COSMIC: High‐Resolution Cancer Genetics Using the Catalogue of Somatic Mutations in Cancer

Forbes, Simon; Beare, David; Bindal, Nidhi; Bamford, Sally; Ward, Sari; Cole, Charlotte G.; Jia, Mingming; Kok, Chai Yin; Boutselakis, Harry; De, Tisham; Sońdka, Zbysław; Ponting, Laura; Stefancsik, Raymund; Harsha, Bhavana; Tate, John; Dawson, Elisabeth; Thompson, Samantha L.; Jubb, Harry; Campbell, Peter J.

doi:10.1002/cphg.21

Cited by 123 publications

(131 citation statements)

References 21 publications

(25 reference statements)

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“…Further, violin plots are displayed to visualize the distribution, median and interquartile range of methylation profiles of the query CpG site in relation to patient characteristics such as age ( Figure 2C), sex ( Figure 2D), clinical stage ( Figure 2E), etc. We also provide a link to external browsers including 'GeneCards' [37], 'COSMIC' [38] and 'Gene Ontology' [39] to explore additional information related to the query gene.…”

Section: Construction Of the Web Toolmentioning

confidence: 99%

MethSurv: A Web Tool to Perform Multivariable Survival Analysis Using DNA Methylation Data

et al. 2017

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Aim:To develop a web tool for survival analysis based on CpG methylation patterns. Materials & methods: We utilized methylome data from 'The Cancer Genome Atlas' and used the Cox proportional-hazards model to develop an interactive web interface for survival analysis. Results: MethSurv enables survival analysis for a CpG located in or around the proximity of a query gene. For further mining, cluster analysis for a query gene to associate methylation patterns with clinical characteristics and browsing of top biomarkers for each cancer type are provided. MethSurv includes 7358 methylomes from 25 different human cancers. Conclusion: The MethSurv tool is a valuable platform for the researchers without programming skills to perform the initial assessment of methylation-based cancer biomarkers.

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Section: Construction Of the Web Toolmentioning

confidence: 99%

MethSurv: A Web Tool to Perform Multivariable Survival Analysis Using DNA Methylation Data

et al. 2017

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“…In BC, the most frequently mutated genes are PIK3CA (25%), TP53 (23%), CDH1 (11%), GATA3 (7%), and PTEN (5%) 54,55 . In YWBC, Encinas et al 56 performed a systematic review to analyze whether somatic mutations in five genes were associated with an early age at presentation of BC.…”

Section: Somatic Mutation Profile In Ywbcmentioning

confidence: 99%

Molecular Biology In Young Women With Breast Cancer: From Tumor Gene Expression To Dna Mutations

Gómez-Flores-Ramos¹,

Castro-Sánchez

Peña-Curiel

et al. 2017

RIC

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Young women with breast cancer (YWBC) represent roughly 15% of breast cancer (BC) cases in Latin America and other developing regions. Breast tumors occurring at an early age are more aggressive and have an overall worse prognosis compared to breast tumors in postmenopausal women. The expression of relevant proliferation biomarkers such as endocrine receptors and human epidermal growth factor receptor 2 appears to be unique in YWBC. Moreover, histopathological, molecular, genetic, and genomic studies have shown that YWBC exhibit a higher frequency of aggressive subtypes, differential tumor gene expression, increased genetic susceptibility, and specific genomic signatures, compared to older women with BC. This article reviews the current knowledge on tumor biology and genomic signatures in YWBC.

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“…Approximately 4 million coding mutations have been identified, defining 500 genes that act as functional cancer drivers [5,6], many of which participate in core cancer pathways [7]. The ability to define hyperactivated signaling pathways that are commonly deregulated allows for development of new therapies.…”

Section: Identification Of Key Driver Mutations In Hematopoietic Cancermentioning

confidence: 99%

Emerging therapeutic targets in myeloproliferative neoplasms and peripheral T-cell leukemia and lymphomas

Orlova

Wingelhofer

Neubauer

et al. 2017

Expert Opinion on Therapeutic Targets

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Introduction: Hematopoietic neoplasms are often driven by gain-of-function mutations of the JAK-STAT pathway together with mutations in chromatin remodeling and DNA damage control pathways. The interconnection between the JAK-STAT pathway, epigenetic regulation or DNA damage control is still poorly understood in cancer cell biology. Areas covered: Here, we focus on a broader description of mutational insights into myeloproliferative neoplasms and peripheral T-cell leukemia and lymphomas, since sequencing efforts have identified similar combinations of driver mutations in these diseases covering different lineages. We summarize how these pathways might be interconnected in normal or cancer cells, which have lost differentiation capacity and drive oncogene transcription. Expert opinion: Due to similarities in driver mutations including epigenetic enzymes, JAK-STAT pathway activation and mutated checkpoint control through TP53, we hypothesize that similar therapeutic approaches could be of benefit in these diseases. We give an overview of how driver mutations in these malignancies contribute to hematopoietic cancer initiation or progression, and how these pathways can be targeted with currently available tools.

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COSMIC: High‐Resolution Cancer Genetics Using the Catalogue of Somatic Mutations in Cancer

Cited by 123 publications

References 21 publications

MethSurv: A Web Tool to Perform Multivariable Survival Analysis Using DNA Methylation Data

MethSurv: A Web Tool to Perform Multivariable Survival Analysis Using DNA Methylation Data

Molecular Biology In Young Women With Breast Cancer: From Tumor Gene Expression To Dna Mutations

Emerging therapeutic targets in myeloproliferative neoplasms and peripheral T-cell leukemia and lymphomas

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