Tamborero D., Gonzalez-Perez A., Suphavilai C., Ko J.Y., Khurana E., Park P.J., Van Allen E.M., Liang H., Caesar-Johnson S.J., Demchok J.A., Felau I., Kasapi M., Ferguson M.L., Hutter C.M., Sofia H.J., Tarnuzzer R., Yang L., Zenklusen J.C., Zhang J.J., Chudamani S., Liu J., Lolla L., Naresh R., Pihl T., Sun Q., Wan Y., Wu Y., Cho J., DeFreitas T., Frazer S., Gehlenborg N., Getz G., Heiman D.I., Lawrence M.S., Lin P., Meier S., Noble M.S., Saksena G., Voet D., Zhang H., Bernard B., Chambwe N., Dhankani V., Knijnenburg T., Kramer R., Leinonen K., Liu Y., Miller M., Reynolds S., Shmulevich I., Thorsson V., Zhang W., Akbani R., Broom B.M., Hegde 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Danilova L., Bootwalla M.S., Lai P.H., Maglinte D.T., Van Den Berg D.J., Weisenberger D.J., Auman J.T., Balu S., Bodenheimer T., Fan C., Hoadley K.A., Hoyle A.P., Jefferys S.R., Jones C.D., Meng S., Mieczkowski P.A., Mose L.E., Perou A.H., Perou C.M., Roach J., Shi Y., Simons J.V., Skelly T., Soloway M.G., Tan D., Veluvolu U., Fan H., Hinoue T., Laird P.W., Shen H., Zhou W., Bellair M., Chang K., Covington K., Creighton C.J., Dinh H., Doddapaneni H., Donehower L.A., Drummond J., Gibbs R.A., Glenn R., Hale W., Han Y., Hu J., Korchina V., Lee S., Lewis L., Li W., Liu X., Morgan M., Morton D., Muzny D., Santibanez J., Sheth M., Shinbrot E., Wang L., Wang M., Wheeler D.A., Xi L., Zhao F., Hess J., Appelbaum E.L., Bailey M., Cordes M.G., Ding L., Fronick C.C., Fulton L.A., Fulton R.S., Kandoth C., Mardis E.R., McLellan M.D., Miller C.A., Schmidt H.K., Wilson R.K., Crain D., Curley E., Gardner J., Lau K., Mallery D., Morris S., Paulauskis J., Penny R., Shelton C., Shelton T., Sherman M., 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B., Govindan R., Heath S., Ley T., Van Tine B., Westervelt P., Rubin M.A., Lee J.I., Aredes N.D., Mariamidze A., Godzik A., Lopez-Bigas N., Stuart J., Wheeler D., Chen K., and Karchin R.

Subjects
0301 basic medicine, Oncology, Entropy, Programmed Cell Death 1 Receptor, biochemistry, genetics, molecular Biology (all), Biochemistry, B7-H1 Antigen, structure analysi, Principal Component Analysi, Neoplasms, Databases, Genetic, LS2_1, LS4_6, Missense mutation, Statistical analysis, 610 Medicine & health, Exome sequencing, Confusion, Principal Component Analysis, Melanoma, Sciences bio-médicales et agricoles, structure analysis, Algorithm, oncology, Cancer gene, Adenocarcinoma, Microsatellite Instability, ALGORITMOS, medicine.symptom, Algorithms, Human, medicine.medical_specialty, driver gene discovery, Computational biology, Biology, Characterization (mathematics), General Biochemistry, Genetics and Molecular Biology, Article, NO, 03 medical and health sciences, Internal medicine, medicine, Humans, mutations of clinical relevance, Gene, Biochemistry, Genetics and Molecular Biology(all), Microsatellite instability, Computational Biology, Cancer, medicine.disease, Cancérologie, 030104 developmental biology, Precision oncology, Mutation, Neoplasm, Human genome, Colon adenocarcinoma, human activities, Genetics and Molecular Biology(all)
Abstract

Identifying molecular cancer drivers is critical for precision oncology. Multiple advanced algorithms to identify drivers now exist, but systematic attempts to combine and optimize them on large datasets are few. We report a PanCancer and PanSoftware analysis spanning 9,423 tumor exomes (comprising all 33 of The Cancer Genome Atlas projects) and using 26 computational tools to catalog driver genes and mutations. We identify 299 driver genes with implications regarding their anatomical sites and cancer/cell types. Sequence- and structure-based analyses identified >3,400 putative missense driver mutations supported by multiple lines of evidence. Experimental validation confirmed 60%–85% of predicted mutations as likely drivers. We found that >300 MSI tumors are associated with high PD-1/PD-L1, and 57% of tumors analyzed harbor putative clinically actionable events. Our study represents the most comprehensive discovery of cancer genes and mutations to date and will serve as a blueprint for future biological and clinical endeavors. A comprehensive analysis of oncogenic driver genes and mutations in >9,000 tumors across 33 cancer types highlights the prevalence of clinically actionable cancer driver events in TCGA tumor samples., 0, info:eu-repo/semantics/published

Published
2018

6. Molecular Basis of childhood deafness resulting from mutations in the GJB2 (connexin26) gene

Author

Paolo Gasparini, Leopoldo Zelante, Salvatore Melchionda, Nuria Lopez-Bigas, Maria L. Arbonés, Raquel Rabionet, Gabriella Restagno, Leonardo D'Agruma, Xavier Estivill, Rabionet, R, Zelante, L, LOPEZ BIGAS, N, D?agruma, L, Melchionda, S, Restagno, G, Arbones, Ml, Gasparini, Paolo, and Estivill, X.

Subjects
Hearing Loss, Sensorineural, media_common.quotation_subject, Nonsense, Mutation, Missense, Genes, Recessive, medicine.disease_cause, Connexins, Frameshift mutation, otorhinolaryngologic diseases, Genetics, medicine, Humans, Missense mutation, Allele, Child, Frameshift Mutation, Gene, Alleles, Genetics (clinical), media_common, Mutation, biology, Phenotype, Connexin 26, biology.protein, Gene Deletion, GJB6
Abstract

Mutations in the GJB2 gene have been identified in many patients with childhood deafness, 35delG being the most common mutation in Caucasoid populations. We have analyzed a total of 576 families/unrelated patients with recessive or sporadic deafness from Italy and Spain, 193 of them being referred as autosomal recessive, and the other 383 as apparently sporadic cases (singletons). Of the 1,152 unrelated GJB2 chromosomes analyzed from these patients, 37% had GJB2 mutations. Twenty-three different mutations were detected (1 in-frame deletion, 4 nonsense, 5 frameshift, and 13 missense mutations). Mutation 35delG was the most common, accounting for 82% of all GJB2 deafness alleles. The relative frequency of 35delG in Italy and Spain was different, representing 88% of the alleles in Italian patients and only 55% in the Spanish cases. Eight non-35delG mutations were detected more than once (V37I, E47X, 167delT, L90P, 312de114, 334delAA, R143W, and R184P), with relative frequencies ranging between 0.5 and 1.6% of the GJB2 deafness alleles. The information based on conservation of amino acid residues, coexistence with a second GJB2 mutation or absence of the mutation in non-deaf control subjects, suggests that most of these missense changes should be responsible for the deafness phenotype.

Published
2000

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