1
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Guthrie JL, Teatero S, Zittermann S, Chen Y, Sullivan A, Rilkoff H, Joshi E, Sivaraman K, de Borja R, Sundaravadanam Y, Laszloffy M, Heisler L, Allen VG, Simpson JT, Fittipaldi N. Detection of the novel SARS-CoV-2 European lineage B.1.177 in Ontario, Canada. Journal of Clinical Virology Plus 2021; 1:100010. [PMID: 35261998 PMCID: PMC8009655 DOI: 10.1016/j.jcvp.2021.100010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/01/2022] Open
Abstract
Background Travel-related dissemination of SARS-CoV-2 continues to contribute to the global pandemic. A novel SARS-CoV-2 lineage (B.1.177) reportedly arose in Spain in the summer of 2020, with subsequent spread across Europe linked to travel by infected individuals. Surveillance and monitoring through the use of whole genome sequencing (WGS) offers insights into the global and local movement of pathogens such as SARS-CoV-2 and can detect introductions of novel variants. Methods We analysed the genomes of SARS-CoV-2 sequenced for surveillance purposes from specimens received by Public Health Ontario (Sept 6 – Oct 10, 2020), collected from individuals in eastern Ontario, which comprised the study sample. Taxonomic lineages were identified using pangolin (v2.08) and phylogenetic analysis incorporated publicly available genomes covering the same time period as the study sample. Epidemiological data collected from laboratory requisitions and standard reportable disease case investigation was integrated into the analysis. Results Genomic surveillance identified a COVID-19 case with SARS-CoV-2 lineage B.1.177 from an individual in eastern Ontario in late September, 2020. The individual had recently returned from Europe. Genomic analysis with publicly available data indicate the most closely related genomes to this specimen were from Southern Europe. Genomic surveillance did not identify further cases with this lineage. Conclusions Genomic surveillance allowed for early detection of a novel SARS-CoV-2 lineage in Ontario which was deemed to be travel related. This type of genomic-based surveillance is a key tool to measure the effectiveness of public health measures such as mandatory self-isolation for returned travellers, aimed at preventing onward transmission of newly introduced lineages of SARS-CoV-2.
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Affiliation(s)
- Jennifer L Guthrie
- Public Health Ontario, 661 University Ave, Toronto, Ontario, M5G 1M1, Canada
| | - Sarah Teatero
- Public Health Ontario, 661 University Ave, Toronto, Ontario, M5G 1M1, Canada
| | - Sandra Zittermann
- Public Health Ontario, 661 University Ave, Toronto, Ontario, M5G 1M1, Canada
| | - Yao Chen
- Public Health Ontario, 661 University Ave, Toronto, Ontario, M5G 1M1, Canada
| | | | - Heather Rilkoff
- Public Health Ontario, 661 University Ave, Toronto, Ontario, M5G 1M1, Canada
| | - Esha Joshi
- Public Health Ontario, 661 University Ave, Toronto, Ontario, M5G 1M1, Canada
| | | | | | | | | | | | - Vanessa G Allen
- Public Health Ontario, 661 University Ave, Toronto, Ontario, M5G 1M1, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jared T Simpson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
| | - Nahuel Fittipaldi
- Public Health Ontario, 661 University Ave, Toronto, Ontario, M5G 1M1, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
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2
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Vladoiu MC, El-Hamamy I, Donovan LK, Farooq H, Holgado BL, Sundaravadanam Y, Ramaswamy V, Hendrikse LD, Kumar S, Mack SC, Lee JJY, Fong V, Juraschka K, Przelicki D, Michealraj A, Skowron P, Luu B, Suzuki H, Morrissy AS, Cavalli FMG, Garzia L, Daniels C, Wu X, Qazi MA, Singh SK, Chan JA, Marra MA, Malkin D, Dirks P, Heisler L, Pugh T, Ng K, Notta F, Thompson EM, Kleinman CL, Joyner AL, Jabado N, Stein L, Taylor MD. Childhood cerebellar tumours mirror conserved fetal transcriptional programs. Nature 2019; 572:67-73. [PMID: 31043743 PMCID: PMC6675628 DOI: 10.1038/s41586-019-1158-7] [Citation(s) in RCA: 234] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 03/22/2019] [Indexed: 11/25/2022]
Abstract
Study of the origin and development of cerebellar tumours has been hampered by the complexity and heterogeneity of cerebellar cells that change over the course of development. Here we use single-cell transcriptomics to study more than 60,000 cells from the developing mouse cerebellum and show that different molecular subgroups of childhood cerebellar tumours mirror the transcription of cells from distinct, temporally restricted cerebellar lineages. The Sonic Hedgehog medulloblastoma subgroup transcriptionally mirrors the granule cell hierarchy as expected, while group 3 medulloblastoma resembles Nestin+ stem cells, group 4 medulloblastoma resembles unipolar brush cells, and PFA/PFB ependymoma and cerebellar pilocytic astrocytoma resemble the prenatal gliogenic progenitor cells. Furthermore, single-cell transcriptomics of human childhood cerebellar tumours demonstrates that many bulk tumours contain a mixed population of cells with divergent differentiation. Our data highlight cerebellar tumours as a disorder of early brain development and provide a proximate explanation for the peak incidence of cerebellar tumours in early childhood.
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Affiliation(s)
- Maria C Vladoiu
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Ibrahim El-Hamamy
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Laura K Donovan
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hamza Farooq
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Borja L Holgado
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yogi Sundaravadanam
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vijay Ramaswamy
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Haematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Liam D Hendrikse
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Sachin Kumar
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Stephen C Mack
- Brain Tumor Program, Children's Cancer Center and Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - John J Y Lee
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Vernon Fong
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kyle Juraschka
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - David Przelicki
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Antony Michealraj
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Patryk Skowron
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Betty Luu
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hiromichi Suzuki
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - A Sorana Morrissy
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Florence M G Cavalli
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Livia Garzia
- Cancer Research Program, McGill University Health Centre Research Institute, Montreal, Quebec, Canada
| | - Craig Daniels
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xiaochong Wu
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Maleeha A Qazi
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Sheila K Singh
- Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Department of Surgery, McMaster University, Hamilton, Ontario, Canada
| | - Jennifer A Chan
- Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Peter Dirks
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lawrence Heisler
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Trevor Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Karen Ng
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Eric M Thompson
- Department of Neurosurgery, Duke University Medical Center, Durham, NC, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Research Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Alexandra L Joyner
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Nada Jabado
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada.
| | - Lincoln Stein
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.
| | - Michael D Taylor
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada.
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Surgery and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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3
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Vinayak B, Liu L, Espirritu S, Lalonde E, Yamaguchi T, Heisler L, Livingstone J, Huang V, Shiah YJ, Sabelnykova V, Yousif F, Fraser M, Chua M, Van Der Kwast T, Liu SK, Boutros PC, Bristow RG. The molecular hallmarks and clinical consequences of tumor hypoxia in prostate cancer. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.7_suppl.81] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
81 Background: Localised prostate cancers are classified into risk-groups using clinical measurements like grade and stage to inform treatment decisions. However, these groupings are imprecise: ~30% of intermediate-risk patients suffer relapse of their disease despite precision image-guided radiotherapy or radical prostatectomy. One reason for this variability in response to treatment is the underlying cellular and molecular heterogeneity of tumours. Prostate tumour cells exist within a microenvironment characterized by gradients of oxygen levels and prostate tumours with low levels of oxygen (hypoxia) have poor clinical outcomes. Methods: Hypoxia was measured using multiple mRNA-based signatures. We examined 548 patients with localised prostate cancer and statistically assessed the association of hypoxia with copy-number alterations (CNAs), single-nucleotide variants (SNVs), genomic rearrangements, focal genomic events ( i.e. kataegis, chromothripsis), telomere length, clinical indices ( i.e. grade, stage) and subclonal architecture. Results: Elevated hypoxia was associated with allelic loss of PTEN, higher rates of chromothripsis and intraductal and cribriform carcinoma (IDC-CA). To translate these findings into a biomarker for prostate cancer precision medicine, we integrated tumour microenvironmental data with genomic and pathological information to stratify patients into distinct prognostic groups. Patients with localized prostate cancer that have polyclonal tumours with elevated hypoxia, allelic loss of PTEN and IDC-CA were at the highest risk of rapid biochemical failure (P = 3.48 x10-3, Logrank test) and metastasis (P = 4.61 x 10-3, Logrank test), even after controlling for T-category, Gleason score and pre-treatment PSA. Conclusions: These data suggest that the aggressiveness of prostate cancers is driven by the interplay of the tumour microenvironment, tumour evolutionary trajectories and its genomic mutational profile.
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Affiliation(s)
| | - Lydia Liu
- Ontario Institute for Cancer Reserach, Toronto, ON, Canada
| | | | - Emilie Lalonde
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | | | | | - Vincent Huang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Fouad Yousif
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Michael Fraser
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Melvin Chua
- National Cancer Centre Singapore, Singapore, Singapore
| | | | - Stanley K. Liu
- Odette Cancer Centre, Sunnybrook Health Sciences Centre, Toronto, ON, Canada
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4
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Abelson S, Collord G, Ng SWK, Weissbrod O, Mendelson Cohen N, Niemeyer E, Barda N, Zuzarte PC, Heisler L, Sundaravadanam Y, Luben R, Hayat S, Wang TT, Zhao Z, Cirlan I, Pugh TJ, Soave D, Ng K, Latimer C, Hardy C, Raine K, Jones D, Hoult D, Britten A, McPherson JD, Johansson M, Mbabaali F, Eagles J, Miller JK, Pasternack D, Timms L, Krzyzanowski P, Awadalla P, Costa R, Segal E, Bratman SV, Beer P, Behjati S, Martincorena I, Wang JCY, Bowles KM, Quirós JR, Karakatsani A, La Vecchia C, Trichopoulou A, Salamanca-Fernández E, Huerta JM, Barricarte A, Travis RC, Tumino R, Masala G, Boeing H, Panico S, Kaaks R, Krämer A, Sieri S, Riboli E, Vineis P, Foll M, McKay J, Polidoro S, Sala N, Khaw KT, Vermeulen R, Campbell PJ, Papaemmanuil E, Minden MD, Tanay A, Balicer RD, Wareham NJ, Gerstung M, Dick JE, Brennan P, Vassiliou GS, Shlush LI. Prediction of acute myeloid leukaemia risk in healthy individuals. Nature 2018; 559:400-404. [PMID: 29988082 PMCID: PMC6485381 DOI: 10.1038/s41586-018-0317-6] [Citation(s) in RCA: 506] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 05/03/2018] [Indexed: 02/07/2023]
Abstract
The incidence of acute myeloid leukaemia (AML) increases with age and mortality exceeds 90% when diagnosed after age 65. Most cases arise without any detectable early symptoms and patients usually present with the acute complications of bone marrow failure1. The onset of such de novo AML cases is typically preceded by the accumulation of somatic mutations in preleukaemic haematopoietic stem and progenitor cells (HSPCs) that undergo clonal expansion2,3. However, recurrent AML mutations also accumulate in HSPCs during ageing of healthy individuals who do not develop AML, a phenomenon referred to as age-related clonal haematopoiesis (ARCH)4-8. Here we use deep sequencing to analyse genes that are recurrently mutated in AML to distinguish between individuals who have a high risk of developing AML and those with benign ARCH. We analysed peripheral blood cells from 95 individuals that were obtained on average 6.3 years before AML diagnosis (pre-AML group), together with 414 unselected age- and gender-matched individuals (control group). Pre-AML cases were distinct from controls and had more mutations per sample, higher variant allele frequencies, indicating greater clonal expansion, and showed enrichment of mutations in specific genes. Genetic parameters were used to derive a model that accurately predicted AML-free survival; this model was validated in an independent cohort of 29 pre-AML cases and 262 controls. Because AML is rare, we also developed an AML predictive model using a large electronic health record database that identified individuals at greater risk. Collectively our findings provide proof-of-concept that it is possible to discriminate ARCH from pre-AML many years before malignant transformation. This could in future enable earlier detection and monitoring, and may help to inform intervention.
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Affiliation(s)
- Sagi Abelson
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
| | - Grace Collord
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Stanley W K Ng
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Omer Weissbrod
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Netta Mendelson Cohen
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Elisabeth Niemeyer
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Barda
- Clalit Research Institute, Tel Aviv, Israel
| | | | | | | | - Robert Luben
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Shabina Hayat
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Ting Ting Wang
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Zhen Zhao
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
| | - Iulia Cirlan
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - David Soave
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Karen Ng
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Calli Latimer
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Claire Hardy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Keiran Raine
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - David Jones
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Diana Hoult
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Abigail Britten
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | | | - Mattias Johansson
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | | | - Jenna Eagles
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | - Lee Timms
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Philip Awadalla
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Rui Costa
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Philip Beer
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Sam Behjati
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Inigo Martincorena
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Jean C Y Wang
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, Ontario, Canada
| | - Kristian M Bowles
- Department of Molecular Haematology, Norwich Medical School, The University of East Anglia, Norwich, UK
- Department of Haematology, Norfolk and Norwich University Hospitals NHS Trust, Norwich, UK
| | | | - Anna Karakatsani
- Hellenic Health Foundation, Athens, Greece
- 2nd Pulmonary Medicine Department, School of Medicine, National and Kapodistrian University of Athens, "ATTIKON" University Hospital, Haidari, Athens, Greece
| | - Carlo La Vecchia
- Hellenic Health Foundation, Athens, Greece
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | | | - Elena Salamanca-Fernández
- Escuela Andaluza de Salud Pública, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
- CIBER Epidemiology and Public Health CIBERESP, Madrid, Spain
| | - José M Huerta
- CIBER Epidemiology and Public Health CIBERESP, Madrid, Spain
- Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, Murcia, Spain
| | - Aurelio Barricarte
- CIBER Epidemiology and Public Health CIBERESP, Madrid, Spain
- Navarra Public Health Institute, Pamplona, Spain
- Navarra Institute for Health Research, Pamplona, Spain
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rosario Tumino
- Cancer Registry and Histopathology Department, Civic-M. P. Arezzo Hospital, Azienda Sanitaria Provinciale, Ragusa, Italy
| | - Giovanna Masala
- Cancer Risk Factors and Life-Style Epidemiology Unit, Cancer Research and Prevention Institute - ISPO, Florence, Italy
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition (DIfE), Potsdam-Rehbrücke, Germany
| | - Salvatore Panico
- Dipartimento Di Medicina Clinica E Chirurgia, Federico II University, Naples, Italy
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Alwin Krämer
- Clinical Cooperation Unit Molecular Hematology/Oncology, German Cancer Research Center (DKFZ) and Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Matthieu Foll
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - James McKay
- International Agency for Research on Cancer, World Health Organization, Lyon, France
| | | | - Núria Sala
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program and Translational Research Laboratory, Catalan Institute of Oncology, ICO-IDIBELL, Barcelona, Spain
| | | | - Roel Vermeulen
- Division of Environmental Epidemiology and Veterinary Public Health, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Elli Papaemmanuil
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Center for Molecular Oncology and Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark D Minden
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Medical Oncology and Hematology, University Health Network, Toronto, Ontario, Canada
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | | | | | - Moritz Gerstung
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
- European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Wellcome Genome Campus, Hinxton, UK.
| | - John E Dick
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| | - Paul Brennan
- International Agency for Research on Cancer, World Health Organization, Lyon, France.
| | - George S Vassiliou
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - Liran I Shlush
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario, Canada.
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
- Division of Hematology, Rambam Healthcare Campus, Haifa, Israel.
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5
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Spears M, Kalatskaya I, Trinh QM, Liao L, Chong TM, Crozier C, Dion D, Heisler L, Timms L, Stein LD, Pritchard KI, Levine MN, Shepherd L, Twelves CJ, Bartlett JMS. Abstract P2-10-04: Targeted sequencing in early breast cancer: Identification of novel candidate mutations predictive of anthracycline benefit. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-10-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background The use of chemotherapies such as anthracyclines and taxanes have improved overall and disease free survival in breast cancer. For all patients, anthracyclines can have significant toxicities including cardiotoxicity and leukemia. It is therefore essential to select the subset of patients who will receive the optimal overall benefit from anthracycline therapy and to identify molecular pathways driving resistance. To fully understand the impact of mutations in the context of current breast cancer therapy, requires a comprehensive mapping of key molecular events in the context of treatment. We sequenced 101 genes, that were prioritized based on not only gene frequency, but also taking into account the importance of amino acid substitution, type of mutation and network connectivity, in 692 primary tumours to both identify driver genes and pathway cassettes and to understand their clinical significance in response to anthracycline treatment.
Methods We performed targeted sequencing in patients from the BR9601 (n=374) and CCTG MA.5 (n=703) clinical trials. The BR9601 and MA.5 clinical trials examined the effectiveness of combination chemotherapy consisting of CMF (cyclophosphamide, methotrexate and 5-fluorouracil) with or without epirubicin. DNA was extracted, samples were sequenced using AmpliSeq Technology adapted to Illumina and somatic mutations were called using a novel mutation calling pipeline (ISOWN). A priori analyses were performed using distant recurrence free survival (DRFS) as the primary endpoint.
Results: In 692 successfully analysed samples 509 (73.6%) samples exhibited at least one single nucleotide mutation (range 0-54). 94/101 genes were mutated in at least one patient. Only variants in PIK3CA, TP53, CDH1, TLE6, MLL3 and USH2A were detected in 5% or more of samples. TSC22D1, RB1 and ZNF565 were associated with increased risk of distant relapse in multivariate analyses corrected for clinic-pathological variables. No single genes were predictive of anthracycline treatment compared to CMF in multivariate analyses corrected for clinic-pathological variables. Signaling cassettes/modules were designed based on the pathway database, Reactome. Within the signaling cassettes one module was predictive of anthracycline failure. Patients with one or more mutations in this module had an increased risk of distant relapse (HR 0.52, 95% CI 0.29-0.95, p=0.034) when treated with an anthracycline containing chemotherapy regimen compared to CMF (HR 1.34 95% CI 1.05-1.72, p=0.019).
Conclusions: We successfully performed a signaling pathway-based targeted sequencing analysis within predefined signaling modules. We identified a single signaling cassette linked to anthracycline resistance in early breast cancer. However, further work to validate this study in a separate clinical trial is warranted.
Citation Format: Spears M, Kalatskaya I, Trinh QM, Liao L, Chong TM, Crozier C, Dion D, Heisler L, Timms L, Stein LD, Pritchard KI, Levine MN, Shepherd L, Twelves CJ, Bartlett JMS. Targeted sequencing in early breast cancer: Identification of novel candidate mutations predictive of anthracycline benefit [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-10-04.
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Affiliation(s)
- M Spears
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - I Kalatskaya
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - QM Trinh
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Liao
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - TM Chong
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - C Crozier
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - D Dion
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Heisler
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Timms
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - LD Stein
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - KI Pritchard
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - MN Levine
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - L Shepherd
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - CJ Twelves
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
| | - JMS Bartlett
- Ontario Institute for Cancer Research, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada; Sunnybrook Odette Cancer, Toronto, ON, Canada; McMaster University and Hamilton Health Sciences, Hamilton, ON, Canada; Canadian Cancer Trials Group, Kingston, ON, Canada; Leeds Institute of Cancer and Pathology and Cancer Research UK Centre, Leeds, United Kingdom; Edinburgh Cancer Research UK Centre, Edinburgh, United Kingdom
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Shlush LI, Mitchell A, Heisler L, Abelson S, Ng SWK, Trotman-Grant A, Medeiros JJF, Rao-Bhatia A, Jaciw-Zurakowsky I, Marke R, McLeod JL, Doedens M, Bader G, Voisin V, Xu C, McPherson JD, Hudson TJ, Wang JCY, Minden MD, Dick JE. Tracing the origins of relapse in acute myeloid leukaemia to stem cells. Nature 2017; 547:104-108. [DOI: 10.1038/nature22993] [Citation(s) in RCA: 339] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/17/2017] [Indexed: 01/06/2023]
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Bartlett J, Kalatskaya I, Yousif F, Bayani J, Trinh QM, Heisler L, Timms L, Lee S, Buchner N, Milacic M, Rothfels K, Crozier C, Drake C, Hasenburg A, Kieback DG, Rea D, McPherson J, Boutros PC, Stein LD. Targeted sequencing in a phase III trial of luminal breast cancer: Identification of novel targets. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
505 Background: The International Cancer Genome Consortium and The Cancer Genome Atlas have had a global transformative impact on our understanding of cancer. These programs have mapped the genomic landscape of common and rare tumors setting the scene for a comprehensive change in the approach to cancer diagnosis and treatment. However, the task remains incomplete until these mutational events are linked to clinical outcomes in the context of current therapeutic intervention to drive future stratified medicine approaches. Methods: We performed targeted sequencing in patients from the Tamoxifen Exemestane Adjuvant Multicentre trial. DNA was extracted and a 101 gene panel analysed using a novel mutation calling pipeline. Both a priori and machine learning analyses were performed using distant recurrence free survival as the primary endpoint. Results: In 1,491 successfully analyzed samples 1,070 (71.76%) samples exhibited at least one single nucleotide mutation (range 0-94, 1.828+/-0.133, mean+/-s.e.). 98/101 genes were mutated in at least one patient. Only variants in PIK3CA, TP53, MLL3, CDH1 were detected in 5% or more of samples. Twenty genes were associated with increased risk of recurrence in multivariate analyses corrected for clinic-pathological variables, 50% of these genes were involved in transcriptional regulation or RNA/protein processing. In a multivariate analysis, two combined signalling modules were independently prognostic for residual risk following hormone therapy (HRvalidation 3.10 95%CI 1.78-5.40 and HRvalidation 2.70 95%CI 1.57-4.64). Conclusions: We successfully performed a signalling pathway-based targeted sequencing analysis within predefined signalling modules. In supervised and unsupervised analyses we identified multiple signalling cassettes linked to poor outcome in patients with ER+ve breast cancers treated with modern endocrine therapy in the context of a phase III clinical trial. These results identify novel candidates as targets to treat endocrine refractory breast cancers.
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Affiliation(s)
- John Bartlett
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Fouad Yousif
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jane Bayani
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Quang M Trinh
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Lee Timms
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Shawna Lee
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Marija Milacic
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Karen Rothfels
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Cheryl Crozier
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Camilla Drake
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | | | - Daniel Rea
- Cancer Research UK Institute for Cancer Studies, Birmingham, United Kingdom
| | - John McPherson
- University of California Davis Comprehensive Cancer Center, Sacramento, CA
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8
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Fox NS, Lalonde E, Livingstone J, Hopkins J, Shiah YJ, Huang V, Yamaguchi T, Sabelnykova V, Heisler L, Fraser M, van der Kwast T, Bristow RG, Boutros PC. Integrated somatic subtypes of localized intermediate-risk prostate cancer. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.6_suppl.e560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e560 Background: Approximately two thirds of intermediate risk prostate cancer patients are over- or under- treated because we cannot correctly prognose this risk group; therefore we require novel biomarkers to better direct patient therapies and avoid subjecting patients to side effects without benefit. One reason genomic biomarkers are not currently used in clinical settings is because they are notoriously difficult to validate in follow-up studies. Furthermore, the lack of clear prostate cancer subtypes prevents the development of subtype specific biomarkers as is standard practice in breast cancer. We aim to improve biomarker validation rates by defining prostate cancer subtypes that can be used to create subtype specific biomarkers. Methods: First, we assess large scale genomic patterns using whole genome sequencing and methylation data and create integrative subtypes for intermediate risk prostate cancer. Second, we assess associations between specific aberrations and subtypes, and determine whether certain types of molecular aberrations are more important background aberrations for subtype specific biomarker development. Finally, we assess biases in prognostic performance of the published Lalonde biomarker between groups associated with patient subtypes to show that subtype aware biomarkers are necessary. Results: We demonstrate that the Lalonde biomarker is biased by the cohorts’ proportion of TMPRSS2-ERG (T2E) aberrations illustrating the need to develop different biomarkers for patients with T2E and patients without T2E. Further, we suggest integrative subtypes can be used to select patients with similar genomic profiles for biomarker analysis to improve biomarker validation rates. Conclusions: This analysis provides direct guidance for future biomarker development and addresses an important barrier to clinical use of genomic biomarkers for prostate cancer.
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Affiliation(s)
- Natalie S Fox
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Emilie Lalonde
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Julie Livingstone
- Informatics & Biocomputing Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Julia Hopkins
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Vincent Huang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | | | | | - Michael Fraser
- Radiation Medicine Program, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Theodorus van der Kwast
- Department of Laboratory Medicine and Pathology, University Health Network, University of Toronto, Toronto, ON, Canada
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9
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Notta F, Chan-Seng-Yue M, Lemire M, Li Y, Wilson GW, Connor AA, Denroche RE, Liang SB, Brown AMK, Kim JC, Wang T, Simpson JT, Beck T, Borgida A, Buchner N, Chadwick D, Hafezi-Bakhtiari S, Dick JE, Heisler L, Hollingsworth MA, Ibrahimov E, Jang GH, Johns J, Jorgensen LGT, Law C, Ludkovski O, Lungu I, Ng K, Pasternack D, Petersen GM, Shlush LI, Timms L, Tsao MS, Wilson JM, Yung CK, Zogopoulos G, Bartlett JMS, Alexandrov LB, Real FX, Cleary SP, Roehrl MH, McPherson JD, Stein LD, Hudson TJ, Campbell PJ, Gallinger S. Erratum: A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns. Nature 2016; 542:124. [PMID: 27851734 DOI: 10.1038/nature20164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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10
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Notta F, Chan-Seng-Yue M, Lemire M, Li Y, Wilson GW, Connor AA, Denroche RE, Liang SB, Brown AMK, Kim JC, Wang T, Simpson JT, Beck T, Borgida A, Buchner N, Chadwick D, Hafezi-Bakhtiari S, Dick JE, Heisler L, Hollingsworth MA, Ibrahimov E, Jang GH, Johns J, Jorgensen LGT, Law C, Ludkovski O, Lungu I, Ng K, Pasternack D, Petersen GM, Shlush LI, Timms L, Tsao MS, Wilson JM, Yung CK, Zogopoulos G, Bartlett JMS, Alexandrov LB, Real FX, Cleary SP, Roehrl MH, McPherson JD, Stein LD, Hudson TJ, Campbell PJ, Gallinger S. A renewed model of pancreatic cancer evolution based on genomic rearrangement patterns. Nature 2016; 538:378-382. [PMID: 27732578 DOI: 10.1038/nature19823] [Citation(s) in RCA: 351] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 09/02/2016] [Indexed: 12/11/2022]
Abstract
Pancreatic cancer, a highly aggressive tumour type with uniformly poor prognosis, exemplifies the classically held view of stepwise cancer development. The current model of tumorigenesis, based on analyses of precursor lesions, termed pancreatic intraepithelial neoplasm (PanINs) lesions, makes two predictions: first, that pancreatic cancer develops through a particular sequence of genetic alterations (KRAS, followed by CDKN2A, then TP53 and SMAD4); and second, that the evolutionary trajectory of pancreatic cancer progression is gradual because each alteration is acquired independently. A shortcoming of this model is that clonally expanded precursor lesions do not always belong to the tumour lineage, indicating that the evolutionary trajectory of the tumour lineage and precursor lesions can be divergent. This prevailing model of tumorigenesis has contributed to the clinical notion that pancreatic cancer evolves slowly and presents at a late stage. However, the propensity for this disease to rapidly metastasize and the inability to improve patient outcomes, despite efforts aimed at early detection, suggest that pancreatic cancer progression is not gradual. Here, using newly developed informatics tools, we tracked changes in DNA copy number and their associated rearrangements in tumour-enriched genomes and found that pancreatic cancer tumorigenesis is neither gradual nor follows the accepted mutation order. Two-thirds of tumours harbour complex rearrangement patterns associated with mitotic errors, consistent with punctuated equilibrium as the principal evolutionary trajectory. In a subset of cases, the consequence of such errors is the simultaneous, rather than sequential, knockout of canonical preneoplastic genetic drivers that are likely to set-off invasive cancer growth. These findings challenge the current progression model of pancreatic cancer and provide insights into the mutational processes that give rise to these aggressive tumours.
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Affiliation(s)
- Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | | | - Mathieu Lemire
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Yilong Li
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Gavin W Wilson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Ashton A Connor
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Robert E Denroche
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Sheng-Ben Liang
- UHN Program in BioSpecimen Sciences, Department of Pathology, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Andrew M K Brown
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Jaeseung C Kim
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Tao Wang
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Jared T Simpson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada
| | - Timothy Beck
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Ayelet Borgida
- Eppley Institute for Research in Cancer, Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Nicholas Buchner
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Dianne Chadwick
- UHN Program in BioSpecimen Sciences, Department of Pathology, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Sara Hafezi-Bakhtiari
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,UHN Program in BioSpecimen Sciences, Department of Pathology, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - John E Dick
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Lawrence Heisler
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer, Nebraska Medical Center, Omaha, Nebraska 68198, USA
| | - Emin Ibrahimov
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Jeremy Johns
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | | | - Calvin Law
- Division of Surgical Oncology, Sunnybrook Health Sciences Centre, Odette Cancer Centre, Toronto, Ontario M4N 3M5, Canada
| | - Olga Ludkovski
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Ilinca Lungu
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Karen Ng
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | | | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Liran I Shlush
- Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Lee Timms
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Ming-Sound Tsao
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - Julie M Wilson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Christina K Yung
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - George Zogopoulos
- Research Institute of the McGill University Health Centre, Montreal, Québec, Canada, H3H 2L9
| | - John M S Bartlett
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Ludmil B Alexandrov
- Theoretical Biology and Biophysics (T-6) and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico, USA, 87545
| | - Francisco X Real
- Epithelial Carcinogenesis Group, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain
| | - Sean P Cleary
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Surgery, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Michael H Roehrl
- UHN Program in BioSpecimen Sciences, Department of Pathology, University Health Network, Toronto, Ontario M5G 2C4, Canada.,Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, Ontario M5G 2M9, Canada
| | - John D McPherson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Lincoln D Stein
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.,Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Department of Surgery, University Health Network, Toronto, Ontario M5G 2C4, Canada
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Tomson BN, Crisucci EM, Heisler L, Gebbia M, Nislow C, Arndt KM. Characterization of snoRNA 3’‐end formation in
Saccharomyces cerevisiae
reveals a broad role for the Paf1 complex and locus‐specific roles for histone post‐translational modifications. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.lb97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | | | | | | | - Karen M Arndt
- Biological SciencesUniversity of PittsburghPittsburghPA
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Hyrcza MD, Kovacs C, Loutfy M, Halpenny R, Heisler L, Yang S, Wilkins O, Ostrowski M, Der SD. Distinct transcriptional profiles in ex vivo CD4+ and CD8+ T cells are established early in human immunodeficiency virus type 1 infection and are characterized by a chronic interferon response as well as extensive transcriptional changes in CD8+ T cells. J Virol 2007; 81:3477-86. [PMID: 17251300 PMCID: PMC1866039 DOI: 10.1128/jvi.01552-06] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Accepted: 01/16/2007] [Indexed: 11/20/2022] Open
Abstract
Changes in T-cell function are a hallmark of human immunodeficiency virus type 1 (HIV-1) infection, but the pathogenic mechanisms leading to these changes are unclear. We examined the gene expression profiles in ex vivo human CD4+ and CD8+ T cells from untreated HIV-1-infected individuals at different clinical stages and rates of disease progression. Profiles of pure CD4+ and CD8+ T-cell subsets from HIV-1-infected nonprogressors with controlled viremia were indistinguishable from those of individuals not infected with HIV-1. Similarly, no gene clusters could distinguish T cells from individuals with early infection from those seen in chronic progressive HIV-1 infection, whereas differences were observed between uninfected individuals or nonprogressors versus early or chronic progressors. In early and chronic HIV-1 infection, three characteristic gene expression signatures were observed. (i) CD4+ and CD8+ T cells showed increased expression of interferon-stimulated genes (ISGs). However, some ISGs, including CXCL9, CXCL10, and CXCL11, and the interleukin-15 alpha receptor were not upregulated. (ii) CD4+ and CD8+ T cells showed a cluster similar to that observed in thymocytes. (iii) More genes were differentially regulated in CD8+ T cells than in CD4+ T cells, including a cluster of genes downregulated exclusively in CD8+ T cells. In conclusion, HIV-1 infection induces a persistent T-cell transcriptional profile, early in infection, characterized by a dramatic but potentially aberrant interferon response and a profile suggesting an active thymic output. These findings highlight the complexity of the host-virus relationship in HIV-1 infection.
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Affiliation(s)
- Martin D Hyrcza
- Clinical Sciences Division, University of Toronto, Medical Sciences Building, Rm. 6271, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada
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Sander T, Olson S, Hall J, Siebert M, Grooms K, Heisler L, de Arruda M, Neri B. Comparison of detection platforms and post-polymerase chain reaction DNA purification methods for use in conjunction with Cleavase fragment length polymorphism analysis. Electrophoresis 1999. [PMID: 10380752 DOI: 10.1002/(sici)1522-2683(19990101)20:6<1131::aid-elps1131>3.0.co;2-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The removal of impurities and contaminants from PCR-amplified fragments is important for mutation detection methods which identify mutations based on shifts in electrophoretic mobility. This is particularly critical for assays and detection methods which use target DNA that is labeled prior to analysis and electrophoretic detection. We examined several procedures for purifying DNA amplified by the polymerase chain reaction (PCR) and their use in conjunction with a novel DNA scanning method, the Cleavase fragment length polymorphism (CFLP)* assay. In this study, a 480 bp DNA fragment, fluorescently labeled on the 5'-end of one strand, was amplified and subjected to various widely used purification procedures, including several commercially available clean-up kits. We demonstrate that visualization of the fluorescent label, as opposed to simple ethidium bromide staining, reveals the presence of considerable levels of labeled, truncated, amplification products. The various procedures were evaluated on the basis of their ability to remove these unwanted DNA fragments as well as on the degree to which they inhibited or promoted the CFLP reaction. Several procedures are recommended for use with CFLP analysis, including isopropanol precipitation, gel excision, and several commercially available spin columns. Concurrently, we evaluated (compared) a number of commonly used visualization platforms, including fluorescence imaging, chemiluminescence, and post-electrophoretic staining, for the ability to detect CFLP pattern changes. The advantages and disadvantages of different methods are discussed and amounts of DNA to be used for CFLP analysis on different detection platforms are recommended.
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Affiliation(s)
- T Sander
- Third Wave Technologies, Madison, WI 53719, USA
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Sander T, Olson S, Hall J, Siebert M, Grooms K, Heisler L, de Arruda M, Neri B. Comparison of detection platforms and post-polymerase chain reaction DNA purification methods for use in conjunction with Cleavase fragment length polymorphism analysis. Electrophoresis 1999; 20:1131-40. [PMID: 10380752 DOI: 10.1002/(sici)1522-2683(19990101)20:6<1131::aid-elps1131>3.0.co;2-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The removal of impurities and contaminants from PCR-amplified fragments is important for mutation detection methods which identify mutations based on shifts in electrophoretic mobility. This is particularly critical for assays and detection methods which use target DNA that is labeled prior to analysis and electrophoretic detection. We examined several procedures for purifying DNA amplified by the polymerase chain reaction (PCR) and their use in conjunction with a novel DNA scanning method, the Cleavase fragment length polymorphism (CFLP)* assay. In this study, a 480 bp DNA fragment, fluorescently labeled on the 5'-end of one strand, was amplified and subjected to various widely used purification procedures, including several commercially available clean-up kits. We demonstrate that visualization of the fluorescent label, as opposed to simple ethidium bromide staining, reveals the presence of considerable levels of labeled, truncated, amplification products. The various procedures were evaluated on the basis of their ability to remove these unwanted DNA fragments as well as on the degree to which they inhibited or promoted the CFLP reaction. Several procedures are recommended for use with CFLP analysis, including isopropanol precipitation, gel excision, and several commercially available spin columns. Concurrently, we evaluated (compared) a number of commonly used visualization platforms, including fluorescence imaging, chemiluminescence, and post-electrophoretic staining, for the ability to detect CFLP pattern changes. The advantages and disadvantages of different methods are discussed and amounts of DNA to be used for CFLP analysis on different detection platforms are recommended.
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Affiliation(s)
- T Sander
- Third Wave Technologies, Madison, WI 53719, USA
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15
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O'Connell CD, Atha DH, Oldenburg MC, Tian J, Siebert M, Handrow R, Grooms K, Heisler L, de Arruda M. Detection of p53 gene mutations: analysis by single-strand conformation polymorphism and Cleavase fragment length polymorphism. Electrophoresis 1999; 20:1211-23. [PMID: 10380761 DOI: 10.1002/(sici)1522-2683(19990101)20:6<1211::aid-elps1211>3.0.co;2-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have generated a collection of clones containing single point mutations within the exon 5-9 hot spot regions of the p53 gene by using polymerase chain reaction (PCR) to amplify select regions of the gene from characterized cell lines. These clones were then used to address the sensitivity of mutation detection using slab-gel single-strand conformation polymorphism (SSCP) and Cleavase fragment length polymorphism (CFLP) assay systems. Both methods exhibited high sensitivities for the detection of mutations in cloned p53 mutations in this study: 97% for CFLP and 94% for SSCP. In addition to resulting in higher sensitivity of mutation detection, CFLP has the capability to analyze longer fragments. In this study, CFLP identified five intronic mutations which were not investigated in the exon-specific SSCP assay. These results agree with those found elsewhere and demonstrate that CFLP scanning can have practical advantages when used for the identification of sequence alterations within the p53 gene.
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Affiliation(s)
- C D O'Connell
- Biotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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Martin-Tanguy J, Tepfer D, Paynot M, Burtin D, Heisler L, Martin C. Inverse Relationship between Polyamine Levels and the Degree of Phenotypic Alteration Induced by the Root-Inducing, Left-Hand Transferred DNA from Agrobacterium rhizogenes. Plant Physiol 1990; 92:912-8. [PMID: 16667405 PMCID: PMC1062395 DOI: 10.1104/pp.92.4.912] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Floral induction in plants is a paradigm for signal perception, transduction, and physiological response. The introduction of root-inducing, left-hand transferred DNA (Ri T-DNA) into the genomes of several plants results in modifications of flowering (D Tepfer [1984] Cell 47: 959-967), including a delay in flowering in tobacco (Nicotiana tabacum). Conjugated polyamines are markers for flowering in numerous species of plants. In tobacco their accumulation is correlated with the onset of flowering (F Cabanne et al. [1981] Physiol Plant 53: 399-404). Using tobacco, we have explored the possibility of a correlation between the expression of Ri TL-DNA and changes in polyamine metabolism. We made use of two levels of phenotypic change, designated T and T', that retard flowering by 5 to 10 and 15 to 20 days, respectively. We show that delay in flowering is correlated with a reduction in polyamine accumulation and with a delay in appearance of conjugated polyamines, and we propose that genes carried by the Ri TL-DNA intervene either directly in polyamine metabolism or that polyamine metabolism is closely linked to direct effects of Ri T-DNA expression.
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Affiliation(s)
- J Martin-Tanguy
- Station de Physiopathologie Végétale, INRA, BV 1540, 21034 Dijon Cedex, France
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Affiliation(s)
- J Piscitelli
- Division of Pulmonary and Critical Care Medicine, Long Island Jewish Medical Center, New Hyde Park, NY 11042
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Portnoy J, Mendelson J, Clecner B, Heisler L. Asymptomatic gonorrhea in the male. Can Med Assoc J 1974; 110:169 passim. [PMID: 4203950 PMCID: PMC1947122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In a prospective study, 133 male contacts of 102 women with gonorrhea were examined. A diagnosis of gonorrhea was made in 63 patients, indicating an infection rate of 47% after exposure. Forty-three percent of the patients with gonorrhea were asymptomatic. The duration of the asymptomatic period ranged from 3 to 154 days. The epidemiologic importance of this hidden infectious reservoir is stressed.
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