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COSMIC: somatic cancer genetics at high-resolution

Simon A. Forbes, David Beare, Harry Boutselakis, Sally Bamford, Nidhi Bindal, John Tate, Charlotte G. Cole, Sari Ward, Elisabeth Dawson, Laura Ponting, Raymund Stefancsik, Bhavana Harsha (+7 others)
2016 Nucleic Acids Research  
COSMIC, the Catalogue of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk) is a high-resolution resource for exploring targets and trends in the genetics of human cancer.  ...  COSMIC now details the genetics of drug resistance, novel somatic gene mutations which allow a tumour to evade therapeutic cancer drugs.  ...  Further funds supporting additional curation and website development have been provided via licensing of the COSMIC database to commercial organisations.  ... 
doi:10.1093/nar/gkw1121 pmid:27899578 pmcid:PMC5210583 fatcat:pj6xanlwqrhbnfbfvv2gy7oay4

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

Simon A. Forbes, David Beare, Prasad Gunasekaran, Kenric Leung, Nidhi Bindal, Harry Boutselakis, Minjie Ding, Sally Bamford, Charlotte Cole, Sari Ward, Chai Yin Kok, Mingming Jia (+5 others)
2014 Nucleic Acids Research  
COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://cancer.sanger.ac.uk) is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer.  ...  Combination of almost 20 000 published studies gives substantial resolution of how mutations and phenotypes relate in human cancer, providing insights into the stratification of mutations and biomarkers  ...  Somatic mutations in cancer are now described across almost all human genes.  ... 
doi:10.1093/nar/gku1075 pmid:25355519 pmcid:PMC4383913 fatcat:i5aiafyob5dalppyerjp7esowe

COSMIC: the catalogue of somatic mutations in cancer

Nidhi Bindal, Simon A Forbes, David Beare, Prasad Gunasekaran, Kenric Leung, Chai Kok, Mingming Jia, Sally Bamford, Charlotte Cole, Sari Ward, Jon Teague, Michael R Stratton (+2 others)
2011 Genome Biology  
The expression values for these proteins in FlyAtlas showed that The Catalogue Of Somatic Mutations In Cancer (COSMIC)[1] is one of the largest repositories of information on somatic mutations in human  ...  We identifi ed more than 7.2 million signifi cant interactions at single-gene resolution using the RH data.  ...  Mutations in Cancer (COSMIC) database.  ... 
doi:10.1186/gb-2011-12-s1-p3 fatcat:m3f5onqq55ajtgfh6g3ucpso7y

Evaluating biomarkers to model cancer risk post cosmic ray exposure

Deepa M. Sridharan, Aroumougame Asaithamby, Steve R. Blattnig, Sylvain V. Costes, Paul W. Doetsch, William S. Dynan, Philip Hahnfeldt, Lynn Hlatky, Yared Kidane, Amy Kronenberg, Mamta D. Naidu, Leif E. Peterson (+8 others)
2016 Life Sciences in Space Research  
Chronic exposure to cosmic rays in the context of the complex deep space environment may place astronauts at high cancer risk.  ...  Other biomarkers discussed, often assayed for at longer points post exposure, include mutations, chromosome aberrations, reactive oxygen species and telomere length changes.  ...  at high dose rates and close to linearity at low dose rates (LDR).  ... 
doi:10.1016/j.lssr.2016.05.004 pmid:27345199 pmcid:PMC5613937 fatcat:3geic35wtjc3tilibs45oxm67y

Long-Term Rearing of Medaka Aboard ISS to Clarify the Trans-Generation Effects in Vertebrates Induced by Cosmic Ray Irradiation

Shoji ODA, Yusuke URUSHIHARA, Yukie HIGA, Toyoko KUNO, Yasuhiro KAMEI, Tomoko ISHIKAWA, Chiaki MUKAI, Takeshi TODO, Hiroshi MITANI
2010 TRANSACTIONS OF THE JAPAN SOCIETY FOR AERONAUTICAL AND SPACE SCIENCES AEROSPACE TECHNOLOGY JAPAN  
The effect of cosmic ray irradiation on astronaut health is a major problem to be addressed in the near future, however, it is not clear whether or not long-term irradiation of cosmic ray has trans-generation  ...  Cosmic-ray irradiation would induce deletion type DNA lesions and a sperm would lose fluorescence if the deletion occurs in the transgenes in the sperm genome.  ...  These characters make medaka to be an excellent experimental animal for decades in physiology, developmental biology, genetics, cancer biology and radiation biology.  ... 
doi:10.2322/tastj.8.tp_1 fatcat:3sb2ozcp6vcelhkx6y6mhcxswu

Understanding the impacts of missense mutations on structures and functions of human cancer-related genes: A preliminary computational analysis of the COSMIC Cancer Gene Census

Sony Malhotra, Ali F. Alsulami, Yang Heiyun, Bernardo Montano Ochoa, Harry Jubb, Simon Forbes, Tom L. Blundell, Yang Zhang
2019 PLoS ONE  
To complement the wealth of information on the genetics of cancer in COSMIC, the most comprehensive database for cancer somatic mutations available, structural information obtained experimentally has been  ...  Even where structural information is available for a gene in the Cancer Gene Census, a list of genes in COSMIC with substantial evidence supporting their impacts in cancer, this information is quite often  ...  COSMIC [3] , the Catalogue of Somatic Mutations in Cancer, is currently the most comprehensive database of mutations in cancer.  ... 
doi:10.1371/journal.pone.0219935 pmid:31323058 pmcid:PMC6641202 fatcat:7o3ijgdk2zdmjgnglv4tywttry

Target genes discovery through copy number alteration analysis in human hepatocellular carcinoma

De-Leung Gu
2013 World Journal of Gastroenterology  
High-throughput short-read sequencing of exomes and whole cancer genomes in multiple human hepatocellular carcinoma (HCC) cohorts confirmed previously identified frequently mutated somatic genes, such  ...  Recently developed high-throughput short-read sequencing technologies were used to identify somatic mutations in HCC cancer genomes at genome-wide scales.  ...  and provide lines [57] COSMIC Catalogue of somatic mutations in cancer http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/ Forbes et al [58] ICGC International Cancer Genome Consortium provides  ... 
doi:10.3748/wjg.v19.i47.8873 pmid:24379610 pmcid:PMC3870538 fatcat:bg3zh4ptnvhqlapkkeg4gxbsyu

OncoBase: a platform for decoding regulatory somatic mutations in human cancers

Xianfeng Li, Leisheng Shi, Yan Wang, Jianing Zhong, Xiaolu Zhao, Huajing Teng, Xiaohui Shi, Haonan Yang, Shasha Ruan, MingKun Li, Zhong Sheng Sun, Qimin Zhan (+1 others)
2018 Nucleic Acids Research  
Herein, we present OncoBase (http://www.oncobase.biols.ac.cn/), an integrated database for annotating 81 385 242 somatic mutations in 68 cancer types from more than 120 cancer projects by exploring their  ...  Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers, and the vast majority of them are located outside of coding sequences, making  ...  ACKNOWLEDGEMENTS We thank Dr Chenghang Du in the Beijing Institutes of Life Science, Chinese Academy of Sciences for his help in maintaining the high performance computing systems.  ... 
doi:10.1093/nar/gky1139 pmid:30445567 pmcid:PMC6323961 fatcat:wt3bpdaiavgb5csjxdkxaw67qe

Whole-exome sequencing of pediatric acute lymphoblastic leukemia

H Lilljebjörn, M Rissler, C Lassen, J Heldrup, M Behrendtz, F Mitelman, B Johansson, T Fioretos
2011 Leukemia  
Acknowledgements This work was supported by grants from the Swedish Cancer Society, the Swedish Childhood Cancer Foundation, the Swedish Research Council (personal project grant to T.F.; Hemato-Linne and  ...  BioCARE strategic research program grants), the Inga-Britt and Arne Lundberg Foundation, the Gunnar Nilsson Cancer Foundation, and the Medical Faculty of Lund University.  ...  For example, eight of the genes with protein altering mutations (besides FLT3) are known from COSMIC to display somatic mutations in other types of cancer.  ... 
doi:10.1038/leu.2011.333 pmid:22094584 fatcat:vak3yzro3jh35haqvz5ilf4xhy

Novel Candidate Cancer Genes Identified by a Large-Scale Cross-Species Comparative Oncogenomics Approach

J. Mattison, J. Kool, A. G. Uren, J. de Ridder, L. Wessels, J. Jonkers, G. R. Bignell, A. Butler, A. G. Rust, M. Brosch, C. H. Wilson, L. van der Weyden (+8 others)
2010 Cancer Research  
Here we combine high-resolution CGH analysis of 598 human cancer cell lines with insertion sites isolated from 1,005 mouse tumors induced with the murine leukemia virus (MuLV).  ...  Collectively, this work provides a rich catalogue of new candidate cancer genes for functional analysis. Cancer Res; 70(3); 883-95.  ...  profile of candidate cancer genes at high resolution.  ... 
doi:10.1158/0008-5472.can-09-1737 pmid:20103622 pmcid:PMC2880710 fatcat:zv4rjudzpje4pljmahdm7767ym

Systematic analysis of somatic mutations driving cancer: uncovering functional protein regions in disease development

Bálint Mészáros, András Zeke, Attila Reményi, István Simon, Zsuzsanna Dosztányi
2016 Biology Direct  
These results indicate that the accumulation of local somatic mutations can be used to pinpoint genes responsible for cancer formation and can also help to understand the effect of cancer mutations at  ...  Conclusions: While local somatic mutations correspond to only a subset of genetic variations that can lead to cancer, our systematic analyses revealed that they represent an accompanying feature of most  ...  Methods COSMIC somatic mutations Cancer related somatic mutations were collected from version 73 of the COSMIC database (http://cancer. sanger.ac.uk/cosmic/) [8] .  ... 
doi:10.1186/s13062-016-0125-6 pmid:27150584 pmcid:PMC4858844 fatcat:5oq7dbbjjjamdmaqbia3mhnjkq

Classification of Cancer Primary Sites Using Machine Learning and Somatic Mutations

Yukun Chen, Jingchun Sun, Liang-Chin Huang, Hua Xu, Zhongming Zhao
2015 BioMed Research International  
The available big data of somatic mutations provides us a great opportunity to investigate cancer classification using machine learning.  ...  Here, we explored the patterns of 1,760,846 somatic mutations identified from 230,255 cancer patients along with gene function information using support vector machine.  ...  genome-wide mic-roRNA sequencing, and epigenomics, providing the highest resolution (base-pair resolution) of genetic and genomic information in cancer.  ... 
doi:10.1155/2015/491502 pmid:26539502 pmcid:PMC4619847 fatcat:zcummxlfsrhcfivnuly67itszm

Whole-Exome Sequencing Reveals Frequent Genetic Alterations in BAP1, NF2, CDKN2A, and CUL1 in Malignant Pleural Mesothelioma

G. Guo, J. Chmielecki, C. Goparaju, A. Heguy, I. Dolgalev, M. Carbone, S. Seepo, M. Meyerson, H. I. Pass
2014 Cancer Research  
Cancer Res; 75(2); 264-9. Ó2014 AACR.  ...  Integrative analysis of mutations and somatic copy-number alterations revealed frequent genetic alterations in BAP1, NF2, CDKN2A, and CUL1.  ...  Advances in technologies for high-throughput sequencing of DNA have enabled the comprehensive characterization of somatic mutations in different cancer types at an unprecedented resolution (6) .  ... 
doi:10.1158/0008-5472.can-14-1008 pmid:25488749 fatcat:3uik4yuno5getmawd4ugonqy5e

Mutation Screening of 1,237 Cancer Genes across Six Model Cell Lines of Basal-Like Breast Cancer

Eleonor Olsson, Christof Winter, Anthony George, Yilun Chen, Therese Törngren, Pär-Ola Bendahl, Åke Borg, Sofia K. Gruvberger-Saal, Lao H. Saal, Alvaro Galli
2015 PLoS ONE  
; COSMIC). 125 novel mutations were confirmed by Sanger sequencing (59 exonic, 48 3'UTR and 10 5'UTR, 1 splicing), with a validation rate of 94% of high confidence variants.  ...  In total, 658 somatic variants were identified, of which 378 were non-silent (average 63 per cell line, range 37-146) and 315 were novel (not present in the Catalogue of Somatic Mutations in Cancer database  ...  Acknowledgments We thank members of the Translational Oncogenomics Unit and Anders Kvist for valuable discussion, and Jeanette Valcich, Ulrika Åström, Ingrid Wilson, Björn Frostner, and Susanne André at  ... 
doi:10.1371/journal.pone.0144528 pmid:26670335 pmcid:PMC4684399 fatcat:rgowgwcjuzfuhflbycsf32y2ti

Toxicogenomics and Cancer Susceptibility: Advances with Next-Generation Sequencing

Baitang Ning, Zhenqiang Su, Nan Mei, Huixiao Hong, Helen Deng, Leming Shi, James C. Fuscoe, William H. Tolleson
2014 Journal of Environmental Science And Health Part C - Environmental Carcinogenesis & Ecotoxicology Reviews  
alterations with single-base resolution.  ...  Cancer is primarily a genetic disease in which genetic factors and environmental stimuli interact to cause genetic and epigenetic aberrations in human cells.  ...  [9] to next-generation sequencing (NGS) technology, which provides very high resolution genetic information relevant to carcinogenesis [10] .  ... 
doi:10.1080/10590501.2014.907460 pmid:24875441 pmcid:PMC5712441 fatcat:wmz5ezl2e5ag3glcdsj6fre37e
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