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115 results on '"Cotton, R.G.H."'

2. General mutation databases: analysis and review

Author

George, R.A., Smith, T.D., Callaghan, S., Hardman, L., Pierides, C., Horaitis, O., Wouters, M.A., and Cotton, R.G.H.

Subjects
Gene mutations -- Information management, Databases -- Usage, CD-ROM catalog, CD-ROM database, Database, Company systems management, Health
Published
2008

7. Deciphering the Colon Cancer Genes-Report of the InSiGHT-Human Variome Project Workshop, UNESCO, Paris 2010

Author

Kohonen-Corish, M.R.J., Macrae, F., Genuardi, M., Aretz, S., Bapat, B., Bernstein, I.T., Burn, J., Cotton, R.G.H., Dunnen, J.T. den, Frebourg, T., Greenblatt, M.S., Hofstra, R., Holinski-Feder, E., Lappalainen, I., Lindblom, A., Maglott, D., Moller, P., Morreau, H., Moslein, G., Sijmons, R., Spurdle, A.B., Tavtigian, S., Tops, C.M.J., Weber, T.K., Wind, N. de, Woods, M.O., Contributors InSiGHT-HVP Workshop, Faculteit Medische Wetenschappen/UMCG, and Guided Treatment in Optimal Selected Cancer Patients (GUTS)

Subjects
MISMATCH-REPAIR GENES, COLORECTAL-CANCER, SEQUENCE VARIANTS, CLASSIFICATION, MUTATIONS, DATABASE, MLH1, Colorectal cancer, Human Variome Project, Library science, HNPCC, Biology, Settore MED/03 - GENETICA MEDICA, Data submission, Bioinformatics, Genetics, medicine, Pilot program, cancer, Pathogenicity, Genetics (clinical), colon, Cancer, medicine.disease, Tumor Pathology, variant, HVP, InSiGHT
Abstract

The Human Variome Project (HVP) has established a pilot program with the International Society for Gastrointestinal Hereditary Tumours (InSiGHT) to compile all inherited variation affecting colon cancer susceptibility genes. An HVP-InSiGHT Workshop was held on May 10, 2010, prior to the HVP Integration and Implementation Meeting at UNESCO in Paris, to review the progress of this pilot program. A wide range of topics were covered, including issues relating to genotype-phenotype data submission to the InSiGHT Colon Cancer Gene Variant Databases (chromium.liacs.nl/LOVD2/colon_cancer/home.php). The meeting also canvassed the recent exciting developments in models to evaluate the pathogenicity of unclassified variants using in silico data, tumor pathology information, and functional assays, and made further plans for the future progress and sustainability of the pilot program. Hum Mutat 32: 491-494, 2011. (C) 2011 Wiley-Liss, Inc.

Published
2011

10. Mutation (variation) databases and registries: a rationale for coordination of efforts

Author

Auerbach, A.D., Burn, J., Cassiman, J.J., Claustres, M., Cotton, R.G.H., Cutting, G., Dunnen, J.T. den, El-Ruby, M., Vargas, A.F., Greenblatt, M.S., Macrae, F., Matsubara, Y., Rimoin, D.L., Vihinen, M., Broeckhoven, C. van, Human Variome Project, Department of Clinical Genetics/EMGO Institute for Health and Care research, Laboratoire de génétique des maladies rares. Pathologie moleculaire, etudes fonctionnelles et banque de données génétiques (LGMR), IFR3, Université Montpellier 1 (UM1)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier), United Kingdom Met Office [Exeter], Johns Hopkins University School of Medicine [Baltimore], Department of Human Genetics, Leiden University Medical Center (LUMC), Department of Colorectal Medicine and Genetics, The Royal Melbourne Hospital, Medical Genetics Institute, Department of Experimental Medical Science, Lund University [Lund], Neurodegenerative Brain Diseases Group, and VIB

Subjects
[SDV]Life Sciences [q-bio], Human Variome Project, Developing country, computer.software_genre, 03 medical and health sciences, Annotation, 0302 clinical medicine, Resource (project management), Databases, Genetic, Genetics, Humans, Medicine, Relevance (information retrieval), Biology, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Database, business.industry, Biobank, 3. Good health, Incentive, Mutation (genetic algorithm), Human medicine, business, computer, 030217 neurology & neurosurgery
Abstract

Here we argue that coor-dination of international efforts for develop -ing comprehensive mutation databases and patient phenotype registries is essential for optimal genetic health care.Well-funded international efforts for set -ting up mutation databases or registries are crucial for several reasons. Many variants that are found during clinical testing world-wide are not submitted to databases, where they could form an important resource for patient care. Many laboratories and clini-cians do not have the capacity or incentive to submit data to databases. This is espe-cially the case in developing countries owing mainly to technical insufficiency, lack of public awareness, lack of international com -munications, the absence of the concept of DNA biobanking, national authority restric -tions and lack of translation from original languages to English. The Human Variome Project (HVP) was initiated to facilitate the collection of all variants in all genes from all countries and to include annotation of these variants for pathogenicity and relevance to clinical medicine

Published
2011
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11. Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities

Author

Falk, M.J. (Marni J.), Shen, L. (Lishuang), Gonzalez, M. (Michael), Leipzig, J. (Jeremy), Lott, M.T. (Marie T.), Stassen, A.P.M. (Alphons P.M.), Diroma, M.A. (Maria Angela), Navarro-Gomez, D. (Daniel), Yeske, P. (Philip), Bai, R. (Renkui), Boles, R.G. (Richard G.), Brilhante, V. (Virginia), Ralph, D. (David), DaRe, J.T. (Jeana T.), Shelton, R. (Robert), Terry, S.F. (Sharon), Zhang, Z. (Zhe), Copeland, W.C. (William C.), Oven, M. (Mannis) van, Prokisch, H. (Holger), Wallace, D.C., Attimonelli, M. (Marcella), Krotoski, D. (Danuta), Zuchner, S. (Stephan), Gai, X. (Xiaowu), Bale, S. (Sherri), Bedoyan, J. (Jirair), Behar, D.M. (Doron), Bonnen, P. (Penelope), Brooks, L. (Lisa), Calabrese, C. (Claudia), Calvo, S. (Sarah), Chinnery, P.F. (Patrick), Christodoulou, J. (John), Church, D. (Deanna), Clima, R. (Rosanna), Cohen, B.H. (Bruce H.), Cotton, R.G.H. (Richard), Coo, I.F.M. (René) de, Derbenevoa, O. (Olga), Dunnen, J.T. (Johan) den, Dimmock, D. (David), Enns, G. (Gregory), Gasparre, G. (Giuseppe), Goldstein, A. (Amy), Gonzalez, I. (Iris), Gwinn, K. (Katrina), Hahn, S. (Sihoun), Haas, R.H. (Richard H.), Hakonarson, H. (Hakon), Hirano, M. (Michio), Kerr, D. (Douglas), Li, D. (Dong), Lvova, M. (Maria), Macrae, F. (Finley), Maglott, D. (Donna), McCormick, E. (Elizabeth), Mitchell, G. (Grant), Mootha, V.K. (Vamsi K.), Okazaki, Y. (Yasushi), Pujol, A. (Aurora), Parisi, M. (Melissa), Perin, J.C. (Juan Carlos), Pierce, E.A. (Eric A.), Procaccio, V. (Vincent), Rahman, S. (Shamima), Reddi, H. (Honey), Rehm, H. (Heidi), Riggs, E. (Erin), Rodenburg, R.J.T. (Richard), Rubinstein, Y. (Yaffa), Saneto, R. (Russell), Santorsola, M. (Mariangela), Scharfe, C. (Curt), Sheldon, C. (Claire), Shoubridge, E.A. (Eric), Simone, D. (Domenico), Smeets, B. (Bert), Smeitink, J.A.M. (Jan), Stanley, C. (Christine), Suomalainen, A. (Anu), Tarnopolsky, M.A. (Mark), Thiffault, I. (Isabelle), Thorburn, D.R. (David R.), Hove, J.V. (Johan Van), Wolfe, L. (Lynne), Wong, L.-J. (Lee-Jun), Falk, M.J. (Marni J.), Shen, L. (Lishuang), Gonzalez, M. (Michael), Leipzig, J. (Jeremy), Lott, M.T. (Marie T.), Stassen, A.P.M. (Alphons P.M.), Diroma, M.A. (Maria Angela), Navarro-Gomez, D. (Daniel), Yeske, P. (Philip), Bai, R. (Renkui), Boles, R.G. (Richard G.), Brilhante, V. (Virginia), Ralph, D. (David), DaRe, J.T. (Jeana T.), Shelton, R. (Robert), Terry, S.F. (Sharon), Zhang, Z. (Zhe), Copeland, W.C. (William C.), Oven, M. (Mannis) van, Prokisch, H. (Holger), Wallace, D.C., Attimonelli, M. (Marcella), Krotoski, D. (Danuta), Zuchner, S. (Stephan), Gai, X. (Xiaowu), Bale, S. (Sherri), Bedoyan, J. (Jirair), Behar, D.M. (Doron), Bonnen, P. (Penelope), Brooks, L. (Lisa), Calabrese, C. (Claudia), Calvo, S. (Sarah), Chinnery, P.F. (Patrick), Christodoulou, J. (John), Church, D. (Deanna), Clima, R. (Rosanna), Cohen, B.H. (Bruce H.), Cotton, R.G.H. (Richard), Coo, I.F.M. (René) de, Derbenevoa, O. (Olga), Dunnen, J.T. (Johan) den, Dimmock, D. (David), Enns, G. (Gregory), Gasparre, G. (Giuseppe), Goldstein, A. (Amy), Gonzalez, I. (Iris), Gwinn, K. (Katrina), Hahn, S. (Sihoun), Haas, R.H. (Richard H.), Hakonarson, H. (Hakon), Hirano, M. (Michio), Kerr, D. (Douglas), Li, D. (Dong), Lvova, M. (Maria), Macrae, F. (Finley), Maglott, D. (Donna), McCormick, E. (Elizabeth), Mitchell, G. (Grant), Mootha, V.K. (Vamsi K.), Okazaki, Y. (Yasushi), Pujol, A. (Aurora), Parisi, M. (Melissa), Perin, J.C. (Juan Carlos), Pierce, E.A. (Eric A.), Procaccio, V. (Vincent), Rahman, S. (Shamima), Reddi, H. (Honey), Rehm, H. (Heidi), Riggs, E. (Erin), Rodenburg, R.J.T. (Richard), Rubinstein, Y. (Yaffa), Saneto, R. (Russell), Santorsola, M. (Mariangela), Scharfe, C. (Curt), Sheldon, C. (Claire), Shoubridge, E.A. (Eric), Simone, D. (Domenico), Smeets, B. (Bert), Smeitink, J.A.M. (Jan), Stanley, C. (Christine), Suomalainen, A. (Anu), Tarnopolsky, M.A. (Mark), Thiffault, I. (Isabelle), Thorburn, D.R. (David R.), Hove, J.V. (Johan Van), Wolfe, L. (Lynne), and Wong, L.-J. (Lee-Jun)

Abstract

Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The "Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium" is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (. https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through the use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is integr

Published
2015
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12. How to catch all those mutations--the report of the third Human Variome Project Meeting, UNESCO Paris, May 2010

Author

Kohonen-Corish, M.R.J., Al-Aama, J.Y., Auerbach, A.D., Axton, M., Barash, C.I., Bernstein, I., Beroud, C., Burn, J., Cunningham, F., Cutting, G.R., Dunnen, J.T. den, Greenblatt, M.S., Kaput, J., Katz, M., Lindblom, A., Macrae, F., Maglott, D., Moslein, G., Povey, S., Ramesar, R., Richards, S., Seminara, D., Sobrido, M.J., Tavtigian, S., Taylor, G., Vihinen, M., Winship, I., Cotton, R.G.H., Contributors Human Variome Project, HNPCC-register, Hvidovre Hospital, University of Copenhagen = Københavns Universitet (KU), Laboratoire de génétique des maladies rares. Pathologie moleculaire, etudes fonctionnelles et banque de données génétiques (LGMR), Université Montpellier 1 (UM1)-IFR3, Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (JHU), Metabolic Unit, Dept Clinical Chemistry, University of Vermont College of Medicine, University of Vermont [Burlington], University of Massachusetts [Amherst] (UMass Amherst), University of Massachusetts System (UMASS), Department of Clinical Genetics, Karolinska University Hospital [Stockholm], Department of Colorectal Medicine and Genetics, The Royal Melbourne Hospital, National Center for Biotechnology Information (NCBI), Dept of Genetics, Evolution and Environment [London] (UCL-GEE), University College of London [London] (UCL), National Cancer Institute [Bethesda] (NCI-NIH), National Institutes of Health [Bethesda] (NIH), Fundacion Publica Galega de Medicina Xenomica, Fundación Pública Galega de Medicina Xenómica, Department of Oncological Sciences, University of Utah-Huntsman Cancer Institute, Imperial College London, Department of Experimental Medical Science, Lund University [Lund], University of Copenhagen = Københavns Universitet (UCPH), IFR3, and Université Montpellier 1 (UM1)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Santé et de la Recherche Médicale (INSERM)

Subjects
education, Human Variome Project, Library science, Human genetic variation, Biology, computer.software_genre, Article, 03 medical and health sciences, 0302 clinical medicine, Health care, Genetics, Genetics (clinical), 030304 developmental biology, 0303 health sciences, Data collection, business.industry, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, 3. Good health, Variome, Incentive, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, 030220 oncology & carcinogenesis, Sustainability, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, computer, Data integration
Abstract

International audience; The third Human Variome Project (HVP) Meeting "Integration and Implementation" was held under UNESCO Patronage in Paris, France, at the UNESCO Headquarters May 10-14, 2010. The major aims of the HVP are the collection, curation, and distribution of all human genetic variation affecting health. The HVP has drawn together disparate groups, by country, gene of interest, and expertise, who are working for the common good with the shared goal of pushing the boundaries of the human variome and collaborating to avoid unnecessary duplication. The meeting addressed the 12 key areas that form the current framework of HVP activities: Ethics; Nomenclature and Standards; Publication, Credit and Incentives; Data Collection from Clinics; Overall Data Integration and Access-Peripheral Systems/Software; Data Collection from Laboratories; Assessment of Pathogenicity; Country Specific Collection; Translation to Healthcare and Personalized Medicine; Data Transfer, Databasing, and Curation; Overall Data Integration and Access-Central Systems; and Funding Mechanisms and Sustainability. In addition, three societies that support the goals and the mission of HVP also held their own Workshops with the view to advance disease-specific variation data collection and utilization: the International Society for Gastrointestinal Hereditary Tumours, the Micronutrient Genomics Project, and the Neurogenetics Consortium.

Published
2010
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16. Response to Stenson et al on the review of general mutation databases

Author

George, R.A., Smith, T.D., Callaghan, S., Hardman, L., Pierides, C., Horaitis, O., Wouters, M.A., and Cotton, R.G.H.

Subjects
Gene mutations -- Information management, Databases -- Evaluation, CD-ROM catalog, CD-ROM database, Database, Company systems management, Health
Published
2008

18. Mutation detection

Author

Cotton, R.G.H. and Malcolm, A.D.B.

Subjects
Genetic screening -- Research, Gel electrophoresis -- Usage, Mutation (Biology) -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Published
1991

19. Genetic Tests Need the Human Variome Project

Author

Cotton, R.G.H., Vihinen, M., Dunnen, J.T. den, and Human Variome Project Nomenclature

Subjects
medicine.medical_specialty, Political science, Human Variome Project, medicine, Medical genetics, General Medicine, Data science, Genetics (clinical)
Published
2011
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20. Somatic mutation databases as tools for molecular epidemiology and molecular pathology of cancer: Proposed guidelines for improving data collection, distribution, and integration

Author

Olivier, M., primary, Petitjean, A., additional, Teague, J., additional, Forbes, S., additional, Dunnick, J.K., additional, den Dunnen, J.T., additional, Langerød, A., additional, Wilkinson, J.M., additional, Vihinen, M., additional, Cotton, R.G.H., additional, and Hainaut, P., additional

Published
2008
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22. Recommendations for locus-specific databases and their curation

Author

Cotton, R.G.H., primary, Auerbach, A.D., additional, Beckmann, J.S., additional, Blumenfeld, O.O., additional, Brookes, A.J., additional, Brown, A.F., additional, Carrera, P., additional, Cox, D.W., additional, Gottlieb, B., additional, Greenblatt, M.S., additional, Hilbert, P., additional, Lehvaslaiho, H., additional, Liang, P., additional, Marsh, S., additional, Nebert, D.W., additional, Povey, S., additional, Rossetti, S., additional, Scriver, C.R., additional, Summar, M., additional, Tolan, D.R., additional, Verma, I.C., additional, Vihinen, M., additional, and den Dunnen, J.T., additional

Published
2007
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28. Analysis of Sequence Contexts Flanking T·G Mismatches Leads to Predictions about Reactivity of the Mismatched T to Osmium Tetroxide

Author

COTTON, R.G.H., primary, DAHL, H.-H.M., additional, FORREST, S, additional, HOWELLS, D.W., additional, RAMUS, S.J., additional, BISHOP, R.E., additional, DIANZANI, I., additional, SALEEBA, J.A., additional, PALOMBO, E., additional, ANDERSON, M.J., additional, MILNER, C.M., additional, and CAMPBELL, R.D., additional

Published
1993
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32. Somatic mutation databases as tools for molecular epidemiology and molecular pathology of cancer: Proposed guidelines for improving data collection, distribution, and integration.

Author

Olivier, M., Petitjean, A., Teague, J., Forbes, S., Dunnick, J.K., den Dunnen, J.T., Langerød, A., Wilkinson, J.M., Vihinen, M., Cotton, R.G.H., and Hainaut, P.

Abstract

There are currently less than 40 locus-specific databases (LSDBs) and one large general database that curate data on somatic mutations in human cancer genes. These databases have different scope and use different annotation standards and database systems, resulting in duplicated efforts in data curation, and making it difficult for users to find clear and consistent information. As data related to somatic mutations are generated at an increasing pace it is urgent to create a framework for improving the collecting of this information and making it more accessible to clinicians, scientists, and epidemiologists to facilitate research on biomarkers. Here we propose a data flow for improving the connectivity between existing databases and we provide practical guidelines for data reporting, database contents, and annotation standards. These proposals are based on common standards recommended by the Human Genome Variation Society (HGVS) with additions related to specific requirements of somatic mutations in cancer. Indeed, somatic mutations may be used in molecular pathology and clinical studies to characterize tumor types, help treatment choice, predict response to treatment and patient outcome, or in epidemiological studies as markers for tumor etiology or exposure assessment. Thus, specific annotations are required to cover these diverse research topics. This initiative is meant to promote collaboration and discussion on these issues and the development of adequate resources that would avoid the loss of extremely valuable information generated by years of basic and clinical research. Hum Mutat 0,1-8, 2008. © 2008 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Published
2009
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34. Recommendations for locus-specific databases and their curation.

Author

Cotton, R.G.H., Auerbach, A.D., Beckmann, J.S., Blumenfeld, O.O., Brookes, A.J., Brown, A.F., Carrera, P., Cox, D.W., Gottlieb, B., Greenblatt, M.S., Hilbert, P., Lehvaslaiho, H., Liang, P., Marsh, S., Nebert, D.W., Povey, S., Rossetti, S., Scriver, C.R., Summar, M., and Tolan, D.R.

Abstract

Expert curation and complete collection of mutations in genes that affect human health is essential for proper genetic healthcare and research. Expert curation is given by the curators of gene-specific mutation databases or locus-specific databases (LSDBs). While there are over 700 such databases, they vary in their content, completeness, time available for curation, and the expertise of the curator. Curation and LSDBs have been discussed, written about, and protocols have been provided for over 10 years, but there have been no formal recommendations for the ideal form of these entities. This work initiates a discussion on this topic to assist future efforts in human genetics. Further discussion is welcome. Hum Mutat 29(1), 2-5, 2008. © 2007 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Published
2008
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