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6. P003 Implementation of High Throughput Parallel Sequencing in a Diagnostic Setting: Multiplexed Amplicon Sequencing of the Breast Cancer Genes BRCA1 and 2

Author

Zogopoulos G, Tomi Pastinen, Sivanandan K, Vaca F, Kinoshita T, Johannes B, Leguis E, Jansen-van der Weide M, Learn L, Godlewski D, Ed Saunders, Montserrat Rué, Vaisman A, de Bock G, Ángel Segura, Sabbaghian N, Mohammad Amin Kerachian, Pelletier S, Metcalfe K, Lilge L, Stockle E, Cheng S, Burger C, Woike A, Michelle Guy, Ragone A, Y. J. Bignon, Bronkhorst Y, Patricia N. Tonin, Lima M, Mieke Kriege, Karsan A, Zweemer R, Prady C, Beattie M, Panchal S, Kathleen Claes, van Zon P, Diane Provencher, Ummels A, Kang I, Shumak R, Arcusa Â, Yosr Hamdi, Alonso Mc, Dolman L, Houssami N, Olivier Delattre, Yannick Bidet, Claude Houdayer, Mercedes Durán, Ganschow P, Isabel Chirivella, Domingo S, Rebsamen M, Giustina Simone, Orland Diez, Chapman J, An tSaoir C, Jeanna McCuaig, Blayney J, Bosdet I, Treacy R, Esther Darder, Ando J, Luc Dehaspe, García-Casado Z, Duffy J, Harkin D, Z Kote-Jarai, Kasamatsu T, Ulf Kristoffersson, Membrez, Priston M, Noreau-Heisz D, Trivedi A, Begoña Graña, Ghadirian P, Ashuryk O, Consol López, Wenzel L, Vogel R, Joseph G, Poll A, Kennedy R, Patton S, Pérez C, Mónica Cornet, Panighetti A, Cassart P, Burke K, Mes-Masson A, Llacuachaqui M, Marc Tischkowitz, Wong N, Arcand S, Kotsopoulos J, Meschino W, Hall A, Marles S, Docking R, Haroun I, Marie Plante, Rachel Laframboise, Daniel Sinnett, Luce J, Sekiguchi I, Edenir Inêz Palmero, de Winter J, Christopher J. Lord, Hamel N, Pruski-Clark J, Lee D, Rusnak A, Carson N, Marta Santamariña, Knoppers B, Oakhill K, Bruce R. Rosen, Pierre O. Chappuis, Bruce Poppe, Stanislaw C, Catts Z, Brood M, van der Wall E, Yip C, Christine Walsh, Hoodfar E, Pressman A, Andrulis I, Alicia Barroso, D. Leongamornlert, Gillian Mitchell, Akira Hirasawa, Shen Z, Sameer Parpia, Horgan M, van Echtelt J, Chun K, Lubinski J, Rebecca Sutphen, Terespolsky D, Richard D, McDyer F, Floquet A, Lambo R, Bathurst L, Brown G, Kidd M, Nicolas Sevenet, Mourits M, Vencken P, Tatiana Popova, Garcia N, Armel S, van Amstel H, Valentini A, Ellen Warner, Hofland N, Hanna D, Kim J, Osann K, Enmore M, Loranger K, Sulivan I, J. Oliveira, Meijers H, Jansen R, Edmundo Carvalho Mauad, Kirkpatrick R, Danilo V Viana, Ian G. Campbell, Mil S, E J Sawyer, J. Balmaña, Samra Turajlic, Graham G, Alonso C, Inanc Birol, Sinclair F, van Tuil M, Pascual Bolufer, Micheli R, Andrew R. Green, Junyent N, Whittaker J, Monnerat C, Rhéaume J, Livingston D, Chan S, L. Ramadan, Lee R, Katarzyna Durda, De Leeneer K, Grados C, Côté C, Kyle B. Matchett, Robert Winqvist, Bonner D, Brunella Pilato, Mohd Taib N, Judy Garber, Kleiderman E, Murakami S, Sharifi N, Kimberley Hill, Desbiens C, Robert Royer, Jasperson K, Hsieh S, De Summa S, Dominique Stoppa-Lyonnet, de Lima J, Stuart McIntosh, Shakeri M, Wendy Kohlmann, Albert-Green A, de Hullu J, Pasick R, Avard D, Pathania S, van der Groep P, Laura Fachal, Bruno Zeitouni, Susan M. Domchek, Davey S, Richard Marais, Powell C, Hans J. J. P. Gille, Greenberg R, Kamata H, Cina, Gaarenstroom K, Lakhal Chaieb M, Kavanagh L, Gaelle Benais-Pont, Sun P, Jansen L, Matthew Parker, Barjhoux L, Russ H, Simon J. Furney, Willems A, Robb L, David E. Goldgar, Young S, Natalia Campacci, Mark G. Thomas, Doug Easton, Klugman S, Barrault M, Calvo N, Adriana C. Flora, Littell R, Narod S, Fragoso, N. Bosch, Finch A, Paul M. Wilkerson, Teo S, Tomasz Huzarski, Manuel Salto-Tellez, Moseley M, Davis S, Olga M. Sinilnikova, Iturbe A, Joan Brunet, Tierney M, Tsai E, Navarro de Souza A, Leclerc M, Lorenzo Manti, Gutiérrez-Enríquez S, Milewski B, Simon S. McDade, Kaplan C, Buckley N, Eva Esteban-Cardeñosa, Richter S, Shimizu C, Li J, Elena Castro, Iwanka Kozarewa, Harley I, Atocha Romero, Carlos E. Andrade, Carole Verny-Pierre, Barouk E, Vian D, Montserrat Baiget, Chan J, Sandra Bonache, Andrew Y Shuen, van der Merwe N, Kaklewski K, Mohar A, Tamura C, Heale E, Rooyadeh M, van Asperen C, Gemma Llort, Alan Mackay, Denroche R, Seelaus C, Zbuk K, McCluggage W, van der Luijt R, Maaike P.G. Vreeswijk, Edelweiss M, Crossan G, Arseneau J, Ambus I, Verheul H, Rodrigo Augusto Depieri Michelli, Juul T. Wijnen, Gross-Lester J, Britta Weigelt, Pedro Pérez-Segura, Richard A. Moore, Cornelissen C, Larouche G, McAlpine J, Daniel Nava Rodrigues, Trim L, Furnival J, Elser C, Muszyńka M, Adriana Lasa, Tuya Pal, Greuter. M, Ng K, Dorval M, Bresee C, Reimnitz G, Gaëtan MacGrogan, Perry Maxwell, Barnadas A, Hwang E, Powell B, Knapke S, Griskevicius. L, Alvarez R, Mester J, Anne-Bine Skytte, Eladio Velasco, Vidal S, Australie K, Leunen K, Ben-Yishay M, Van Houdt J, Phuah S, Amy E Taylor, Pinto R, Fonseca T, Champine M, Gammon A, Hollema H, Menko F, Feng B, David Olmos, Chong G, Tomasz Byrski, Patrick J. Morrison, Gregoire J, André Lopes Carvalho, Don B. Plewes, Rabeneck L, Carrol J, Alan Ashworth, Terlinge A, A Jakubowska, Odette Mariani, Setareh Moghadasi, Reitsma W, Rothenmund H, Herrera L, Anna Tenés, Angel Izquierdo, Asunción Torres, Stawicka M, Goh C, Hirst M, Drummond J, Osorio A, Ostrovsky R, Jeffrey N. Weitzel, Gareth W. Irwin, Fehniger J, Sugano K, Spriggs E, Dęniak T, Volenik A, Thorne H, Piccinin C, Amie Blanco, Jinno H, Robert A. Holt, Stephen B. Fox, Julia J. Gorski, Gilpin C, Herschorn S, Vega A, E. Page, Hamet P, McKenna D, Fabrice Bonnet, Yoshida T, Kienan I. Savage, Petzel S, Elizabeth Bancroft, Schneider S, Warwick L, Stewart S, William D. Foulkes, Colizza K, Bell K, Demsky R, Malgorzata Tymrakiewicz, Caldés T, Fons G, Bowen D, Côté S, Clouston D, Kitagawa Y, Gordon Glendon, Jenny Lester, Kinney A, Nelson E, Silke Hollants, Macrae L, Cajal T, Andrew J. Mungall, Ferrell B, Creighton B, Bressler L, Uy P, Makishima K, Haffaf Z, Ramūnas Janavičius, Einstein G, Zakalik D, Chiarelli A, Cantu D, Croce S, Kalloger S, Lin F, Ian O. Ellis, Benedito Mauro Rossi, R A Wilkinson, Mulligan J, Murphy J, Vadaparampil S, Smith E, Slangen B, Loiselle C, Iqbal J, Palma L, Cooper K, Jorge S. Reis-Filho, Chen. L, Quinten Waisfisz, Haneda E, Banks P, Vermeulen K, Visser B, Montalbán G, McCabe N, Honeyford J, Naseri S, Ng J, Ali A, Sandrine Viala, Mensa I, Kamarainen O, Guerra C, Mazzola E, David A. Schwartz, Marjanka K. Schmidt, Simon R, Fergus J. Couch, Margreet G. E. M. Ausems, Anne Vincent-Salomon, Olinski R, Zewald R, Moreno R, Semple J, McPherson J, Lamers E, Kharbanda A, Kessler L, Biemans D, Au A, Bordeleau L, Jean Feunteun, Mar Infante, Mullan P, Rudaitis, Molenda A, Rachael Natrajan, Pawar, Boman B, Kok T, Andrew A. Brown, Geller M, Monfared N, Bart J, Murata P, Crawford N, Butterfield Y, Bargalló J, Katherine L. Tucker, Cook-Wiens G, Rhodes A, Elodie Manié, Rubio E, Oram L, Shandiz F, Hayden R, Crawford B, Parmigiani G, Harkin P, Müller C, Grant M, Maryou B. Lambros, Thong M, Grzegorz Sukiennicki, Wouts J, Haddock P, Ramon y Cajal T, Kenneth C. Anderson, Michel Longy, Batiste W, Carroll J, Matte C, Hojyo T, Zhao Y, Caroline Seynaeve, Wai P, Simard J, Hurley K, Bolton D, Karlan B, Javier Benítez, Miriam Masas, Tołczko-Grabarek A, de Dueñas E, Geneviève Michils, Moncoutier, Nancy Uhrhammer, MacDonald D, Keyserlingk J, Osher D, Gilks C, Christopher T. Elliott, Scharf L, Gabram-Mendola S, Grondin K, Dohany L, van Diest P, Joris Vermeesch, Jan C. Oosterwijk, M’Baïlara K, DePuit M, Jacek Gronwald, Stefania Tommasi, de la Hoya M, Bouchard K, Black L, Lui M, Soucy P, Rosalind A. Eeles, Gert Matthijs, Graham T, Andrea Eisen, Bacha O, Alvaro N.A. Monteiro, Yoon S, Caron T, Smith D, Marc-Henri Stern, Hampson E, Kurz R, Gaasbeek W, Mundt E, Angela Velasco, Quinn J, Jocelyne Chiquette, Marquez T, Adam B. Murphy, Bakker J, Neus Gadea, Anita Grigoriadis, Aoki D, Dean S, Looi L, Paradiso A, Agostina Stradella, K. Govindasami, Lovell N, Eva Tomiak, Siesling S, Belanger M, Feilotter H, Knight J, Emmanuel Barillot, Huang M, Raquel Andrés, Kang P, Somerman C, Gackowski D, Rimel B, Nakamura S, McClellan K, Barrros E, Henriette Roed Nielsen, Rui Manuel Reis, Greening S, Ayme A, Carmen Guillen, de Vries E, and Katarzyna Jaworska

Subjects
Oncology, Education and Communication, medicine.medical_specialty, endocrine system diseases, medicine.diagnostic_test, business.industry, Psycho-Oncology, medicine.disease, Meeting Abstracts, Transcriptome, Basic Research, Clinical Management, Germline mutation, Breast cancer, Applied Research, Internal medicine, Mutation (genetic algorithm), medicine, Genetic Counselling, Human genome, skin and connective tissue diseases, business, Ovarian cancer, Comparative genomic hybridization, Fluorescence in situ hybridization
Abstract

Background: Germline mutation screening of BRCA1 and BRCA2 genes is performed in suspected familial breast cancer cases, but a causative mutation is found in only 30% of patients. The development of additional methods to identify good candidates for BRCA1 and BRCA2 analysis would therefore increase the efficacy of diagnostic mutation screening. With this in mind, we developed a study to determine molecular signatures of BRCA1—or BRCA2—mutated breast cancers. Materials and Methods: Array-cgh (comparative genomic hybridization) and transcriptomic analysis were performed on a series of 103 familial breast cancers. The series included 7 breast cancers with a BRCA1 mutation and 5 breast cancers with a BRCA2 mutation. The remaining 91 cases were obtained from 73 families selected on the basis of at least 3 affected first-degree relatives or at least 2 affected first-degree relatives with breast cancer at an average age of 45 years. Array-cgh analyses were performed on a 4407 BAC-array (CIT-V8) manufactured by IntegraGen. Transcriptomic analyses were performed using an Affymetrix Human Genome U133 Plus 2.0 chip. Results: Using supervised clustering analyses we identified two transcriptomic signatures: one for BRCA1-mutated breast cancers consisting of 600 probe sets and another for BRCA2-mutated breast cancers also consisting of 600 probes sets. We also defined cgh-array signatures, based on the presence of specific genomic rearrangements, one for BRCA1-mutated breast cancers and one for BRCA2-mutated breast cancers. Conclusions: This study identified molecular signatures of breast cancers with BRCA1 or BRCA2 germline mutations. Genes present in these signatures could be exploited to find new markers for such breast cancers. We also identified specific genomic rearrangements in these breast cancers, which could be screened for in a diagnostic setting using fluorescence in situ hybridization, thus improving patient selection for BRCA1 and BRCA2 molecular genetic analysis.

Published
2009
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9. Diversity of Molecular Phenotypes in Acute Leukemias

Author

Mizutani, S., Nakamura, K., Ozaki, M., Tamura, C., Sasaki, M., Tsunematsu, Y., Fujimoto, J., Hata, J., Kobayashi, N., Neth, Rolf, editor, Gallo, Robert C., editor, Greaves, Melvyn F., editor, Gaedicke, Gerhard, editor, Gohla, Sven, editor, Mannweiler, Klaus, editor, and Ritter, Jörg, editor

Published
1989
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11. A causal relationship between Bordetella pertussis and Bordetella parapertussis infections

Author

H Kawai, Tamura C, Murase Y, A Imaizumi, and Aoyama T

Subjects
Microbiology (medical), DNA, Bacterial, Bordetella pertussis, Ratón, Bordetella, medicine.disease_cause, Polymerase Chain Reaction, Bordetella parapertussis, Microbiology, Mice, Pregnancy, medicine, Animals, Colonization, Virulence Factors, Bordetella, Whooping cough, Pertussis Vaccine, General Immunology and Microbiology, biology, Toxin, Vaccination, Outbreak, General Medicine, biology.organism_classification, medicine.disease, Virology, Antibodies, Bacterial, Infectious Diseases, Animals, Newborn, biology.protein, Pregnancy, Animal, Female, Antibody
Abstract

Bordetella parapertussis is isolated during the late stages of pertussis outbreaks and occasionally from patients infected with pertussis. The relationship between Bordetella pertussis and B. parapertussis was investigated in mice with monoinfections and mixed infections. Four groups of 10 2-week-old suckling mice were studied: mice born to mice vaccinated against pertussis during pregnancy and unvaccinated controls consequently did and did not receive antipertussis toxin (PT) antibody transcolostrally. The mice were infected transnasally with B. parapertussis strain 422 and 2 identical groups were infected transnasally with B. parapertussis strain 422 and B. pertussis strain 18-323. Bacterial colonization of the lungs and trachea was studied at 1, 2, and 3 weeks after challenge. No persistent colonization by B. parapertussis of the lungs or trachea of monoinfected suckling mice were observed. Persistent colonization by B. parapertussis was observed when suckling mice that received anti-PT antibody transcolostrally were infected with both species. These findings are consistent with the clinical characteristics of B. parapertussis. The results of this study demonstrate that B. pertussis infection facilitates B. parapertussis infection.

Published
1996

12. Correction to “A geomagnetic record over the last 3.5 million years from deep-tow magnetic anomaly profiles across the Central Indian Ridge” by Gaud Pouliquen, Yves Gallet, Jérôme Dyment, Philippe Patriat, and Chiori Tamura

Author

Pouliquen, G, Gallet, Y, Dyment, J, Patriat, P, Tamura, C, Pouliquen, G, Gallet, Y, Dyment, J, Patriat, P, and Tamura, C

Abstract

High-resolution records of the geomagnetic field intensity over the last 3.5 Myr provided by paleomagnetic analyses of marine sediments and volcanics have shown the occurrence of short-lived low field intensity features associated with excursions or short polarity intervals. In order to evaluate the ability of marine magnetic anomalies to record the same geomagnetic events, we have collected six deep-tow (similar to500 m above the seafloor) and several sea surface magnetic anomaly profiles from the Central Indian Ridge across the Brunhes, Matuyama, and Gauss chrons (i.e., from the ridge axis to anomaly 2A). After removal of topography, latitude, and azimuth effects, we converted distances into time sequences using well-dated polarity reversal anomalies as tie points. We calculated the average signal to test the robustness of the short-wavelength anomalies. The resulting stacked profile is very similar to stacked sea surface and downward continued profiles from the Central Indian Ridge, the East Pacific Rise, and the Pacific-Antarctic Ridge. Our results suggest that in addition to polarity reversals, geomagnetic field intensity variations represent the major contributor to the detailed shape of recent marine magnetic anomalies in investigated areas. We observe a dense succession of microanomalies that are correlated to previously suggested geomagnetic events (subchrons or excursions) within the Brunhes and Matuyama chrons. A new small-scale magnetic anomaly, likely generated by several closely spaced excursions (Ontong Java 1 and 2, and Gilsa), is found after the Olduvai chron. The near-bottom results support the existence of three geomagnetic features between the Gauss-Matuyama boundary and Olduvai. They also suggest three geomagnetic events during the C2A. In subchron within the Gauss chron. This study emphasizes the potential of deep-tow magnetic surveys in detecting fluctuations in geomagnetic field intensity and, in particular, short-lived excursions, a poorly c

Published
2001
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43. ChemInform Abstract: Metacyclophanes and Related Compounds. Part 18. Preparation of anti‐ 5,14‐Di‐tert‐butyl‐8,17‐dimethyl(2.3)metacyclophan‐1‐ene and anti‐5,15‐ Di‐tert‐butyl‐8,18‐dimethyl(2.4)metacyclophan‐1‐enes with Dichlorocarbene.

Author

YAMATO, T., primary, KOBAYASHI, K., additional, ARIMURA, T., additional, TASHIRO, M., additional, YOSHIHIRA, K., additional, KAWAZOE, K., additional, SATO, S., additional, and TAMURA, C., additional

Published
1987
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