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2. Evaluation of conventional and molecular strategies for the rapid diagnosis and molecular characterisation of strains of Mycobacterium tuberculosis

Author

Gilpin, C. M.

Subjects
616, R Medicine (General), QH301 Biology, Health and Wellbeing
Abstract

Laboratory diagnosis of tuberculosis is often difficult and time consuming. This study has evaluated some new strategies for improved isolation and detection of Mycobacterium tuberculosis in clinical specimens. This work was conducted over several years examining samples from the a high tuberculosis prevalence population in Jeddah, Saudi Arabia and in the low tuberculosis prevalence setting in Queensland, Australia. Commercial nucleic acid amplification technologies were evaluated and compared with in-house real-time quantitative PCR strategies for both pulmonary and extrapulmonary specimens and for paraffin embedded tissue samples. The study examined strategies for the detection of multidrug resistance strains through the use of Lipa assay to detect mutations in the rpoB gene. Variable numbers of tandem DNA repeat (VNTR) typing was applied to samples from Saudi Arabia and Queensland, Australia to assess their discriminatory power and to demonstrate the diversity and uniqueness of strains of M. tuberculosis in distinct geographical regions. A combination of VNTR typing targeting six ETR loci and an additional three polymorphic MIRU loci was applied to a strains of MTB to enhance discrimination of strains. The results demonstrated that culture remains the "gold standard" for diagnosis and that a liquid culture system is essential for timely isolation of mycobacteria. Direct nucleic acid techniques are valuable diagnostic tools in samples where AFBs can be demonstrated but have markedly reduced sensitivity in AFB smear negative MTB culture positive samples. A combination of VNTR and MIRU typing provides excellent discrimination of strains of Mycobacterium tuberculosis. This stable typing strategy relies on PCR which allows for real-time epidemiology of transmission to be monitored.

Published
2003

14. Survival Benefit for Individuals With Constitutional Mismatch Repair Deficiency Undergoing Surveillance

Author

Durno, C, Ercan, AB, Bianchi, V, Edwards, M, Aronson, M, Galati, M, Atenafu, EG, Abebe-Campino, G, Al-Battashi, A, Alharbi, M, Azad, VF, Baris, HN, Basel, D, Bedgood, R, Bendel, A, Ben-Shachar, S, Blumenthal, DT, Blundell, M, Bornhorst, M, Bronsema, A, Cairney, E, Rhode, S, Caspi, S, Chamdin, A, Chiaravalli, S, Constantini, S, Crooks, B, Das, A, Dvir, R, Farah, R, Foulkes, WD, Frenkel, Z, Gallinger, B, Gardner, S, Gass, D, Ghalibafian, M, Gilpin, C, Goldberg, Y, Goudie, C, Hamid, SA, Hampel, H, Hansford, JR, Harlos, C, Hijiya, N, Hsu, S, Kamihara, J, Kebudi, R, Knipstein, J, Koschmann, C, Kratz, C, Larouche, V, Lassaletta, A, Lindhorst, S, Ling, SC, Link, MP, De Mola, RL, Luiten, R, Lurye, M, Maciaszek, JL, MagimairajanIssai, V, Maher, OM, Massimino, M, McGee, RB, Mushtaq, N, Mason, G, Newmark, M, Nicholas, G, Nichols, KE, Nicolaides, T, Opocher, E, Osborn, M, Oshrine, B, Pearlman, R, Pettee, D, Rapp, J, Rashid, M, Reddy, A, Reichman, L, Remke, M, Robbins, G, Roy, S, Sabel, M, Samuel, D, Scheers, I, Schneider, KW, Sen, S, Stearns, D, Sumerauer, D, Swallow, C, Taylor, L, Thomas, G, Toledano, H, Tomboc, P, Van Damme, A, Winer, I, Yalon, M, Yen, LY, Zapotocky, M, Zelcer, S, Ziegler, DS, Zimmermann, S, Hawkins, C, Malkin, D, Bouffet, E, Villani, A, Tabori, U, Durno, C, Ercan, AB, Bianchi, V, Edwards, M, Aronson, M, Galati, M, Atenafu, EG, Abebe-Campino, G, Al-Battashi, A, Alharbi, M, Azad, VF, Baris, HN, Basel, D, Bedgood, R, Bendel, A, Ben-Shachar, S, Blumenthal, DT, Blundell, M, Bornhorst, M, Bronsema, A, Cairney, E, Rhode, S, Caspi, S, Chamdin, A, Chiaravalli, S, Constantini, S, Crooks, B, Das, A, Dvir, R, Farah, R, Foulkes, WD, Frenkel, Z, Gallinger, B, Gardner, S, Gass, D, Ghalibafian, M, Gilpin, C, Goldberg, Y, Goudie, C, Hamid, SA, Hampel, H, Hansford, JR, Harlos, C, Hijiya, N, Hsu, S, Kamihara, J, Kebudi, R, Knipstein, J, Koschmann, C, Kratz, C, Larouche, V, Lassaletta, A, Lindhorst, S, Ling, SC, Link, MP, De Mola, RL, Luiten, R, Lurye, M, Maciaszek, JL, MagimairajanIssai, V, Maher, OM, Massimino, M, McGee, RB, Mushtaq, N, Mason, G, Newmark, M, Nicholas, G, Nichols, KE, Nicolaides, T, Opocher, E, Osborn, M, Oshrine, B, Pearlman, R, Pettee, D, Rapp, J, Rashid, M, Reddy, A, Reichman, L, Remke, M, Robbins, G, Roy, S, Sabel, M, Samuel, D, Scheers, I, Schneider, KW, Sen, S, Stearns, D, Sumerauer, D, Swallow, C, Taylor, L, Thomas, G, Toledano, H, Tomboc, P, Van Damme, A, Winer, I, Yalon, M, Yen, LY, Zapotocky, M, Zelcer, S, Ziegler, DS, Zimmermann, S, Hawkins, C, Malkin, D, Bouffet, E, Villani, A, and Tabori, U

Abstract

PURPOSE: Constitutional mismatch repair deficiency syndrome (CMMRD) is a lethal cancer predisposition syndrome characterized by early-onset synchronous and metachronous multiorgan tumors. We designed a surveillance protocol for early tumor detection in these individuals. PATIENTS AND METHODS: Data were collected from patients with confirmed CMMRD who were registered in the International Replication Repair Deficiency Consortium. Tumor spectrum, efficacy of the surveillance protocol, and malignant transformation of low-grade lesions were examined for the entire cohort. Survival outcomes were analyzed for patients followed prospectively from the time of surveillance implementation. RESULTS: A total of 193 malignant tumors in 110 patients were identified. Median age of first cancer diagnosis was 9.2 years (range: 1.7-39.5 years). For patients undergoing surveillance, all GI and other solid tumors, and 75% of brain cancers were detected asymptomatically. By contrast, only 16% of hematologic malignancies were detected asymptomatically (P < .001). Eighty-nine patients were followed prospectively and used for survival analysis. Five-year overall survival (OS) was 90% (95% CI, 78.6 to 100) and 50% (95% CI, 39.2 to 63.7) when cancer was detected asymptomatically and symptomatically, respectively (P = .001). Patient outcome measured by adherence to the surveillance protocol revealed 4-year OS of 79% (95% CI, 54.8 to 90.9) for patients undergoing full surveillance, 55% (95% CI, 28.5 to 74.5) for partial surveillance, and 15% (95% CI, 5.2 to 28.8) for those not under surveillance (P < .0001). Of the 64 low-grade tumors detected, the cumulative likelihood of transformation from low-to high-grade was 81% for GI cancers within 8 years and 100% for gliomas in 6 years. CONCLUSION: Surveillance and early cancer detection are associated with improved OS for individuals with CMMRD.

Published
2021

18. Germline E-cadherin mutations in hereditary diffuse gastric cancer: assessment of 42 new families and review of genetic screening criteria

Author

Brooks-Wilson, A R, Kaurah, P, Suriano, G, Leach, S, Senz, J, Grehan, N, Butterfield, Y S N, Jeyes, J, Schinas, J, Bacani, J, Kelsey, M, Ferreira, P, MacGillivray, B, MacLeod, P, Micek, M, Ford, J, Foulkes, W, Australie, K, Greenberg, C, LaPointe, M, Gilpin, C, Nikkel, S, Gilchrist, D, Hughes, R, Jackson, C E, Monaghan, K G, Oliveira, M J, Seruca, R, Gallinger, S, Caldas, C, and Huntsman, D

Published
2004

25. 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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26. Worldwide Emergence of Extensively Drug-resistant Tuberculosis

Author

Shah, NS, Wright, A, Bai, GH, Barrera, L, Boulahbal, F, Martín-Casabona, N, Drobniewski, F, Gilpin, C, Havelková, M, Lepe, R, Lumb, R, Metchock, B, Portaels, F, Rodrigues, MF, Rüsch-Gerdes, S, Van Deun, A, Vincent, V, Laserson, K, Wells, C, and Cegielski, JP

Subjects
Microbiology (medical), medicine.medical_specialty, Tuberculosis, Epidemiology, Bacterial diseases, Population, multidrug-resistant, Antitubercular Agents, lcsh:Medicine, Drug resistance, Multidrug resistance, Pharmacology, Global Health, infectious diseases, lcsh:Infectious and parasitic diseases, Mycobacterium tuberculosis, Internal medicine, Tuberculosis, Multidrug-Resistant, Global health, Medicine, Humans, lcsh:RC109-216, education, second-line drugs, education.field_of_study, biology, business.industry, Public health, Research, emerging, lcsh:R, Extensively drug-resistant tuberculosis, Global, medicine.disease, biology.organism_classification, Multiple drug resistance, First-line drugs, tuberculosis, Communicable Disease Control, business, Laboratories, Sentinel Surveillance
Abstract

Mycobacterium tuberculosis strains are becoming resistant to not only the most powerful first-line drugs but also many second-line drugs., Mycobacterium tuberculosis strains that are resistant to an increasing number of second-line drugs used to treat multidrug-resistant tuberculosis (MDR-TB) are becoming a threat to public health worldwide. We surveyed the Network of Supranational Reference Laboratories for M. tuberculosis isolates that were resistant to second-line anti-TB drugs during 2000–2004. We defined extensively drug-resistant TB (XDR-TB) as MDR-TB with further resistance to ≥3 of the 6 classes of second-line drugs. Of 23 eligible laboratories, 14 (61%) contributed data on 17,690 isolates, which reflected drug susceptibility results from 48 countries. Of 3,520 (19.9%) MDR-TB isolates, 347 (9.9%) met criteria for XDR-TB. Further investigation of population-based trends and expanded efforts to prevent drug resistance and effectively treat patients with MDR-TB are crucial for protection of public health and control of TB.

Published
2007

27. Germline and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type

Author

Witkowski, L. Carrot-Zhang, J. Albrecht, S. Fahiminiya, S. Hamel, N. Tomiak, E. Grynspan, D. Saloustros, E. Nadaf, J. Rivera, B. Gilpin, C. Castellsagué, E. Silva-Smith, R. Plourde, F. Wu, M. Saskin, A. Arseneault, M. Karabakhtsian, R.G. Reilly, E.A. Ueland, F.R. Margiolaki, A. Pavlakis, K. Castellino, S.M. Lamovec, J. Mackay, H.J. Roth, L.M. Ulbright, T.M. Bender, T.A. Georgoulias, V. Longy, M. Berchuck, A. Tischkowitz, M. Nagel, I. Siebert, R. Stewart, C.J.R. Arseneau, J. McCluggage, W.G. Clarke, B.A. Riazalhosseini, Y. Hasselblatt, M. Majewski, J. Foulkes, W.D.

Abstract

Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is the most common undifferentiated ovarian malignancy in women under 40 years of age. We sequenced the exomes of six individuals from three families with SCCOHT. After discovering segregating deleterious germline mutations in SMARCA4 in all three families, we tested DNA from a fourth affected family, which also carried a segregating SMARCA4 germline mutation. All the familial tumors sequenced harbored either a somatic mutation or loss of the wild-type allele. Immunohistochemical analysis of these cases and additional familial and non-familial cases showed loss of SMARCA4 (BRG1) protein in 38 of 40 tumors overall. Sequencing of cases with available DNA identified at least one germline or somatic deleterious SMARCA4 mutation in 30 of 32 cases. Additionally, the SCCOHT cell line BIN-67 had biallelic deleterious mutations in SMARCA4. Our findings identify alterations in SMARCA4 as the major cause of SCCOHT, which could lead to improvements in genetic counseling and new treatment approaches. © 2014 Nature America, Inc. All rights reserved.

Published
2014

30. Emergence of mycobacterium tuberculosis with extensive resistance to second-line drugs--worldwide, 2000-2004

Author

Wright, A., Bai, G., Barrera, L., Boulahbal, F., Martin-Casabona, N., Gilpin, C., Drobniewski, F., Havelkova, M., Lepe, R., Lumb, R., Metchock, B., Portaels, F., Rodrigues, M., Rusch-Gerdes, S., Van Deun, A., Vincent, V., Leimane, V., Riekstina, V., Skenders, G., Holtz, T., Pratt, R., Laserson, K., Wells, C., Cegielski, P., and Shah, N.S.

Subjects
Tuberculosis -- Causes of, Tuberculosis -- Risk factors, Tuberculosis -- Reports
Abstract

During the 1990s, multidrug-resistant (MDR) tuberculosis (TB), defined as resistance to at least isoniazid and rifampin, emerged as a threat to TB control, both in the United States (1) and [...]

Published
2006

34. Infections of the subcutis and skin of dogs caused by rapidly growing mycobacteria

Author

Malik, R., Shaw, S.E., Griffin, C., Stanley, B., Burrows, A.K., Bryden, S.L., Titmarsh, J., Stutsel, M-J., Carter, S-A., Warner, A., Martin, P., Wigney, D.I., Gilpin, C., Malik, R., Shaw, S.E., Griffin, C., Stanley, B., Burrows, A.K., Bryden, S.L., Titmarsh, J., Stutsel, M-J., Carter, S-A., Warner, A., Martin, P., Wigney, D.I., and Gilpin, C.

Abstract

Nine dogs with panniculitis due to rapidly growing mycobacteria (RGM) were examined over 17 years. Dogs were two to 15 years; five were male, four were female. All were obese or in good condition. Antecedent injury, typically a dog bite or vehicular trauma, could be identified in some patients, while one bitch had hyperadrenocorticism. Infections involved different locations, although the cervicothoracic region, dorsum or flank were most often affected. Patients were systemically well, apart from one dog with pyrexia and two with pain or lameness. Cytology demonstrated pyogranulomatous inflammation, but in only one case was it possible to see acid‐fast bacilli (AFB) in smears. Histology demonstrated chronic active pyogranulomatous panniculitis and dermatitis; AFB could be detected in only four specimens. Culture of aspirates or resected tissues demonstrated RGM in all cases, comprising six Mycobacterium smegmatis group and three Mycobacterium fortuitum group isolates. Resection of infected tissues, perioperative injectable antimicrobials and long courses of oral antimicrobials chosen according to susceptibility data generally effected a cure, although some cases recurred.

Published
2004

37. A cluster of tuberculosis associated with use of a marijuana water pipe

Author

Munckhof, W.J., Konstantinos, A., Wamsley, M., Mortlock, M., Gilpin, C., Munckhof, W.J., Konstantinos, A., Wamsley, M., Mortlock, M., and Gilpin, C.

Abstract

SETTING: New cases of pulmonary tuberculosis (TB) were noted in a cluster of young Caucasian males, an unusual ethnic group for this disease in Queensland, Australia. It was noted that marijuana water pipe ('bong') smoking was common amongst cases and contacts. OBJECTIVE: To report this cluster of TB and to investigate whether shared use of a marijuana water pipe was associated with transmission of TB. DESIGN: All contacts were identified and screened according to standard protocols. Cases were asked to list contacts with whom they had shared a marijuana water pipe. RESULTS: Five cases of open pulmonary TB were identified clinically and on sputum culture, and all isolates of Mycobacterium tuberculosis were identical on typing. Of 149 contacts identified, 114 (77%) completed screening, and 57 (50%) had significant tuberculin skin test (TST) reactions on follow-up. Of 45 contacts who had shared a marijuana water pipe with a case, 29 (64%) had a significant TST reaction. CONCLUSION: Sharing a marijuana water pipe with a case of pulmonary TB was associated with transmission of TB (OR 2.22, 95% CI 0.96-5.17), although the most important risk factor for acquiring TB infection in this cluster was close household contact with a case (OR 4.91, 95% CI 1.13-20.70).

Published
2003

38. X-Ray Microanalysis with the Environmental Scanning Electron Microscope: Interpretation of Data Obtained Under Different Atmospheric Conditions

Author

Sigee, D. C. and Gilpin, C.

Subjects
Blue-green algae, X-ray microanalysis, ESEM, Biology, Environmental scanning electron microscopy
Abstract

X-ray microanalysis of non-biological and biological specimens was carried out in an environmental scanning electron microscope (ESEM) over a range of atmospheric conditions. Introduction of water vapour into the specimen chamber lead to direct X-ray contribution from oxygen atoms, an increase in extraneous background (causing reduced P/B ratios of other elements), X-ray absorption (also reducing P/B ratios) and broadening (skirting) of the electron beam. Similar results were obtained after introduction of an argon atmosphere. These effects were reduced under conditions of minimal chamber atmospheric pressure and maximal accelerating voltage. Because of beam skirting, quantitative X-ray microanalysis of biological specimens in a water vapour atmosphere was only valid where the sample was spread over a wide area (leading to mean elemental values for the whole preparation). Unless appropriate correction factors or changes in instrumentation can be implemented, quantitative analysis of wet specimens in ESEM cannot be applied to discrete specimens or to limited areas within a mixed sample.

Published
1994

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