Search
Results: 87011
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...
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...
Surveillance recommendations for DICER1 pathogenic variant carriers
Jette J Bakhuizen, Helen Hanson, Karin van der Tuin, Fiona Lalloo, Marc Tischkowitz, Karin Wadt, Marjolijn CJ Jongmans, SIOPE Host Genome Working Group, CanGene-CanVar Clinical Guideline Working Group, Expert Network Members
Oct 01, 2021
DICER1 syndrome is a rare genetic disorder that predisposes to a wide spectrum of tumors. Developing surveillance protocols for this syndrome is challenging because uncertainty exists about the clinical efficacy of surveillance...
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...
Genomic footprints of activated telomere maintenance mechanisms in cancer.
Lina Sieverling, Chen Hong, Sandra D Koser, Philip Ginsbach, Kortine Kleinheinz, Barbara Hutter, Delia M Braun, Isidro Cortés-Ciriano, Ruibin Xi, Rolf Kabbe, Peter J Park, Roland Eils, Matthias Schlesner, PCAWG-Structural Variation Working Group, Benedikt Brors, Karsten Rippe, David TW Jones, Lars Feuerbach, PCAWG Consortium
Mar 05, 2021
Cancers require telomere maintenance mechanisms for unlimited replicative potential. They achieve this through TERT activation or alternative telomere lengthening associated with ATRX or DAXX loss. Here, as part of the ICGC/TCGA...
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...
Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer.
Kadir C Akdemir, Victoria T Le, Sahaana Chandran, Yilong Li, Roel G Verhaak, Rameen Beroukhim, Peter J Campbell, Lynda Chin, Jesse R Dixon, P Andrew Futreal, PCAWG Structural Variation Working Group, PCAWG Consortium
Feb 04, 2021
Chromatin is folded into successive layers to organize linear DNA. Genes within the same topologically associating domains (TADs) demonstrate similar expression and histone-modification profiles, and boundaries separating...
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Yiqun Zhang, Fengju Chen, Nuno A Fonseca, Yao He, Masashi Fujita, Hidewaki Nakagawa, Zemin Zhang, Alvis Brazma, PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, Chad J Creighton, PCAWG Consortium
Feb 04, 2021
The impact of somatic structural variants (SVs) on gene expression in cancer is largely unknown. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole-genome sequencing...
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...
Pathway and network analysis of more than 2500 whole cancer genomes.
Matthew A Reyna, David Haan, Marta Paczkowska, Lieven PC Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, Gad Getz, Michael S Lawrence, Jakob Skou Pedersen, Mark A Rubin, David A Wheeler, Søren Brunak, Jose MG Izarzugaza, Ekta Khurana, Kathleen Marchal, Christian von Mering, S Cenk Sahinalp, Alfonso Valencia, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, Joshua M Stuart, Benjamin J Raphael, PCAWG Consortium
Feb 04, 2021
The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding...
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...
Gestational diabetes
Ponnusamy Saravanan, Diabetes in Pregnancy Working Group, Maternal Medicine Clinical Study Group, UK Royal College of Obstetricians and Gynaecologists
Apr 30, 2021
Gestational diabetes, the most common medical disorder in pregnancy, is defined as glucose intolerance resulting in hyperglycaemia that begins or is first diagnosed in pregnancy. Gestational diabetes is associated with increased...
Integrative pathway enrichment analysis of multivariate omics data.
Marta Paczkowska, Jonathan Barenboim, Nardnisa Sintupisut, Natalie S Fox, Helen Zhu, Diala Abd-Rabbo, Miles W Mee, Paul C Boutros, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, PCAWG Consortium
Feb 04, 2021
Adenocarcinoma Apoptosis Breast Neoplasms Chromatin Immunoprecipitation Computational Biology Databases Factual Female Gene Dosage Gene Expression Profiling Gene Regulatory Networks Genomics Hippo Signaling Pathway Humans Metabolic Networks and Pathways Mutation Neoplasms Prognosis Protein Serine-Threonine Kinases RNA Messenger Sequence Analysis RNA Signal Transduction
The Neurology and Neurosurgery Interest Group (NANSIG)-ten years of cultivating interest in clinical neurosciences.
Jay J Park, Setthasorn Zhi Yang Ooi, Conor S Gillespie, Soham Bandyopadhyay, Yasir A Chowdhury, Georgios Solomou, Melissa Gough, Ulrick Sidney Kanmounye, Alvaro Yanez Touzet, Michael TC Poon, Andreas K Demetriades, Michael D Jenkinson, Alistair Jenkins, Neurology and Neurosurgery Interest Group (NANSIG)
Feb 18, 2022
Collaboration and successful teamworking are important components of clinical practise, and these skills should be cultivated early in medical school. The breadth of current medical school curricula means that students often...
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
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.
Bernardo Rodriguez-Martin, Eva G Alvarez, Adrian Baez-Ortega, Jorge Zamora, Fran Supek, Jonas Demeulemeester, Martin Santamarina, Young Seok Ju, Javier Temes, Daniel Garcia-Souto, Harald Detering, Yilong Li, Jorge Rodriguez-Castro, Ana Dueso-Barroso, Alicia L Bruzos, Stefan C Dentro, Miguel G Blanco, Gianmarco Contino, Daniel Ardeljan, Marta Tojo, Nicola D Roberts, Sonia Zumalave, Paul A Edwards, Joachim Weischenfeldt, Montserrat Puiggròs, Zechen Chong, Ken Chen, Eunjung Alice Lee, Jeremiah A Wala, Keiran M Raine, Adam Butler, Sebastian M Waszak, Fabio CP Navarro, Steven E Schumacher, Jean Monlong, Francesco Maura, Niccolo Bolli, Guillaume Bourque, Mark Gerstein, Peter J Park, David C Wedge, Rameen Beroukhim, David Torrents, Jan O Korbel, Iñigo Martincorena, Rebecca C Fitzgerald, Peter Van Loo, Haig H Kazazian, Kathleen H Burns, PCAWG Structural Variation Working Group, Peter J Campbell, Jose MC Tubio, PCAWG Consortium
Jan 14, 2019
About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from...
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
The GRAPPA-OMERACT Working Group
Ying Ying Leung, William Tillett, Ana-Maria Orbai, Alexis Ogdie, Lihi Eder, Laura C Coates, Richard Holland, Anna Antony, Niti Goel, Philip J Mease
Jun 30, 2020
The Group for Research and Assessment of Psoriasis and Psoriatic Arthritis (GRAPPA)-Outcome Measures in Rheumatology (OMERACT) Psoriatic Arthritis (PsA) working group provided updates at the 2019 GRAPPA annual meeting on its...
Annexin A1 expression in a pooled breast cancer series
Marcelo Sobral-Leite, Jelle Wesseling, Vincent T H B M Smit, Heli Nevanlinna, Martine H van Miltenburg, Joyce Sanders, Ingrid Hofland, Fiona M Blows, Penny Coulson, Gazinska Patrycja, Jan H M Schellens, Rainer Fagerholm, Päivi Heikkilä, Kristiina Aittomäki, Carl Blomqvist, Elena Provenzano, Hamid R Ali, Jonine Figueroa, Mark Sherman, Jolanta Lissowska, Arto Mannermaa, Vesa Kataja, Veli-Matti Kosma, Jaana M Hartikainen, Kelly-Anne Phillips, Fergus J Couch, Janet E Olson, Celine Vachon, Daniel Visscher, Hermann Brenner, Katja Butterbach, Volker Arndt, Bernd Holleczek, Maartje J Hooning, Antoinette Hollestelle, John W. M. Martens, Carolien H M van Deurzen, Bob van de Water, Annegien Broeks, Jenny Chang-Claude, Georgia Chenevix-Trench, Douglas F Easton, Paul D P Pharoah, Montserrat García-Closas, Marjo de Graauw, Marjanka K Schmidt
Sep 29, 2016
Abstract
Background
Annexin A1 (ANXA1) is a protein related with the carcinogenesis process and metastasis formation in many tumors. However, little is known about the prognostic...
The GRAPPA-OMERACT Working Group
Ying Ying Leung, William Tillett, Ana-Maria Orbai, Alexis Ogdie, Lihi Eder, Laura C Coates, Richard Holland, Anna Antony, Niti Goel, Philip J Mease
Jun 30, 2020
The Group for Research and Assessment of Psoriasis and Psoriatic Arthritis (GRAPPA)-Outcome Measures in Rheumatology (OMERACT) Psoriatic Arthritis (PsA) working group provided updates at the 2019 GRAPPA annual meeting on its...
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...
Brain tumor research in the United Kingdom
Kathreena M Kurian, Michael D Jenkinson, Paul M Brennan, Robin Grant, Sarah Jefferies, Alasdair G Rooney, Helen Bulbeck, Sara C Erridge, Samantha Mills, Catherine McBain, Martin G McCabe, Stephen J Price, Silvia Marino, Erica Moyes, Wendy Qian, Adam Waldman, Babar Vaqas, Debbie Keatley, Peter Burchill, Colin Watts
Dec 12, 2017
The National Cancer Research Institute (NCRI) is a partnership of charity and government research funders whose purpose is to improve health and quality of life by accelerating progress in cancer-related research through...
The tale of TILs in breast cancer
Khalid El Bairi, Harry R Haynes, Elizabeth Blackley, Susan Fineberg, Jeffrey Shear, Sophia Turner, Juliana Ribeiro de Freitas, Daniel Sur, Luis Claudio Amendola, Masoumeh Gharib, Amine Kallala, Indu Arun, Farid Azmoudeh-Ardalan, Luciana Fujimoto, Luz F Sua, Shi-Wei Liu, Huang-Chun Lien, Pawan Kirtani, Marcelo Balancin, Hicham El Attar, Prerna Guleria, Wenxian Yang, Emad Shash, I-Chun Chen, Veronica Bautista, Jose Fernando Do Prado Moura, Bernardo L Rapoport, Carlos Castaneda, Eunice Spengler, Gabriela Acosta-Haab, Isabel Frahm, Joselyn Sanchez, Miluska Castillo, Najat Bouchmaa, Reena R Md Zin, Ruohong Shui, Timothy Onyuma, Wentao Yang, Zaheed Husain, Karen Willard-Gallo, An Coosemans, Edith A Perez, Elena Provenzano, Paula Gonzalez Ericsson, Eduardo Richardet, Ravi Mehrotra, Sandra Sarancone, Anna Ehinger, David L Rimm, John MS Bartlett, Giuseppe Viale, Carsten Denkert, Akira I Hida, Christos Sotiriou, Sibylle Loibl, Stephen M Hewitt, Sunil Badve, William Fraser Symmans, Rim S Kim, Giancarlo Pruneri, Shom Goel, Prudence A Francis, Gloria Inurrigarro, Rin Yamaguchi, Hernan Garcia-Rivello, Hugo Horlings, Said Afqir, Roberto Salgado, Sylvia Adams, Marleen Kok, Maria Vittoria Dieci, Stefan Michiels, Sandra Demaria, Sherene Loi, International Immuno-Oncology Biomarker Working Group
Dec 15, 2021
The advent of immune-checkpoint inhibitors (ICI) in modern oncology has significantly improved survival in several cancer settings. A subgroup of women with breast cancer (BC) has immunogenic infiltration of lymphocytes with...
The Neurology and Neurosurgery Interest Group (NANSIG)-ten years of cultivating interest in clinical neurosciences.
Jay J Park, Setthasorn Zhi Yang Ooi, Conor S Gillespie, Soham Bandyopadhyay, Yasir A Chowdhury, Georgios Solomou, Melissa Gough, Ulrick Sidney Kanmounye, Alvaro Yanez Touzet, Michael TC Poon, Andreas K Demetriades, Michael D Jenkinson, Alistair Jenkins, Neurology and Neurosurgery Interest Group (NANSIG)
Mar 31, 2022
Collaboration and successful teamworking are important components of clinical practise, and these skills should be cultivated early in medical school. The breadth of current medical school curricula means that students often...
|
|< |
< |
1 |