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2. A Global Effort to Define the Human Genetics of Protective Immunity to SARS-CoV-2 Infection

Author

Jean-Laurent Casanova, Helen C. Su, Laurent Abel, Alessandro Aiuti, Saleh Almuhsen, Andres Augusto Arias, Paul Bastard, Catherine Biggs, Dusan Bogunovic, Bertrand Boisson, Stephanie Boisson-Dupuis, Alexandre Bolze, Anastasia Bondarenko, Aziz Bousfiha, Petter Brodin, Jacinta Bustamante, Manish Butte, Giorgio Casari, Michael Ciancanelli, Aurelie Cobat, Antonio Condino-Neto, Megan Cooper, Clifton Dalgard, Sara Espinosa, Hagit Feldman, Jacques Fellay, Jose Luis Franco, David Hagin, Yuval Itan, Emmanuelle Jouanguy, Carrie Lucas, Davood Mansouri, Isabelle Meyts, Joshua Milner, Trine Mogensen, Tomohiro Morio, Lisa Ng, Luigi D. Notarangelo, Satoshi Okada, Tayfun Ozcelik, Pere Soler Palacín, Anna Planas, Carolina Prando, Anne Puel, Aurora Pujol, Claire Redin, Laurent Renia, Jose Carlos Rodriguez Gallego, Lluis Quintana-Murci, Vanessa Sancho-Shimizu, Vijay Sankaran, Mikko R.J. Seppänen, Mohammad Shahrooei, Andrew Snow, András Spaan, Stuart Tangye, Jordi Perez Tur, Stuart Turvey, Donald C. Vinh, Horst von Bernuth, Xiaochuan Wang, Pawel Zawadzki, Qian Zhang, Shenying Zhang, Casanova, J. -L., Su, H. C., Abel, L., Aiuti, A., Almuhsen, S., Arias, A. A., Bastard, P., Biggs, C., Bogunovic, D., Boisson, B., Boisson-Dupuis, S., Bolze, A., Bondarenko, A., Bousfiha, A., Brodin, P., Bustamante, J., Butte, M., Casari, G., Ciancanelli, M., Cobat, A., Condino-Neto, A., Cooper, M., Dalgard, C., Espinosa, S., Feldman, H., Fellay, J., Franco, J. L., Hagin, D., Itan, Y., Jouanguy, E., Lucas, C., Mansouri, D., Meyts, I., Milner, J., Mogensen, T., Morio, T., Ng, L., Notarangelo, L. D., Okada, S., Ozcelik, T., Palacin, P. S., Planas, A., Prando, C., Puel, A., Pujol, A., Redin, C., Renia, L., Rodriguez Gallego, J. C., Quintana-Murci, L., Sancho-Shimizu, V., Sankaran, V., Seppanen, M. R. J., Shahrooei, M., Snow, A., Spaan, A., Tangye, S., Tur, J. P., Turvey, S., Vinh, D. C., von Bernuth, H., Wang, X., Zawadzki, P., Zhang, Q., Zhang, S., UKRI Future Leader's Fellowship, and Özçelik, Tayfun

Subjects
Pneumonia, Viral, Disease, Biology, Infections, Virus, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Betacoronavirus, 0302 clinical medicine, Pandemic, Genetic variation, medicine, Humans, Genetic Predisposition to Disease, COVID Human Genetic Effort, Pandemics, 11 Medical and Health Sciences, Genetic Association Studies, 030304 developmental biology, Disease Resistance, 0303 health sciences, Viral Epidemiology, Genome, Human, SARS-CoV-2, Age Factors, Genetic Diseases, Inborn, COVID-19, Genetic Variation, 06 Biological Sciences, biology.organism_classification, medicine.disease, Human genetics, Immunology, Host-Pathogen Interactions, Coronavirus Infections, Pneumonia (non-human), 030217 neurology & neurosurgery, Developmental Biology
Abstract

SARS-CoV-2 infection displays immense inter-individual clinical variability, ranging from silent infection to lethal disease. The role of human genetics in determining clinical response to the virus remains unclear. Studies of outliers—individuals remaining uninfected despite viral exposure and healthy young patients with life-threatening disease—present a unique opportunity to reveal human genetic determinants of infection and disease.

Published
2020
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3. List of Contributors

Author

Roshini Sarah Abraham, Cristina Albanesi, Ilias Alevizos, Juan Anguita, Brendan Antiochos, Cynthia Aranow, John P. Atkinson, Howard A. Austin, Subash Babu, Mark C. Ballow, James E. Balow, John W. Belmont, Claudia Berek, Timothy Beukelman, Tapan Bhavsar, J. Andrew Bird, Sarah E. Blutt, Mark Boguniewicz, Rafael Bonamichi-Santos, Bertrand Boisson, Elena Borzova, Prosper N. Boyaka, Joshua Boyce, Sarah K. Browne, Wesley Burks, Jacinta Bustamante, Virginia L. Calder, Matthew Campbell, Adela Rambi G. Cardones, Jean-Laurent Casanova, Mariana Castells, Lisa A. Cavacini, Edwin S.L. Chan, David D. Chaplin, W. Winn Chatham, Edward S. Chen, Javier Chinen, Lisa Christopher-Stine, Michael Ciancanelli, Andrew P. Cope, David B. Corry, Filippo Crea, Randy Q. Cron, Jennifer M. Cuellar-Rodriguez, Marinos C. Dalakas, Sara M. Dann, Betty Diamond, Terry W. Du, Stéphanie Dupuis-Boisson, Todd N. Eagar, Craig A. Elmets, Doruk Erkan, Laura Fanning, Erol Fikrig, Davide Flego, Thomas A. Fleisher, Luz Fonacier, Andrew P. Fontenot, Alexandra F. Freeman, Anthony J. Frew, Kohtaro Fujihashi, Massimo Gadina, Moshe E. Gatt, M. Eric Gershwin, Susan L. Gillespie, Jörg J. Goronzy, Sangeeta Goswami, Clive E.H. Grattan, Neil S. Greenspan, Sarthak Gupta, Claire E. Gustafson, Russell P. Hall, Robert G. Hamilton, Laurie E. Harrington, Leonard C. Harrison, Sarfaraz A. Hasni, Arthur Helbling, Joanna Hester, Steven M. Holland, Dennis Hourcade, Nicholas D. Huntington, Tracy Hwangpo, John B. Imboden, Fadi Issa, Shai Izraeli, Elaine S. Jaffe, Sirpa Jalkanen, Stacie Jones, Emmanuelle Jouanguy, Sarah Kabbani, Stefan H.E. Kaufmann, Farrah Kheradmand, Donald B. Kohn, Robert Korngold, Anna Kovalszki, Douglas B. Kuhns, Hrishikesh Kulkarni, Caroline Y. Kuo, Arash Lahouti, C. Ola Landgren, Arian Laurence, Joyce S. Lee, Catherine Lemière, Donald Y.M. Leung, Arnold I. Levinson, Ofer Levy, Dorothy E. Lewis, Phoebe Lin, Andreas Linkermann, Giovanna Liuzzo, Michael D. Lockshin, Allison K. Lord, Jay N. Lozier, Amber Luong, Raashid Luqmani, Meggan Mackay, Jonathan S. Maltzman, Peter J. Mannon, Michael P. Manns, James G. Martin, Craig L. Maynard, Samual McCash, Douglas R. McDonald, Peter C. Melby, Stephen D. Miller, Anna L. Mitchell, Amirah Mohd-Zaki, Carolyn Mold, David R. Moller, Dimitrios S. Monos, Scott N. Mueller, Catharina M. Mulders-Manders, Mark J. Mulligan, Ulrich R. Müller, Pashna N. Munshi, Kazunori Murata, Philip M. Murphy, Nicolás Navasa, Pierre Noel, Luigi D. Notarangelo, Robert L. Nussbaum, Thomas B. Nutman, Stephen L. Nutt, João B. Oliveira, Thomas L. Ortel, John J. O'Shea, Sung-Yun Pai, Lavannya Pandit, Mary E. Paul, Simon H.S. Pearce, Daniela Pedicino, Erik J. Peterson, Capucine Picard, Stefania Pittaluga, Debra Long Priel, Jennifer Puck, Anne Puel, Andreas Radbruch, Stephen T. Reece, John D. Reveille, Robert R. Rich, Chaim M. Roifman, Antony Rosen, James T. Rosenbaum, Sergio D. Rosenzweig, Barry T. Rouse, Scott D. Rowley, Shimon Sakaguchi, Marko Salmi, Andrea J. Sant, Sarah W. Satola, Valerie Saw, Marcos C. Schechter, Harry W. Schroeder, Benjamin M. Segal, Carlo Selmi, Sushma Shankar, Anu Sharma, Padmanee Sharma, William T. Shearer, Richard M. Siegel, Anna Simon, Gideon P. Smith, David S. Stephens, Robin Stephens, Alex Straumann, Leyla Y. Teos, Laura Timares, Wulf Tonnus, Raul M. Torres, Gülbü Uzel, Jeroen C.H. van der Hilst, Jos W.M. van der Meer, John Varga, Jatin M. Vyas, Meryl Waldman, Peter Weiser, Peter F. Weller, Cornelia M. Weyand, Fredrick M. Wigley, Robert J. Winchester, James B. Wing, Kathryn J. Wood, Xiaobo Wu, Hui Xu, Cassian Yee, and Shen-Ying Zhang

Published
2019
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4. Whole-exome sequencing to analyze population structure, parental inbreeding, and familial linkage

Author

Anne Puel, Stephanie Boisson-Dupuis, Davood Mansouri, Avinash Abhyankar, Shen-Ying Zhang, Silvia SÁNCHEZ-RAMÓN, Jean-Laurent Casanova, Jacinta Bustamante, Antonio Condino-Neto, Francois Vandenesch, Bertrand Boisson, Vincent Pedergnana, Sara sebnem Kilic, Emmanuelle Jouanguy, Aurélie Cobat, Didier Raoult, Melike Emiroglu, CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), The Wellcome Trust Centre for Human Genetics [Oxford], University of Oxford [Oxford], St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller University [New York], New York Genome Center [New York], New York Genome Center, Hôpital militaire d'instruction Mohammed V [Rabat, Maroc], CHU Ibn Rochd [Casablanca], Université Hassan II [Casablanca] (UH2MC), Howard Hughes Medical Institute [New York] (HHMI), Howard Hughes Medical Institute (HHMI)-New York University School of Medicine, NYU System (NYU)-NYU System (NYU)-Rockefeller University [New York]-Columbia University Irving Medical Center (CUIMC), and Exome/Array Consortium: Waleed Al-Herz, Cigdem Arikan, Peter Arkwright, Cigdem Aydogmus, Olivier Bernard, Lizbeth Blancas-Galicia, Stéphanie Boisson-Dupuis, Damien Bonnet, Omar Boudghene Stambouli, Lobna Boussofara, Jeannette Boutros, Jacinta Bustamante, Michael Ciancanelli, Theresa Cole, Antonio Condino-Neto, Mukesh Desai, Claire Fieschi, José Luis Franco, Philippe Ichai, Emmanuelle Jouanguy, Melike Keser-Emiroglu, Sara S Kilic, Seyed Alireza Mahdaviani, Nizar Mahlhoui, Davood Mansouri, Nima Parvaneh, Capucine Picard, Anne Puel, Didier Raoult, Nima Rezaei, Ozden Sanal, Silvia Sanchez Ramon, François Vandenesch, Guillaume Vogt, Shen-Ying Zhang

Subjects
0301 basic medicine, Male, Genetic Linkage, [SDV]Life Sciences [q-bio], Population, MESH: Genetic Linkage, Genome-wide association study, Runs of Homozygosity, Biology, genotyping array, 03 medical and health sciences, Consanguinity, Middle East, 0302 clinical medicine, Humans, linkage analysis, education, Exome sequencing, MESH: Consanguinity, Linkage (software), Genetics, education.field_of_study, MESH: Humans, Multidisciplinary, Homozygote, population structure, Biological Sciences, Disease gene identification, MESH: Male, MESH: North America, Minor allele frequency, 030104 developmental biology, homozygosity mapping, MESH: Middle East, MESH: Genome-Wide Association Study, North America, Female, exome sequencing, MESH: Female, Inbreeding, 030217 neurology & neurosurgery, MESH: Homozygote, Genome-Wide Association Study
Abstract

International audience; Significance We compared the information provided by whole-exome sequencing (WES) and genome-wide single-nucleotide variant arrays in terms of principal component analysis, homozygosity rate estimation, and linkage analysis using 110 subjects originating from different regions of the world. WES provided an accurate prediction of population substructure using high-quality variants with a minor allele frequency > 2% and reliable estimation of homozygosity rates using runs of homozygosity. Finally, homozygosity mapping in 15 consanguineous families showed that WES led to powerful linkage analyses, particularly in coding regions. Overall, our study shows that WES could be used for several analyses that are very helpful to optimize the search for disease-causing exome variants. AbstractPrincipal component analysis (PCA), homozygosity rate estimations, and linkage studies in humans are classically conducted through genome-wide single-nucleotide variant arrays (GWSA). We compared whole-exome sequencing (WES) and GWSA for this purpose. We analyzed 110 subjects originating from different regions of the world, including North Africa and the Middle East, which are poorly covered by public databases and have high consanguinity rates. We tested and applied a number of quality control (QC) filters. Compared with GWSA, we found that WES provided an accurate prediction of population substructure using variants with a minor allele frequency > 2% (correlation = 0.89 with the PCA coordinates obtained by GWSA). WES also yielded highly reliable estimates of homozygosity rates using runs of homozygosity with a 1,000-kb window (correlation = 0.94 with the estimates provided by GWSA). Finally, homozygosity mapping analyses in 15 families including a single offspring with high homozygosity rates showed that WES provided 51% less genome-wide linkage information than GWSA overall but 97% more information for the coding regions. At the genome-wide scale, 76.3% of linked regions were found by both GWSA and WES, 17.7% were found by GWSA only, and 6.0% were found by WES only. For coding regions, the corresponding percentages were 83.5%, 7.4%, and 9.1%, respectively. With appropriate QC filters, WES can be used for PCA and adjustment for population substructure, estimating homozygosity rates in individuals, and powerful linkage analyses, particularly in coding regions.

Published
2016
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