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Results: 86976
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...
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...
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...
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...
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...
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...
The evolutionary history of 2,658 cancers.
Moritz Gerstung, Clemency Jolly, Ignaty Leshchiner, Stefan C Dentro, Santiago Gonzalez, Daniel Rosebrock, Thomas J Mitchell, Yulia Rubanova, Pavana Anur, Kaixian Yu, Maxime Tarabichi, Amit Deshwar, Jeff Wintersinger, Kortine Kleinheinz, Ignacio Vázquez-García, Kerstin Haase, Lara Jerman, Subhajit Sengupta, Geoff Macintyre, Salem Malikic, Nilgun Donmez, Dimitri G Livitz, Marek Cmero, Jonas Demeulemeester, Steven Schumacher, Yu Fan, Xiaotong Yao, Juhee Lee, Matthias Schlesner, Paul C Boutros, David D Bowtell, Hongtu Zhu, Gad Getz, Marcin Imielinski, Rameen Beroukhim, S Cenk Sahinalp, Yuan Ji, Martin Peifer, Florian Markowetz, Ville Mustonen, Ke Yuan, Wenyi Wang, Quaid D Morris, PCAWG Evolution & Heterogeneity Working Group, Paul T Spellman, David C Wedge, Peter Van Loo, PCAWG Consortium
Feb 04, 2021
Cancer develops through a process of somatic evolution1,2. Sequencing data from a single biopsy represent a snapshot of this process that can reveal the timing of specific genomic aberrations and the changing influence of...
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...
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...
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...
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
Intra-tumor heterogeneity
Multiple subclonal populations of tumor cells can coexist within the same tumor. This intra-tumor heterogeneity will have clinical implications and it is therefore important to identify factors that drive or suppress such...
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...
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...
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...
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...
Intra-tumor heterogeneity
Multiple subclonal populations of tumor cells can coexist within the same tumor. This intra-tumor heterogeneity will have clinical implications and it is therefore important to identify factors that drive or suppress such...
Assessment of venous hemodynamics and volume homeostasis during pregnancy
Venous hemodynamics and volume homeostasis are important aspects of cardiovascular physiology. However, today their relevance is still very much underappreciated. Their most important role is maintenance and control of venous...
maternal hemodynamics plasma volume Pregnancy venous hemodynamics venous return volume homeostasis Blood Flow Velocity cardiac output Cardiovascular Physiological Phenomena Consensus Development Conferences as Topic Female Guidelines as Topic Hemodynamics Homeostasis Humans Maternal Health Pregnancy Pregnancy Complications Cardiovascular Prenatal Diagnosis Uterine Artery
Changing the name of diabetes insipidus
Working Group for Renaming Diabetes Insipidus, Hiroshi Arima, Timothy Cheetham, Mirjam Christ-Crain, Deborah Cooper, Mark Gurnell, Juliana B Drummond, Miles Levy, Ann I McCormack, Joseph Verbalis, John Newell-Price, John AH Wass
Nov 16, 2022
'What's in a name? That which we call a rose/By any other name would smell as sweet' (Juliet, from Romeo and Juliet by William Shakespeare). Shakespeare's implication is that a name is nothing but a word, and it therefore...
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...
Working for the future
Tochukwu Nweze, Mary Basil Nwoke, Juliet Ifeoma Nwufo, Richard Ikechukwu Aniekwu, Florian Lange
Jun 12, 2020
BACKGROUND: The dominant view based on the deficit model of developmental psychopathology is that early adverse rearing impairs cognition. In contrast, an emerging evolutionary-developmental model argues that individuals exposed...
Genomic basis for RNA alterations in cancer.
PCAWG Transcriptome Core Group, Claudia Calabrese, Natalie R Davidson, Deniz Demircioğlu, Nuno A Fonseca, Yao He, André Kahles, Kjong-Van Lehmann, Fenglin Liu, Yuichi Shiraishi, Cameron M Soulette, Lara Urban, Liliana Greger, Siliang Li, Dongbing Liu, Marc D Perry, Qian Xiang, Fan Zhang, Junjun Zhang, Peter Bailey, Serap Erkek, Katherine A Hoadley, Yong Hou, Matthew R Huska, Helena Kilpinen, Jan O Korbel, Maximillian G Marin, Julia Markowski, Tannistha Nandi, Qiang Pan-Hammarström, Chandra Sekhar Pedamallu, Reiner Siebert, Stefan G Stark, Hong Su, Patrick Tan, Sebastian M Waszak, Christina Yung, Shida Zhu, Philip Awadalla, Chad J Creighton, Matthew Meyerson, BF Francis Ouellette, Kui Wu, Huanming Yang, PCAWG Transcriptome Working Group, Alvis Brazma, Angela N Brooks, Jonathan Göke, Gunnar Rätsch, Roland F Schwarz, Oliver Stegle, Zemin Zhang, PCAWG Consortium
Feb 04, 2021
Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is...
Heterogeneity of genomic evolution and mutational profiles in multiple myeloma.
Niccolo Bolli, Hervé Avet-Loiseau, David C Wedge, Peter Van Loo, Ludmil B Alexandrov, Inigo Martincorena, Kevin J Dawson, Francesco Iorio, Serena Nik-Zainal, Graham R Bignell, Jonathan W Hinton, Yilong Li, Jose MC Tubio, Stuart McLaren, Sarah O' Meara, Adam P Butler, Jon W Teague, Laura Mudie, Elizabeth Anderson, Naim Rashid, Yu-Tzu Tai, Masood A Shammas, Adam S Sperling, Mariateresa Fulciniti, Paul G Richardson, Giovanni Parmigiani, Florence Magrangeas, Stephane Minvielle, Philippe Moreau, Michel Attal, Thierry Facon, P Andrew Futreal, Kenneth C Anderson, Peter J Campbell, Nikhil C Munshi
Nov 29, 2018
Multiple myeloma is an incurable plasma cell malignancy with a complex and incompletely understood molecular pathogenesis. Here we use whole-exome sequencing, copy-number profiling and cytogenetics to analyse 84 myeloma samples....
Adult Aged Antigens Nuclear Cohort Studies DNA Copy Number Variations Early Growth Response Protein 1 evolution Molecular Exome GTP Phosphohydrolases Genetic Heterogeneity Humans Lymphotoxin-beta Membrane Proteins Middle Aged multiple myeloma Mutation Mutation Missense Nerve Tissue Proteins Proto-Oncogene Proteins Proto-Oncogene Proteins B-raf Proto-Oncogene Proteins p21(ras) Receptors Immunologic Sequence Analysis DNA Transcription Factors Tumor Suppressor Protein p53 ras Proteins
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