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COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

S. A. Forbes, N. Bindal, S. Bamford, C. Cole, C. Y. Kok, D. Beare, M. Jia, R. Shepherd, K. Leung, A. Menzies, J. W. Teague, P. J. Campbell (+2 others)
2010 Nucleic Acids Research  
ACKNOWLEDGEMENTS We would like to thank Magali Olivier for her substantial help interpreting the IARC p53 R14 database for upload into COSMIC.  ...  With the increasing genomic context in COSMIC, the system has expanded to encompass the complete annotation of somatic mutations across whole genomes, including all coding and non-coding mutations, structural  ...  In the age of whole cancer genome sequencing, it is now possible to describe the genomewide somatic mutation content of a tumour sample, including structural rearrangements and non-coding variants.  ... 
doi:10.1093/nar/gkq929 pmid:20952405 pmcid:PMC3013785 fatcat:abmtyhmnnnhv7jm4pw57loy75q

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.  ...  All these types of somatic mutation are annotated to both the human genome and each affected coding gene, then correlated across disease and mutation types.  ...  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  
increase in the size of the human population.  ...  The unprecedented magnitude of this dataset allowed us to rigorously characterize the large variation in nucleotide diversity among genes (ranging from 0 to 1.32%), as well as the role of positive and  ...  novo copy number variation, de novo point mutations of large eff ect could explain the majority of all mental retardation cases in the population.  ... 
doi:10.1186/gb-2011-12-s1-p3 fatcat:m3f5onqq55ajtgfh6g3ucpso7y

Data mining using the Catalogue of Somatic Mutations in Cancer BioMart

R. Shepherd, S. A. Forbes, D. Beare, S. Bamford, C. G. Cole, S. Ward, N. Bindal, P. Gunasekaran, M. Jia, C. Y. Kok, K. Leung, A. Menzies (+5 others)
2011 Database: The Journal of Biological Databases and Curation  
Catalogue of Somatic Mutations in Cancer (COSMIC) (http://www.sanger.ac.uk/cosmic) is a publicly available resource providing information on somatic mutations implicated in human cancer.  ...  This article describes the data available in COSMIC along with examples of how to successfully mine and integrate data sets using COSMICMart.  ...  COSMIC has been successfully adapted to hold complete catalogues of somatic mutations for individual cancer samples.  ... 
doi:10.1093/database/bar018 pmid:21609966 pmcid:PMC3263736 fatcat:axe4zjyrpvgy7ecqtka66h4lc4

Databases and Web Tools for Cancer Genomics Study

Yadong Yang, Xunong Dong, Bingbing Xie, Nan Ding, Juan Chen, Yongjun Li, Qian Zhang, Hongzhu Qu, Xiangdong Fang
2015 Genomics, Proteomics & Bioinformatics  
The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge.  ...  Here, we describe the web resources for cancer genomics research and rate them on the basis of the diversity of cancer types, sample size, omics data comprehensiveness, and user experience.  ...  Catalogue Of Somatic Mutations In Cancer The Catalogue Of Somatic Mutations In Cancer (COSMIC) is the largest database of somatic mutations and their effects on human cancer [2] .  ... 
doi:10.1016/j.gpb.2015.01.005 pmid:25707591 pmcid:PMC4411507 fatcat:nn4g76i3b5gbln2cqqkzs2irza

Identification of candidate genes for lung cancer somatic mutation test kits

Yong Chen, Jian-Xin Shi, Xu-Feng Pan, Jian Feng, Heng Zhao
2013 Genetics and Molecular Biology  
In this study, we constructed a more complete catalogue of lung cancer mutation events including 145 mutated genes.  ...  In this study, we analyzed the latest lung cancer data in the COSMIC database, in order to find genomic "hotspots" that are frequently mutated in human lung cancer genomes.  ...  To construct a complete dataset of cancer mutation information, we had to start by finding a complete catalogue of gene mutations in lung cancer patients.  ... 
doi:10.1590/s1415-47572013000300022 pmid:24130455 pmcid:PMC3795175 fatcat:7zbabhbwmjexrmm3bpxown6mty

Discovering novel driver mutations from pan-cancer analysis of mutational and gene expression profiles

Houriiyah Tegally, Kevin H. Kensler, Zahra Mungloo-Dilmohamud, Anisah W. Ghoorah, Timothy R. Rebbeck, Shakuntala Baichoo, Sophia N. Karagiannis
2020 PLoS ONE  
As the genomic profile across cancers varies from person to person, patient prognosis and treatment may differ based on the mutational signature of each tumour.  ...  Large-scale cancer genomics initiatives, such as TCGA, ICGC and GENIE have enabled the analysis of thousands of tumour genomes.  ...  in the Catalogue of Somatic Mutations in Cancer (COSMIC) or PLOS ONE not.  ... 
doi:10.1371/journal.pone.0242780 pmid:33232371 pmcid:PMC7685479 fatcat:cju7lhkgcveitf6zuqqkp22ozi

A Cancer Genomics Data Space within the Linked Open Data (LOD) Cloud

Durre Zehra, Alokkumar Jha, Yasar Khan, Ali Hasnain, Mathieu d'Aquin, Ratnesh Sahay
2019 International Semantic Web Conference  
Atlas (TCGA), Catalogue of Somatic Mutations in Cancer (COSMIC), and Copy Number Variation in Disease (CNVD)).  ...  In this paper we provide a short overview of three types of cancer genomics datasets that are transformed from raw formats (csv, tsv, relational, etc.) into a set of linked datasets within the Linked Open  ...  COSMIC 5 is a comprehensive database for exploring somatic mutations in key cancer genes across different cancer samples.  ... 
dblp:conf/semweb/ZehraJKHdS19 fatcat:olnj43ullrdbrosle3wejshtfy

Human variation databases

J. Kuntzer, D. Eggle, S. Klostermann, H. Burtscher
2010 Database: The Journal of Biological Databases and Curation  
This work was supported by the Roche Postdoc Fellowship Program. Conflict of interest. None declared.  ...  of Somatic Mutations in Cancer (COSMIC) http://www.sanger.ac.  ...  , Catalog of Somatic Mutations in Cancer (COSMIC) (42), TCGA (35), Roche Cancer Genome Database (RCGDB) and Human Gene Mutation Database (HGMD Õ ) (43). ...........................................  ... 
doi:10.1093/database/baq015 pmid:20639550 pmcid:PMC2911800 fatcat:aihq3cfy3redpjf2wtm2rngggm

Human cancer databases (Review)

ATHANASIA PAVLOPOULOU, DEMETRIOS A. SPANDIDOS, IOANNIS MICHALOPOULOS
2014 Oncology Reports  
data in the form of raw sequences and polymorphisms to well-annotated, structured data. consequently, the storage, mining, retrieval and analysis of these data in an efficient and meaningful manner pose  ...  cancer is one of the four major non-communicable diseases (ncD), responsible for ~14.6% of all human deaths. currently, there are >100 different known types of cancer and >500 genes involved in cancer.  ...  Immunome Database http://ludwig-sun5.unil.ch/cancerImmunomeDB/ (68) cosMIc catalogue of somatic Mutations in cancer http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/ (18) cosMIcMart  ... 
doi:10.3892/or.2014.3579 pmid:25369839 pmcid:PMC4254674 fatcat:rqs4fdfqsze4fmypfkbqy4ibzu

Somatic synonymous mutations in regulatory elements contribute to the genetic aetiology of melanoma

Di Zhang, Junfeng Xia
2020 BMC Medical Genomics  
We explored the role of somatic synonymous mutations in melanoma samples from TCGA (The Cancer Genome Atlas).  ...  These findings confirm the functional consequences of somatic synonymous mutations in melanoma, emphasizing the significance of research in future studies.  ...  methods and application in medical genomics (part 1).  ... 
doi:10.1186/s12920-020-0685-2 pmid:32241263 fatcat:6ddeq6wxzbebhop2vyqriilfju

Cause of Cambrian Explosion - Terrestrial or Cosmic?

Edward J. Steele, Shirwan Al-Mufti, Kenneth A. Augustyn, Rohana Chandrajith, John P. Coghlan, S.G. Coulson, Sudipto Ghosh, Mark Gillman, Reginald M. Gorczynski, Brig Klyce, Godfrey Louis, Kithsiri Mahanama (+21 others)
2018 Progress in Biophysics and Molecular Biology  
A second focus is the remarkable evolution of intelligent complexity (Cephalopods) culminating in the emergence of the Octopus.  ...  We review the salient evidence consistent with or predicted by the Hoyle-Wickramasinghe (H-W) thesis of Cometary (Cosmic) Biology. Much of this physical and biological evidence is multifactorial.  ...  Conflicts of interest The authors declare no conflict of interest. Author contributions  ... 
doi:10.1016/j.pbiomolbio.2018.03.004 pmid:29544820 fatcat:c2irhaw2nnaoxfzv6fviywkhgm

dbGENVOC: database of GENomic Variants of Oral Cancer, with special reference to India

Sanchari Pradhan, Subrata Das, Animesh K Singh, Chitrarpita Das, Analabha Basu, Partha P Majumder, Nidhan K Biswas
2021 Database: The Journal of Biological Databases and Curation  
Presently, the web-accessible database allows potential users to mine data on ∼24 million clinically relevant somatic and germline variants derived from exomes (n = 100) and whole genomes (n = 5) of Indian  ...  Oral cancer is highly prevalent in India and is the most frequent cancer type among Indian males. It is also very common in southeast Asia.  ...  ) COSMIC Catalogue of Somatic Mutations in Cancer http://cancer.sanger.ac.uk/cancergenome/projects/ cosmic/ (12) MethyCancer A database of human DNA methylation and cancer http://methycancer.psych.ac.cn  ... 
doi:10.1093/database/baab034 pmid:34048545 fatcat:7yohuchcnfbxjntbwer4uh77ta

Identifying the role of Wilms tumor 1 associated protein in cancer prediction using integrative genomic analyses

Li-Sheng Wu, Jia-Yi Qian, Minghai Wang, Haiwei Yang
2016 Molecular Medicine Reports  
By searching the Catalogue of Somatic Mutations in Cancer database, 65 somatic mutations were identified in the human WTAP gene from the cancer tissue samples.  ...  The present study identified 44 complete WTAP genes in the genomes of vertebrates, including fish, amphibians, birds and mammals.  ...  ), and the Priority Academic Program Development of Jiangsu Higher Education Institutions.  ... 
doi:10.3892/mmr.2016.5528 pmid:27430156 fatcat:hqx233l7wfa5jg62tzrpuva7xq

ISOWN: accurate somatic mutation identification in the absence of normal tissue controls

Irina Kalatskaya, Quang M. Trinh, Melanie Spears, John D. McPherson, John M. S. Bartlett, Lincoln Stein
2017 Genome Medicine  
A key step in cancer genome analysis is the identification of somatic mutations in the tumor.  ...  Conclusions: In this work, we describe the development, implementation, and validation of ISOWN, an accurate algorithm for predicting somatic mutations in cancer tissues in the absence of matching normal  ...  of the ISOWN algorithm.  ... 
doi:10.1186/s13073-017-0446-9 pmid:28659176 pmcid:PMC5490163 fatcat:rkvpzz35vzcndpqastvzfk7v4q
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