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Akehurst N, Bamford S, Brooks E. A specialist led back pain service in primary care. Advanced Practice Physiotherapists (APP) working as first contact practitioners (FCPs). Physiotherapy 2019. [DOI: 10.1016/j.physio.2018.11.077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Scharf T, Bamford S, Beach B. UNEQUAL SOCIAL RELATIONSHIPS: EVIDENCE FROM ENGLAND. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.3626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- T. Scharf
- Institute of Health & Society and Institute for Ageing, Newcastle University, Newcastle, United Kingdom,
| | - S. Bamford
- ILC-UK International Longevity Centre, London, United Kingdom
| | - B. Beach
- ILC-UK International Longevity Centre, London, United Kingdom
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Forbes SA, Beare D, Bindal N, Bamford S, Ward S, Cole CG, Jia M, Kok C, Boutselakis H, De T, Sondka Z, Ponting L, Stefancsik R, Harsha B, Tate J, Dawson E, Thompson S, Jubb H, Campbell PJ. COSMIC: High-Resolution Cancer Genetics Using the Catalogue of Somatic Mutations in Cancer. ACTA ACUST UNITED AC 2016; 91:10.11.1-10.11.37. [PMID: 27727438 DOI: 10.1002/cphg.21] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
COSMIC (http://cancer.sanger.ac.uk) is an expert-curated database of somatic mutations in human cancer. Broad and comprehensive in scope, recent releases in 2016 describe over 4 million coding mutations across all human cancer disease types. Mutations are annotated across the entire genome, but expert curation is focused on over 400 key cancer genes. Now encompassing the majority of molecular mutation mechanisms in oncogenetics, COSMIC additionally describes 10 million non-coding mutations, 1 million copy-number aberrations, 9 million gene-expression variants, and almost 8 million differentially methylated CpGs. This information combines a consistent interpretation of the data from the major cancer genome consortia and cancer genome literature with exhaustive hand curation of over 22,000 gene-specific literature publications. This unit describes the graphical Web site in detail; alternative protocols overview other ways the entire database can be accessed, analyzed, and downloaded. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- S A Forbes
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - D Beare
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - N Bindal
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - S Bamford
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - S Ward
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - C G Cole
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - M Jia
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - C Kok
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - H Boutselakis
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - T De
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Z Sondka
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - L Ponting
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - R Stefancsik
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - B Harsha
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - J Tate
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - E Dawson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - S Thompson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - H Jubb
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - P J Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
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Boutselakis C, Forbes SA, Gunasekaran P, Jia M, Beare D, Bindal N, Kok CY, Leung K, Minjie D, Shepherd R, Bamford S, Ward S, Cole C, Teague JW, Stratton M, Campbell P, McDermott U. Abstract 5326: COSMIC: Enhancing the world's knowledge of somatic mutations in human cancer. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-5326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
COSMIC, the Catalogue Of Somatic Mutations In Cancer (http://cancer.sanger.ac.uk) is the world's largest and most comprehensive online resource for exploring the impact of somatic mutations in human cancer. Now running for over 10 years, the 67th release (Oct 2013) describes 1592109 mutations in 947213 tumour samples across 25606 genes. This information is curated manually from the scientific literature, and automatically from genome resequencing consortium data portals. Full curation of the scientific literature provides in-depth understanding of the impact that each gene has in human cancer, and this has been achieved for 127 point-mutated cancer genes, and 185 fusion gene pairs. Curated genes are selected from the Cancer Gene Census (http://cancer.sanger.ac.uk/census), a listing of all genes with substantial evidence implicating them in cancer promotion, currently numbering 513 and updated frequently.
The mutations discovered in the re-sequencing of over 8000 tumour genomes are now present in COSMIC (viewable in isolation from the genic curations, http://cancer.sanger.ac.uk/wgs). In addition, the Sanger has now fully exome sequenced 1015 common cancer cell lines, identifying 1146874 coding mutations annotated for functional significance, and this is available exclusively in COSMIC at (http://cancer.sanger.ac.uk/cell_lines). While COSMIC has focused on point mutations and gene fusions, many other mutation mechanisms cause oncogenesis and these are now being integrated. The 67th COSMIC release includes copy number mutations integrated into the database and major web page views. To allow easy graphical examination of this data, copy number information was reduced to ‘gain’ and ‘loss’ annotations for inclusion in histograms and tables, with much more precise detail available with a further click. Copy number data is available in detail for every gene in COSMIC, and also for every tissue. Exploring cancer via COSMIC’s Cancer Browser (http://cancer.sanger.ac.uk/cosmic/browse/tissue), results not just in a plot of the most mutated genes, but now also a circular genome plot summarizing the copy number gains and losses across all the samples from that tumour type, all explorable in more detail via clicks on the pictures.
As the genomic data increases in COSMIC, it is becoming more important to qualitatively annotate the information, indicating which is more important or significant to oncogenesis. We are now building systems to better highlight known or putative functional mutations, improving the signal-to-noise ratio of cancer genome resequencing.
Citation Format: C Boutselakis, S A. Forbes, P Gunasekaran, M Jia, D Beare, N Bindal, C Y. Kok, K Leung, D Minjie, R Shepherd, S Bamford, S Ward, C Cole, J W. Teague, M Stratton, P Campbell, U McDermott. COSMIC: Enhancing the world's knowledge of somatic mutations in human cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5326. doi:10.1158/1538-7445.AM2014-5326
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Affiliation(s)
- C Boutselakis
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - S A. Forbes
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - P Gunasekaran
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - M Jia
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - D Beare
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - N Bindal
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - C Y. Kok
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - K Leung
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - D Minjie
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - R Shepherd
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - S Bamford
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - S Ward
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - C Cole
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - J W. Teague
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - M Stratton
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - P Campbell
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - U McDermott
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
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Shepherd R, Forbes SA, Beare D, Bamford S, Cole CG, Ward S, Bindal N, Gunasekaran P, Jia M, Kok CY, Leung K, Menzies A, Butler AP, Teague JW, Campbell PJ, Stratton MR, Futreal PA. Data mining using the Catalogue of Somatic Mutations in Cancer BioMart. Database (Oxford) 2011; 2011:bar018. [PMID: 21609966 PMCID: PMC3263736 DOI: 10.1093/database/bar018] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 04/15/2011] [Accepted: 04/19/2011] [Indexed: 01/10/2023]
Abstract
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. Release v51 (January 2011) includes data from just over 19,000 genes, 161,787 coding mutations and 5573 gene fusions, described in more than 577,000 tumour samples. COSMICMart (COSMIC BioMart) provides a flexible way to mine these data and combine somatic mutations with other biological relevant data sets. This article describes the data available in COSMIC along with examples of how to successfully mine and integrate data sets using COSMICMart. DATABASE URL: http://www.sanger.ac.uk/genetics/CGP/cosmic/biomart/martview/.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - P. Andrew Futreal
- Cancer Genome Project, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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Bamford S, Ward R. Predispositions to approach and avoid are contextually sensitive and goal dependent. J Vis 2010. [DOI: 10.1167/8.6.611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, Clements J, Menzies A, Teague JW, Futreal PA, Stratton MR. The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet 2008; Chapter 10:Unit 10.11. [PMID: 18428421 PMCID: PMC2705836 DOI: 10.1002/0471142905.hg1011s57] [Citation(s) in RCA: 572] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
COSMIC is currently the most comprehensive global resource for information on somatic mutations in human cancer, combining curation of the scientific literature with tumor resequencing data from the Cancer Genome Project at the Sanger Institute, U.K. Almost 4800 genes and 250000 tumors have been examined, resulting in over 50000 mutations available for investigation. This information can be accessed in a number of ways, the most convenient being the Web-based system which allows detailed data mining, presenting the results in easily interpretable formats. This unit describes the graphical system in detail, elaborating an example walkthrough and the many ways that the resulting information can be thoroughly investigated by combining data, respecializing the query, or viewing the results in different ways. Alternate protocols overview the available precompiled data files available for download.
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Affiliation(s)
- S A Forbes
- Wellcome Trust Genome Campus, Hinxton, United Kingdom
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Forbes S, Clements J, Dawson E, Bamford S, Webb T, Dogan A, Flanagan A, Teague J, Wooster R, Futreal PA, Stratton MR. COSMIC 2005. Br J Cancer 2006; 94:318-22. [PMID: 16421597 PMCID: PMC2361125 DOI: 10.1038/sj.bjc.6602928] [Citation(s) in RCA: 288] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Catalogue Of Somatic Mutations In Cancer (COSMIC) database and web site was developed to preserve somatic mutation data and share it with the community. Over the past 25 years, approximately 350 cancer genes have been identified, of which 311 are somatically mutated. COSMIC has been expanded and now holds data previously reported in the scientific literature for 28 known cancer genes. In addition, there is data from the systematic sequencing of 518 protein kinase genes. The total gene count in COSMIC stands at 538; 25 have a mutation frequency above 5% in one or more tumour type, no mutations were found in 333 genes and 180 are rarely mutated with frequencies <5% in any tumour set. The COSMIC web site has been expanded to give more views and summaries of the data and provide faster query routes and downloads. In addition, there is a new section describing mutations found through a screen of known cancer genes in 728 cancer cell lines including the NCI-60 set of cancer cell lines.
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Affiliation(s)
- S Forbes
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - J Clements
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - E Dawson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - S Bamford
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - T Webb
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - A Dogan
- Mayo Clinic, Department of Laboratory Medicine and Pathology, 200 First Street SW, Rochester, MN 55905, USA
| | - A Flanagan
- The Institute of Orthopaedics, UCL, Stanmore, Middlesex, HA7 4LP, UK
| | - J Teague
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - R Wooster
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. E-mail:
| | - P A Futreal
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - M R Stratton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
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Bamford S, Dawson E, Forbes S, Clements J, Pettett R, Dogan A, Flanagan A, Teague J, Futreal PA, Stratton MR, Wooster R. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer 2004; 91:355-8. [PMID: 15188009 PMCID: PMC2409828 DOI: 10.1038/sj.bjc.6601894] [Citation(s) in RCA: 931] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The discovery of mutations in cancer genes has advanced our understanding of cancer. These results are dispersed across the scientific literature and with the availability of the human genome sequence will continue to accrue. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website have been developed to store somatic mutation data in a single location and display the data and other information related to human cancer. To populate this resource, data has currently been extracted from reports in the scientific literature for somatic mutations in four genes, BRAF, HRAS, KRAS2 and NRAS. At present, the database holds information on 66 634 samples and reports a total of 10 647 mutations. Through the web pages, these data can be queried, displayed as figures or tables and exported in a number of formats. COSMIC is an ongoing project that will continue to curate somatic mutation data and release it through the website.
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Affiliation(s)
- S Bamford
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - E Dawson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - S Forbes
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - J Clements
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R Pettett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - A Dogan
- Department of Histopathology, Royal Free and University Medical School, University Street, London WC1E 6JJ, UK
| | - A Flanagan
- The Institute of Orthopaedics, UCL, Stanmore, Middlesex HA7 4LP, UK
| | - J Teague
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - P A Futreal
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. E-mail:
| | - M R Stratton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - R Wooster
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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Branchini BR, Hayward MM, Bamford S, Brennan PM, Lajiness EJ. Naphthyl- and quinolylluciferin: green and red light emitting firefly luciferin analogues. Photochem Photobiol 1989; 49:689-95. [PMID: 2756004 DOI: 10.1111/j.1751-1097.1989.tb08442.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In the course of investigations on the possible involvement of the CIEEL (chemically initiated electron-exchange luminescence) mechanism in firefly bioluminescence, we have synthesized two novel firefly luciferin substrate analogues. D-Naphthylluciferin and D-quinolylluciferin were prepared by condensing D-cysteine with 2-cyano-6-hydroxynaphthalene and 2-cyano-6-hydroxyquinoline, respectively. These analogues are the first examples of bioluminescent substrates for firefly luciferase that do not contain a benzothiazole moiety. Firefly luciferase-catalyzed bioluminescence emission spectra revealed that compared to the normal yellow-green light of luciferin (lambda max = 559 nm), the emission from naphthylluciferin is significantly blue-shifted (lambda max = 524 nm); whereas quinolylluciferin emits orange-red light (lambda max = 608 nm). The fluorescence emission spectra, reaction pH optima, relative light yields, light emission kinetics and KM values of the analogues also were measured and compared to those of luciferin. Neither of the analogues produced the characteristic flash kinetics observed for the natural substrate. Instead, slower rise times to peak emission intensity were recorded. It appears that the formation of an intermediate from the analogue adenylates prior to the addition of oxygen is responsible for the slow rise times. The synthetic substrate analogues described here should be useful for future mechanistic studies.
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Milne D, Walker L, Bamford S. Professional coping. Health Visit 1987; 60:49-50. [PMID: 3643910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Mullick S, Bamford S, Mitchell GW, Gilfillan R. Paget's disease of the vulva--a cytogenetic study of skin fibroblasts, tumor cells, andpperipheral blood leukocytes in culture. Acta Cytol 1970; 14:404-10. [PMID: 4322000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Bamford S, Mitchell GW, Cassin C, Corman A, French B. Further observations on neutrophil appendages in sex chromosome aberrations. Acta Cytol 1966; 10:323-30. [PMID: 5230225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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