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Results: 86502
Sex differences in oncogenic mutational processes.
Constance H Li, Stephenie D Prokopec, Ren X Sun, Fouad Yousif, Nathaniel Schmitz, PCAWG Tumour Subtypes and Clinical Translation, Paul C Boutros, PCAWG Consortium
Sep 11, 2020
Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have...
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.
Wei Jiao, Gurnit Atwal, Paz Polak, Rosa Karlic, Edwin Cuppen, PCAWG Tumor Subtypes and Clinical Translation Working Group, Alexandra Danyi, Jeroen de Ridder, Carla van Herpen, Martijn P Lolkema, Neeltje Steeghs, Gad Getz, Quaid D Morris, Lincoln D Stein, PCAWG Consortium
May 14, 2020
In cancer, the primary tumour's organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of...
Reconstructing evolutionary trajectories of mutation signature activities in cancer using TrackSig.
Yulia Rubanova, Ruian Shi, Caitlin F Harrigan, Roujia Li, Jeff Wintersinger, Nil Sahin, Amit G Deshwar, PCAWG Evolution and Heterogeneity Working Group, Quaid D Morris, PCAWG Consortium
Feb 04, 2021
The type and genomic context of cancer mutations depend on their causes. These causes have been characterized using signatures that represent mutation types that co-occur in the same tumours. However, it remains unclear how...
Inferring structural variant cancer cell fraction.
Marek Cmero, Ke Yuan, Cheng Soon Ong, Jan Schröder, PCAWG Evolution and Heterogeneity Working Group, Niall M Corcoran, Tony Papenfuss, Christopher M Hovens, Florian Markowetz, Geoff Macintyre, PCAWG Consortium
Dec 18, 2019
We present SVclone, a computational method for inferring the cancer cell fraction of structural variant (SV) breakpoints from whole-genome sequencing data. SVclone accurately determines the variant allele frequencies of both SV...
CLINICAL AND TRANSLATION RESEARCH DAY
The Rockefeller University
Jan 01, 0001
The Rockefeller University Hospital hosted Clinical and Translation Research Day on September 20th, 2012
Published by: The Rockefeller University
Mitochondrial DNA transcription and translation
Diagnosing primary mitochondrial diseases is challenging in clinical practice. Although, defective oxidative phosphorylation (OXPHOS) is the common final pathway, it is unknown why different mtDNA or nuclear mutations result in...
mitochondrial tRNA modifications mitochondrial tRNA processing mitochondrial tRNA synthetases mitochondrial translation DNA Mitochondrial Electron Transport Humans Mitochondrial Diseases Mitochondrial Proteins Mutation Oxidative Phosphorylation Phenotype Protein Biosynthesis RNA Precursors RNA processing Post-Transcriptional RNA Messenger RNA Transfer Syndrome Transcription Genetic
Cancer LncRNA Census reveals evidence for deep functional conservation of long noncoding RNAs in tumorigenesis.
Joana Carlevaro-Fita, Andrés Lanzós, Lars Feuerbach, Chen Hong, David Mas-Ponte, Jakob Skou Pedersen, PCAWG Drivers and Functional Interpretation Group, Rory Johnson, PCAWG Consortium
Feb 17, 2021
Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive...
Identification of Subtypes of Barrett's Esophagus and Esophageal Adenocarcinoma Based on DNA Methylation Profiles and Integration of Transcriptome and Genome Data.
Sriganesh Jammula, Annalise C Katz-Summercorn, Xiaodun Li, Constanza Linossi, Elizabeth Smyth, Sarah Killcoyne, Daniele Biasci, Vinod V Subash, Sujath Abbas, Adrienn Blasko, Ginny Devonshire, Amber Grantham, Filip Wronowski, Maria O'Donovan, Nicola Grehan, Matthew D Eldridge, Simon Tavaré, Oesophageal Cancer Clinical and Molecular Stratification (OCCAMS) Consortium, Rebecca C Fitzgerald
Jun 05, 2020
BACKGROUND & AIMS: Esophageal adenocarcinomas (EACs) are heterogeneous and often preceded by Barrett's esophagus (BE). Many genomic changes have been associated with development of BE and EAC, but little is known about...
antitumor immune response gene repression prognostic factor response to treatment Adenocarcinoma Aged Antineoplastic Agents Barrett Esophagus Cyclin E DNA Methylation Disease Progression Epigenesis Genetic Esophageal Mucosa Esophageal Neoplasms Female Gene Amplification Gene Expression Regulation Neoplastic Humans Male Middle Aged Oncogene Proteins Promoter Regions Genetic RNA-seq Retrospective Studies Temozolomide whole genome sequencing
Distinct temporal trends in breast cancer incidence from 1997 to 2016 by molecular subtypes
Ines Mesa-Eguiagaray, Sarah H Wild, Philip S Rosenberg, Sheila M Bird, David H Brewster, Peter S Hall, David A Cameron, David Morrison, Jonine D Figueroa
Jun 19, 2021
BACKGROUND: We describe temporal trends in breast cancer incidence by molecular subtypes in Scotland because public health prevention programmes, diagnostic and therapeutic services are shaped by differences in tumour biology....
Distinct temporal trends in breast cancer incidence from 1997 to 2016 by molecular subtypes
Ines Mesa-Eguiagaray, Sarah H. Wild, Philip S. Rosenberg, Sheila M. Bird, David H. Brewster, Peter S. Hall, David A. Cameron, David Morrison, Jonine D. Figueroa
Sep 01, 2020
Abstract: Background: We describe temporal trends in breast cancer incidence by molecular subtypes in Scotland because public health prevention programmes, diagnostic and therapeutic services are shaped by differences in tumour...
Distinct temporal trends in breast cancer incidence from 1997 to 2016 by molecular subtypes
Ines Mesa-Eguiagaray, Sarah H. Wild, Philip S. Rosenberg, Sheila M. Bird, David H. Brewster, Peter S. Hall, David A. Cameron, David Morrison, Jonine D. Figueroa
Feb 09, 2021
Abstract: Background: We describe temporal trends in breast cancer incidence by molecular subtypes in Scotland because public health prevention programmes, diagnostic and therapeutic services are shaped by differences in tumour...
A Retrospective Study of Clinical and Histopathological Features of 81 Cases of Canine Apocrine Gland Adenocarcinoma of the Anal Sac
Hannah Wong, Stephanie Byrne, Roberta Rasotto, Randi Drees, Angela Taylor, Simon L Priestnall, Chiara Leo
Nov 23, 2021
Canine apocrine gland anal sac adenocarcinoma (AGASAC) is a malignant tumour with variable clinical progression. The objective of this study was to use robust multivariate models, based on models employed in human medical...
Breast cancer incidence and survival in Scotland by socio-economic deprivation and tumour subtype.
Ines Mesa-Eguiagaray, Sarah H Wild, Sheila M Bird, Linda J Williams, David H Brewster, Peter S Hall, Jonine D Figueroa
Jun 29, 2022
BACKGROUND: Women from socio-economically deprived areas are less likely to develop and then to survive breast cancer (BC). Whether associations between deprivation and BC incidence and survival differ by tumour molecular...
Butler enables rapid cloud-based analysis of thousands of human genomes.
Sergei Yakneen, Sebastian M Waszak, PCAWG Technical Working Group, Michael Gertz, Jan O Korbel, PCAWG Consortium
Feb 04, 2021
We present Butler, a computational tool that facilitates large-scale genomic analyses on public and academic clouds. Butler includes innovative anomaly detection and self-healing functions that improve the efficiency of data...
Associations between genomic stratification of breast cancer and centrally reviewed tumour pathology in the METABRIC cohort.
A Mukherjee, R Russell, Suet-Feung Chin, B Liu, OM Rueda, HR Ali, G Turashvili, B Mahler-Araujo, IO Ellis, S Aparicio, C Caldas, E Provenzano
Mar 13, 2018
The integration of genomic and transcriptomic profiles of 2000 breast tumours from the METABRIC [Molecular Taxonomy of Breast Cancer International Consortium] cohort revealed ten subtypes, termed integrative clusters...
Association between tumour infiltrating lymphocytes, histotype and clinical outcome in epithelial ovarian cancer
Fiona R James, Mercedes Jiminez-Linan, Jennifer Alsop, Marie Mack, Honglin Song, James D Brenton, Paul D P Pharoah, H. R Ali
Sep 21, 2017
Abstract
Background
There is evidence that some ovarian tumours evoke an immune response, which can be assessed by tumour infiltrating lymphocytes (TILs). To facilitate adoption of...
Patterns of somatic structural variation in human cancer genomes.
Yilong Li, Nicola D Roberts, Jeremiah A Wala, Ofer Shapira, Steven E Schumacher, Kiran Kumar, Ekta Khurana, Sebastian Waszak, Jan O Korbel, James E Haber, Marcin Imielinski, PCAWG Structural Variation Working Group, Joachim Weischenfeldt, Rameen Beroukhim, Peter J Campbell, PCAWG Consortium
Feb 04, 2021
A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments that range in size from kilobases to whole chromosomes1-7. Here we develop methods to group...
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Matthew H Bailey, William U Meyerson, Lewis Jonathan Dursi, Liang-Bo Wang, Guanlan Dong, Wen-Wei Liang, Amila Weerasinghe, Shantao Li, Yize Li, Sean Kelso, MC3 Working Group, PCAWG novel somatic mutation calling methods working group, Gordon Saksena, Kyle Ellrott, Michael C Wendl, David A Wheeler, Gad Getz, Jared T Simpson, Mark B Gerstein, Li Ding, PCAWG Consortium
Oct 12, 2020
The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the...
ISSCR Guidelines for Stem Cell Research and Clinical Translation
Robin Lovell-Badge, Eric Anthony, Roger A Barker, Tania Bubela, Ali H Brivanlou, Melissa Carpenter, R Alta Charo, Amander Clark, Ellen Clayton, Yali Cong, George Q Daley, Jianping Fu, Misao Fujita, Andy Greenfield, Steve A Goldman, Lori Hill, Insoo Hyun, Rosario Isasi, Jeffrey Kahn, Kazuto Kato, Jin-Soo Kim, Jonathan Kimmelman, Jürgen A Knoblich, Debra Mathews, Nuria Montserrat, Jack Mosher, Megan Munsie, Hiromitsu Nakauchi, Luigi Naldini, Gail Naughton, Kathy Niakan, Ubaka Ogbogu, Roger Pedersen, Nicolas Rivron, Heather Rooke, Janet Rossant, Jeff Round, Mitinori Saitou, Douglas Sipp, Julie Steffann, Jeremy Sugarman, Azim Surani, Jun Takahashi, Fuchou Tang, Leigh Turner, Patricia J Zettler, Xiaomei Zhai
May 28, 2021
The International Society for Stem Cell Research has updated its Guidelines for Stem Cell Research and Clinical Translation in order to address advances in stem cell science and other relevant fields, together with the...
Association between tumour infiltrating lymphocytes, histotype and clinical outcome in epithelial ovarian cancer.
Fiona R James, Mercedes Jiminez-Linan, Jennifer Alsop, Marie Mack, Honglin Song, James D Brenton, Paul DP Pharoah, H Raza Ali
Nov 29, 2018
BACKGROUND: There is evidence that some ovarian tumours evoke an immune response, which can be assessed by tumour infiltrating lymphocytes (TILs). To facilitate adoption of TILs as a clinical biomarker, a standardised method for...
ISSCR Guidelines for Stem Cell Research and Clinical Translation
Robin Lovell-Badge, Eric Anthony, Roger A Barker, Tania Bubela, Ali H Brivanlou, Melissa Carpenter, R Alta Charo, Amander Clark, Ellen Clayton, Yali Cong, George Q Daley, Jianping Fu, Misao Fujita, Andy Greenfield, Steve A Goldman, Lori Hill, Insoo Hyun, Rosario Isasi, Jeffrey Kahn, Kazuto Kato, Jin-Soo Kim, Jonathan Kimmelman, Jürgen A Knoblich, Debra Mathews, Nuria Montserrat, Jack Mosher, Megan Munsie, Hiromitsu Nakauchi, Luigi Naldini, Gail Naughton, Kathy Niakan, Ubaka Ogbogu, Roger Pedersen, Nicolas Rivron, Heather Rooke, Janet Rossant, Jeff Round, Mitinori Saitou, Douglas Sipp, Julie Steffann, Jeremy Sugarman, Azim Surani, Jun Takahashi, Fuchou Tang, Leigh Turner, Patricia J Zettler, Xiaomei Zhai
Jun 28, 2021
The International Society for Stem Cell Research has updated its Guidelines for Stem Cell Research and Clinical Translation in order to address advances in stem cell science and other relevant fields, together with the...
Published by: Stem Cell Reports
The VENUSS prognostic model to predict disease recurrence following surgery for non-metastatic papillary renal cell carcinoma
Tobias Klatte, Kevin M Gallagher, Luca Afferi, Alessandro Volpe, Nils Kroeger, Silvia Ribback, Alan McNeill, Antony CP Riddick, James N Armitage, Tevita F 'Aho, Tim Eisen, Kate Fife, Axel Bex, Allan J Pantuck, Grant D Stewart
Oct 09, 2019
BACKGROUND: The current World Health Organization classification recognises 12 major subtypes of renal cell carcinoma (RCC). Although these subtypes differ on molecular and clinical levels, they are generally managed as the same...
Adjuvant Localised Papillary Prognosis Recurrence SURVEILLANCE Adult Aged Carcinoma Renal Cell Clinical Trials as Topic Cohort Studies Female Humans Incidence Kidney Neoplasms Male Middle Aged Models Statistical Neoplasm Recurrence Local Neoplasm Staging Predictive Value of Tests Prognosis Prospective Studies Research Design Risk Factors Treatment Outcome
A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns
Wei Jiao, Rosa Karlic, Edwin Cuppen, Alexandra Danyi, Jeroen de Ridder, Carla van Herpen, Martijn P. Lolkema, Neeltje Steeghs, Quaid Morris, Fatima Al-Shahrour, Gurnit Atwal, Peter J. Bailey, Andrew V. Biankin, Paul C. Boutros, Peter J. Campbell, David K. Chang, Susanna L. Cooke, Vikram Deshpande, Bishoy M. Faltas, William C. Faquin, Levi Garraway, Gad Getz, Sean M. Grimmond, Syed Haider, Katherine A. Hoadley, Vera B. Kaiser, Rosa Karlić, Mamoru Kato, Kirsten Kübler, Alexander J. Lazar, Constance H. Li, David N. Louis, Adam Margolin, Sancha Martin, Hardeep K. Nahal-Bose, G. Petur Nielsen, Serena Nik-Zainal, Larsson Omberg, Christine P’ng, Marc D. Perry, Paz Polak, Esther Rheinbay, Mark A. Rubin, Colin A. Semple, Dennis C. Sgroi, Tatsuhiro Shibata, Reiner Siebert, Jaclyn Smith, Lincoln D. Stein, Miranda D. Stobbe, Ren X. Sun, Kevin Thai, Derek W. Wright, Chin-Lee Wu, Ke Yuan, Junjun Zhang
Feb 04, 2021
Abstract: In cancer, the primary tumour’s organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary....
Therapy-induced tumour secretomes promote resistance and tumour progression.
Anna C Obenauf, Yilong Zou, Andrew L Ji, Sakari Vanharanta, Weiping Shu, Hubing Shi, Xiangju Kong, Marcus C Bosenberg, Thomas Wiesner, Neal Rosen, Roger S Lo, Joan Massagué
Feb 12, 2020
Drug resistance invariably limits the clinical efficacy of targeted therapy with kinase inhibitors against cancer. Here we show that targeted therapy with BRAF, ALK or EGFR kinase inhibitors induces a complex network of secreted...
Adenocarcinoma Anaplastic Lymphoma Kinase Animals Cell Line Tumor Cell Movement Cell Proliferation Cell Survival Clone Cells Disease Progression Down-Regulation Drug Resistance Neoplasm Enzyme Activation ErbB Receptors Female Humans Lung Neoplasms Melanoma Metabolome Mice Neoplasm Metastasis Protein Kinase Inhibitors Proto-Oncogene Proteins B-raf Proto-Oncogene Proteins c-akt Proto-Oncogene Proteins c-fos Receptor Protein-Tyrosine Kinases Signal Transduction Tumor Microenvironment
Biological material collection to advance translational research and treatment of children with CNS tumours
Stefan Rutkowski, Piergiorgio Modena, Daniel Williamson, Kornelius Kerl, Karsten Nysom, Barry Pizer, Ute Bartels, Stephanie Puget, François Doz, Antony Michalski, Katja von Hoff, Mathilde Chevignard, Shivaram Avula, Matthew J Murray, Stefan Schönberger, Thomas Czech, Antoinette YN Schouten-van Meeteren, Uwe Kordes, Christof M Kramm, Dannis G van Vuurden, Esther Hulleman, Geert O Janssens, Guirish A Solanki, Marie-Luise C van Veelen, Ulrich Thomale, Martin U Schuhmann, Chris Jones, Felice Giangaspero, Dominique Figarella-Branger, Torsten Pietsch, Steve C Clifford, Stefan M Pfister, Stefaan W Van Gool
Feb 15, 2019
Paediatric CNS tumours are the most common cause of childhood cancer-related morbidity and mortality, and improvements in their diagnosis and treatment are needed. New genetic and epigenetic information about paediatric CNS...
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