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Using Genomic Databases for Sequence-Based Biological Discovery

Baxevanis, Andreas D
Fonte: ScholarOne Publicador: ScholarOne
Tipo: Artigo de Revista Científica
Publicado em //2003 Português
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The inherent potential underlying the sequence data produced by the International Human Genome Sequencing Consortium and other systematic sequencing projects is, obviously, tremendous. As such, it becomes increasingly important that all biologists have the ability to navigate through and cull important information from key publicly available databases. The continued rapid rise in available sequence information, particularly as model organism data is generated at breakneck speed, also underscores the necessity for all biologists to learn how to effectively make their way through the expanding “sequence information space.” This review discusses some of the more commonly used tools for sequence discovery; tools have been developed for the effective and efficient mining of sequence information. These include LocusLink, which provides a gene-centric view of sequence-based information, as well as the 3 major genome browsers: the National Center for Biotechnology Information Map Viewer, the University of California Santa Cruz Genome Browser, and the European Bioinformatics Institute’s Ensembl system. An overview of the types of information available through each of these front-ends is given, as well as information on tutorials and other documentation intended to increase the reader’s familiarity with these tools.

Meeting Report from the Genomic Standards Consortium (GSC) Workshops 6 and 7

Field, Dawn; Sterk, Peter; Kyrpides, Nikos; Kottmann, Renzo; Glöckner, Frank Oliver; Hirschman, Lynette; Garrity, George M.; Wooley, John; Gilna, Paul
Fonte: Michigan State University Publicador: Michigan State University
Tipo: Artigo de Revista Científica
Publicado em 20/07/2009 Português
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This report summarizes the proceedings of the 6th and 7th workshops of the Genomic Standards Consortium (GSC), held back-to-back in 2008. GSC 6 focused on furthering the activities of GSC working groups, GSC 7 focused on outreach to the wider community. GSC 6 was held October 10-14, 2008 at the European Bioinformatics Institute, Cambridge, United Kingdom and included a two-day workshop focused on the refinement of the Genomic Contextual Data Markup Language (GCDML). GSC 7 was held as the opening day of the International Congress on Metagenomics 2008 in San Diego California. Major achievements of these combined meetings included an agreement from the International Nucleotide Sequence Database Consortium (INSDC) to create a “MIGS” keyword for capturing ”Minimum Information about a Genome Sequence” compliant information within INSDC (DDBJ/EMBL /Genbank) records, launch of GCDML 1.0, MIGS compliance of the first set of “Genomic Encyclopedia of Bacteria and Archaea” project genomes, approval of a proposal to extend MIGS to 16S rRNA sequences within a “Minimum Information about an Environmental Sequence”, finalization of plans for the GSC eJournal, “Standards in Genomic Sciences” (SIGS), and the formation of a GSC Board. Subsequently...

National Cancer Institute Prostate Cancer Genetics Workshop

Catalona, William J.; Bailey-Wilson, Joan E.; Camp, Nicola J.; Chanock, Stephen J.; Cooney, Kathleen A.; Easton, Douglas F.; Eeles, Rosalind A.; FitzGerald, Liesel M.; Freedman, Matthew L.; Gudmundsson, Julius; Kittles, Rick A.; Margulies, Elliott H.; McG
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
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Compelling evidence supports a genetic component to prostate cancer (PC) susceptibility and aggressiveness. Recent genome-wide association studies (GWAS) have identified >30 single nucleotide polymorphisms associated with PC susceptibility. It remains unclear, however, whether such genetic variants are associated with disease aggressiveness—one of the most important questions in PC research today. To help clarify this and substantially expand research in the genetic determinants of PC aggressiveness, the first National Cancer Institute Prostate Cancer Genetics Workshop assembled researchers to develop plans for a large new research consortium and patient cohort. The workshop reviewed the prior work in this area and addressed the practical issues in planning future studies. With new DNA sequencing technology, the potential application of sequencing information to patient care is emerging. The workshop, therefore, included state-of-the-art presentations by experts on new genotyping technologies, including sequencing and associated bioinformatics issues, which are just beginning to be applied to cancer genetics.

The Human Proteome Project: Current State and Future Direction

Legrain, Pierre; Aebersold, Ruedi; Archakov, Alexander; Bairoch, Amos; Bala, Kumar; Beretta, Laura; Bergeron, John; Borchers, Christoph H.; Corthals, Garry L.; Costello, Catherine E.; Deutsch, Eric W.; Domon, Bruno; Hancock, William; He, Fuchu; Hochstrass
Fonte: The American Society for Biochemistry and Molecular Biology Publicador: The American Society for Biochemistry and Molecular Biology
Tipo: Artigo de Revista Científica
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After the successful completion of the Human Genome Project, the Human Proteome Organization has recently officially launched a global Human Proteome Project (HPP), which is designed to map the entire human protein set. Given the lack of protein-level evidence for about 30% of the estimated 20,300 protein-coding genes, a systematic global effort will be necessary to achieve this goal with respect to protein abundance, distribution, subcellular localization, interaction with other biomolecules, and functions at specific time points. As a general experimental strategy, HPP research groups will use the three working pillars for HPP: mass spectrometry, antibody capture, and bioinformatics tools and knowledge bases. The HPP participants will take advantage of the output and cross-analyses from the ongoing Human Proteome Organization initiatives and a chromosome-centric protein mapping strategy, termed C-HPP, with which many national teams are currently engaged. In addition, numerous biologically driven and disease-oriented projects will be stimulated and facilitated by the HPP. Timely planning with proper governance of HPP will deliver a protein parts list, reagents, and tools for protein studies and analyses, and a stronger basis for personalized medicine. The Human Proteome Organization urges each national research funding agency and the scientific community at large to identify their preferred pathways to participate in aspects of this highly promising project in a HPP consortium of funders and investigators.

GCAT-SEEKquence: Genome Consortium for Active Teaching of Undergraduates through Increased Faculty Access to Next-Generation Sequencing Data

Buonaccorsi, Vincent P.; Boyle, Michael D.; Grove, Deborah; Praul, Craig; Sakk, Eric; Stuart, Ash; Tobin, Tammy; Hosler, Jay; Carney, Susan L.; Engle, Michael J.; Overton, Barry E.; Newman, Jeffrey D.; Pizzorno, Marie; Powell, Jennifer R.; Trun, Nancy
Fonte: American Society for Cell Biology Publicador: American Society for Cell Biology
Tipo: Artigo de Revista Científica
Publicado em //2011 Português
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To transform undergraduate biology education, faculty need to provide opportunities for students to engage in the process of science. The rise of research approaches using next-generation (NextGen) sequencing has been impressive, but incorporation of such approaches into the undergraduate curriculum remains a major challenge. In this paper, we report proceedings of a National Science Foundation–funded workshop held July 11–14, 2011, at Juniata College. The purpose of the workshop was to develop a regional research coordination network for undergraduate biology education (RCN/UBE). The network is collaborating with a genome-sequencing core facility located at Pennsylvania State University (University Park) to enable undergraduate students and faculty at small colleges to access state-of-the-art sequencing technology. We aim to create a database of references, protocols, and raw data related to NextGen sequencing, and to find innovative ways to reduce costs related to sequencing and bioinformatics analysis. It was agreed that our regional network for NextGen sequencing could operate more effectively if it were partnered with the Genome Consortium for Active Teaching (GCAT) as a new arm of that consortium, entitled GCAT-SEEK(quence). This step would also permit the approach to be replicated elsewhere.

The FaceBase Consortium: A comprehensive program to facilitate craniofacial research

Hochheiser, Harry; Aronow, Bruce J.; Artinger, Kristin; Beaty, Terri H.; Brinkley, James F.; Chai, Yang; Clouthier, David; Cunningham, Michael L.; Dixon, Michael; Donahue, Leah Rae; Fraser, Scott E.; Hallgrimsson, Benedikt; Iwata, Junichi; Klein, Ophir; M
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
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The FaceBase Consortium consists of ten interlinked research and technology projects whose goal is to generate craniofacial research data and technology for use by the research community through a central data management and integrated bioinformatics hub. Funded by the National Institute of Dental and Craniofacial Research (NIDCR) and currently focused on studying the development of the middle region of the face, the Consortium will produce comprehensive datasets of global gene expression patterns, regulatory elements and sequencing; will generate anatomical and molecular atlases; will provide human normative facial data and other phenotypes; conduct follow up studies of a completed genome-wide association study; generate independent data on the genetics of craniofacial development, build repositories of animal models and of human samples and data for community access and analysis; and will develop software tools and animal models for analyzing and functionally testing and integrating these data. The FaceBase website (http://www.facebase.org) will serve as a web home for these efforts, providing interactive tools for exploring these datasets, together with discussion forums and other services to support and foster collaboration within the craniofacial research community.

MetaboLights: towards a new COSMOS of metabolomics data management

Steinbeck, Christoph; Conesa, Pablo; Haug, Kenneth; Mahendraker, Tejasvi; Williams, Mark; Maguire, Eamonn; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Salek, Reza M.; Griffin, Julian L.
Fonte: Springer US Publicador: Springer US
Tipo: Artigo de Revista Científica
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Exciting funding initiatives are emerging in Europe and the US for metabolomics data production, storage, dissemination and analysis. This is based on a rich ecosystem of resources around the world, which has been build during the past ten years, including but not limited to resources such as MassBank in Japan and the Human Metabolome Database in Canada. Now, the European Bioinformatics Institute has launched MetaboLights, a database for metabolomics experiments and the associated metadata (http://www.ebi.ac.uk/metabolights). It is the first comprehensive, cross-species, cross-platform metabolomics database maintained by one of the major open access data providers in molecular biology. In October, the European COSMOS consortium will start its work on Metabolomics data standardization, publication and dissemination workflows. The NIH in the US is establishing 6–8 metabolomics services cores as well as a national metabolomics repository. This communication reports about MetaboLights as a new resource for Metabolomics research, summarises the related developments and outlines how they may consolidate the knowledge management in this third large omics field next to proteomics and genomics.

Challenges of Biobanking in South Africa to Facilitate Indigenous Research in an Environment Burdened with Human Immunodeficiency Virus, Tuberculosis, and Emerging Noncommunicable Diseases

Abayomi, Akin; Christoffels, Alan; Grewal, Ravnit; Karam, Locunda A.; Rossouw, Catherine; Staunton, Ciara; Swanepoel, Carmen; van Rooyen, Beverley
Fonte: Mary Ann Liebert, Inc. Publicador: Mary Ann Liebert, Inc.
Tipo: Artigo de Revista Científica
Publicado em 01/12/2013 Português
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The high burden of infectious diseases and the growing problem of noncommunicable and metabolic disease syndromes in South Africa (SA) forces a more focused research approach to facilitate cutting-edge scientific growth and public health development. Increased SA research on these diseases and syndromes and the collection of associated biospecimens has ensured a plethora of biobanks created by individuals, albeit without the foresight of prospective and collective use by other local and international researchers. As the need for access to high-quality specimens in statistically relevant numbers has increased, so has the necessity for the development of national human biobanks in SA and across the Continent. The prospects of achieving sustainable centralized biobanks are still an emerging and evolving concept, primarily and recently driven by the launch of the H3Africa consortium, which includes the development of harmonized and standardized biobanking operating procedures. This process is hindered by a myriad of complex societal considerations and ethico-legal challenges. Efforts to consolidate and standardize biological sample collections are further compromised by the lack of full appreciation by national stakeholders of the biological value inherent in these collections...

CNBi: the new Brazilian National Consortium for Bioinformatics.

HERAI, R. H.; VIDAL, R. O.; CARAZZOLLE, M. F.; COSTA, G. G. L.; FALCAO, P. R. K.; YAMAGISHI, M. E. B.; FRANCHINI, K. G.; PEREIRA, G. G. A.
Fonte: In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts... [S.l.: s.n.], 2010. Publicador: In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts... [S.l.: s.n.], 2010.
Tipo: Resumo em anais de congresso (ALICE) Formato: p. 110.
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PRESENTATION: The National Consortium for Bioinformatics (CNBi) is a multidisciplinary center dedicated to research, development, management and technical support on questions arising from bioinformatics. It was created by a joint effort between three laboratories from São Paulo state in Brazil: the Genomic and Expression Laboratory (UNICAMP), Applied Bioinformatics Laboratory (EMBRAPA/CNPTIA) and National Laboratory of Biosciences (LNBio), and is organized as a distributed center inside the mentioned laboratories. MISSION: As a national center for bioinformatics, CNBi?s mission is the generation of new biotechnological information and advanced methods of computer-based information processing. Moreover it intends to act in the ?eld of genomics, proteomics (including protein structure and mass cryptography) and systems biology. In this way, CNBi brings together scientists from many knowledge areas, including computer science, molecular biology, genetics, mathematics, and physics, all of whom sharing a common interest. STRUCTURE: CNBi provides an advanced structure with powerful machines. Actually, there are several high-performance computational systems capable to analyze and simulate massive sets of data, very large storage devices to house major data collections...

A brazilian soybean database.

NASCIMENTO, L. C.; COSTA, G. G. L.; MEYER, L.; BINNECK, E.; RODRIGUES, F.; KULCHESKI, F. R.; MARGIS, R.; KIDO, E. A.; MARCELINO, F. C.; NEPOMUCENO, A. L.; ABDELNOOR, R. V.; PEREIRA, G. A. G.; CARAZZOLLE, M. F.
Fonte: In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts book... Ouro Preto: AB3C, 2010. p. 120. X-Meeting 2010. Publicador: In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 6., 2010, Ouro Preto. Abstracts book... Ouro Preto: AB3C, 2010. p. 120. X-Meeting 2010.
Tipo: Resumo em anais de congresso (ALICE)
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Soybean is a legume with large economic importance in the international market, with a world production of almost two hundred and ten million tons in the 2008/2009 harvest. Brazil appears as the second largest producer, with about twenty-five percent of the world production. In 2007, the Brazilian Soybean Genome Consortium (GENOSOJA) was established with the goal of integrating several institutions currently working with soybean genomics in Brazil. The project has an initiative to search for new treats to improve the soybean production process, emphasizing in stresses that affect the national production, like the occurrence of droughts, pests attacks and the Asian Rust disease. Among the objectives of GENOSOJA is the creation of a relational database, integrating the results achieved by different methodologies utilized in the project. In the GENOSOJA context, we created a brazilian soybean database, integrating: (1) public data consisting of genome and predicted genes from JGI, an assembly of 1,276,813 of NCBI ESTs from several cultivars and 4,712 full-length cDNA sequences from one japanese cultivar; and (2) private data consisting of (i ) three cDNA libraries explored by SuperSAGE methodology, resulting in 4,373,053 tags of 26 bp...

Computational investigations in eukaryotes genome de novo assembly using short reads.

CINTRA, L. C.; CINTRA, L.
Fonte: In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 7.; INTERNATIONAL CONFERENCE OF THE IBEROAMERICAN SOCIETY FOR BIOINFORMATICS, 3., 2011, Florianópolis. Proceedings... Florianópolis: Associação Brasileira de Bioinformática e Biologia Computacional, 2011. Publicador: In: INTERNATIONAL CONFERENCE OF THE BRAZILIAN ASSOCIATION FOR BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, 7.; INTERNATIONAL CONFERENCE OF THE IBEROAMERICAN SOCIETY FOR BIOINFORMATICS, 3., 2011, Florianópolis. Proceedings... Florianópolis: Associação Brasileira de Bioinformática e Biologia Computacional, 2011.
Tipo: Resumo em anais de congresso (ALICE) Formato: Não paginado.
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Recently news technologies in molecular biology enormously improved the sequencing data production, making it possible to generate billions of short reads totalizing gibabases of data per experiment. Prices for sequencing are decreasing rapidly and experiments that were impossible in the past because of costs are now being executed. Computational methodologies that were successfully used to solve the genome assembler problem with data obtained by the shotgun strategy, are now inefficient. Efforts are under way to develop new programs. At this moment, a stabilized condition for producing quality assembles is to use paired-end reads to virtually increase the length of reads, but there is a lot of controversy in other points. The works described in literature basically use two strategies: one is based in a high coverage[1] and the other is based in an incremental assembly, using the made pairs with shorter inserts first[2]. Independently of the strategy used the computational resources demanded are actually very high. Basically the present computational solution for the de novo genome assembly involves the generation of a graph of some kind [3], and one because those graphs use as node whole reads or k-mers, and considering that the amount of reads is very expressive; it is possible to infer that the memory resource of the computational system will be very important. Works in literature corroborate this idea showing that multiprocessors computational systems with at least 512 Gb of principal memory were used in de novo projects of eukaryotes [1...

Análise de expressão gênica diferencial entre diversas bibliotecas de soja; Analysis of differential gene expression between different libraries of soybean

Leandro Costa do Nascimento
Fonte: Biblioteca Digital da Unicamp Publicador: Biblioteca Digital da Unicamp
Tipo: Dissertação de Mestrado Formato: application/pdf
Publicado em 09/12/2010 Português
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A soja é uma das principais commodities da economia internacional, sendo sua produção mundial de cerca de 220 milhões de toneladas por safra. Além de ser um alimento rico em proteínas e usado para a fabricação de óleo vegetal, a planta vem ganhando visibilidade devido a possibilidade de ser usada na fabricação de biocombustíveis, principalmente o biodiesel. Para o Brasil, a soja tem grande importância na balança comercial, sendo o país o segundo maior produtor do mundo. Neste contexto, no ano de 2007, o governo brasileiro estabeleceu um consórcio de pesquisas em soja - denominado GENOSOJA - com o objetivo de identificar características genéticas que possam facilitar o processo produtivo da planta, com foco nos diversos estresses que acometem a produção nacional, como a ocorrência de secas, o ataque de pragas e a doença da ferrugem asiática, causada pelo fungo Phakopsora pachyrhizi. Este trabalho está inserido no escopo do GENOSOJA, propondo a construção de bancos de dados contendo informações disponíveis nos diversos bancos públicos (sequências genômicas, ESTs e cDNA full-lenght), integrando-as com as informações geradas no decorrer do projeto (tags de SuperSAGE, bibliotecas subtrativas de cDNA e microRNAs). Além disso...

Criação da base de dados Via/Genoma da Chromobacterium violaceum - CvioCyc e análise das informações geradas pelo Software Pathway Tools

Goudel, Artiva Maria
Fonte: Florianópolis, SC Publicador: Florianópolis, SC
Tipo: Dissertação de Mestrado Formato: XVIII, 165 f.| il., tabs.
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Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro Tecnológico. Programa de Pós-Graduação em Engenharia Química.; Microrganismos, cujo genoma já foram completamente seqüenciados, como é o caso da Chromobacterium violaceum, possuem dados de anotação genômica em geral produzidos por uma equipe que analisa a fisiologia do organismo e os correlaciona com os dados produzidos pelo projeto de seqüenciamento. Esses dados são geralmente armazenados em bases de dados públicas, e precisam muitas vezes ser verificados, ou seja, validados por via experimental. Todavia, os recentes avanços na área de bioinformática e biologia computacional permitem que certas condições fisiológicas sejam verificadas computacionalmente como, por exemplo, a existência ou não de uma dada via metabólica. Vários grupos têm desenvolvido técnicas para predição de vias metabólicas de organismos a partir da anotação do genoma, produzindo bases de dados integradas via/genoma (pathway/genome database). Este trabalho teve como objetivo construir uma base de dados para a C. violaceum (CvioCyc), uma bactéria Gram-negativa, seqüenciada pelo Brazilian National Genome Project Consortium, de grande potencial biotecnológico e biomédico. A C. violaceum produz um pigmento violeta conhecido como violaceína...

GENOSOJA - The Brazilian Soybean Genome Consortium: high throughput omics and beyond.

BENKO-ISEPPON, A. M.; NEPOMUCENO, A. L.; ABDELNOOR, R. V.
Fonte: Genetics and Molecular Biology, Ribeirão Preto, v. 35, n. 1, suppl., p. i-iv, May 2012. Publicador: Genetics and Molecular Biology, Ribeirão Preto, v. 35, n. 1, suppl., p. i-iv, May 2012.
Tipo: Artigo em periódico indexado (ALICE)
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Plant genomes are among the most complex and large ones of our planet, with high levels of redundancy when compared to other eukaryotic groups, leading to intricate processes for gene regulation and evolution. Such a complexity demands interdisciplinary and multidimensional approaches in order to allow a better understanding of the processes able to exploit the whole potential of the existing genes in different species, including crop plants. Among cultivated plants, soybean [Glycine max (L.) Merr.] occupies an outstanding position due to its importance as source of protein and oil that may also be converted into biodiesel. The seeds are rarely consumed in natura, but many traditional food products have been consumed, as soymilk, and tofu, as well as fermented products as soy sauce, and soy paste among others, besides its wide use for animal feed. Soybean cultivation has been highly concentrated geographically, with only four countries (USA, Brazil, Argentina and China) accounting for almost 90% of world output. Asia (excluding China) and Africa, the two regions where most of the food insecure countries are located, account for only 5% of production. Among countries classified as 'undernourished', only India and Bolivia are significant producers of soybeans (FAO...

Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform

Cerdà, Joan; Mercadé, Jaume; Lozano, Juan José; Manchado, Manuel; Tingaud-Sequeira, Angèle; Astola, A.; Infante, Carlos; Halm, Silke; Viñas, Jordi; Castellana, Bárbara; Asensio, Esther; Cañavate, J. Pedro; Martínez-Rodríguez, Gonzalo; Piferrer, F
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artículo Formato: 1697987 bytes; application/pdf
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14 pages, 5 figures, 3 tables.-- PMID: 18973667 [PubMed].-- PMCID: PMC2612027.-- Supporting information available at: http://www.biomedcentral.com/1471-2164/9/508/additional/; [Background] The Senegalese sole, Solea senegalensis, is a highly prized flatfish of growing commercial interest for aquaculture in Southern Europe. However, despite the industrial production of Senegalese sole being hampered primarily by lack of information on the physiological mechanisms involved in reproduction, growth and immunity, very limited genomic information is available on this species.; [Results] Sequencing of a S. senegalensis multi-tissue normalized cDNA library, from adult tissues (brain, stomach, intestine, liver, ovary, and testis), larval stages (pre-metamorphosis, metamorphosis), juvenile stages (post-metamorphosis, abnormal fish), and undifferentiated gonads, generated 10,185 expressed sequence tags (ESTs). Clones were sequenced from the 3'-end to identify isoform specific sequences. Assembly of the entire EST collection into contigs gave 5,208 unique sequences of which 1,769 (34%) had matches in GenBank, thus showing a low level of redundancy. The sequence of the 5,208 unigenes was used to design and validate an oligonucleotide microarray representing 5...

Fine scale mapping of the 5q11.2 breast cancer locus reveals at least three independent risk variants regulating MAP3K1

Glubb, Dylan M.; Maranian, Mel J.; Michailidou, Kyriaki; Pooley, Karen A.; Meyer, Kerstin B.; Kar, Siddhartha; Carlebur, Saskia; O'Reilly, Martin; Betts, Joshua A.; Hillman, Kristine M.; Kaufmann, Susanne; Beesley, Jonathan; Canisius, Sander; Hopper, John
Fonte: Cell/Elsevier Publicador: Cell/Elsevier
Tipo: Article; accepted version
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This is the accepted manuscript. The final version is available from Cell/Elsevier at http://www.cell.com/ajhg/abstract/S0002-9297%2814%2900475-3.; Genome Wide Association Studies (GWAS) revealed SNP rs889312 on 5q11.2 to be associated with breast cancer risk in women of European ancestry. In an attempt to identify the biologically relevant variants, we analysed 909 genetic variants across the 5q11.2 locus in 103,991 breast cancer cases and controls from 52 studies in the Breast Cancer Association Consortium. Multiple logistic regression analyses identified three independent risk signals: The strongest associations are with 15 correlated variants (iCHAV1) where the minor allele of best candidate, rs62355902, associates with significantly increased risks of both estrogen receptor-positive (ER+: OR=1.24, 95% CI 1.21-1.27; P-trend=5.7?10-44) and estrogen receptor-negative tumors (ER-: OR=1.10, 95% CI 1.05-1.15; P-trend=3.0?10-4). After adjustment for rs62355902, we found evidence for the association of a further 173 variants (iCHAV2) containing three subsets with a range of effects, of which the strongest is SNP rs113317823 (P-cond=1.61?10-5); and five variants comprising iCHAV3 (lead rs11949391; ER+: OR=0.90, 95% CI 0.87-0.93; P-cond=1.4x10-4). Twenty six percent of the prioritized candidate variants coincide with four putative regulatory elements that interact with the MAP3K1 promoter through chromatin looping and affect MAP3K1 promoter activity. Functional analysis indicates the cancer risk alleles of four candidates increase MAP3K1 transcriptional activity: rs74345699 and rs62355900 (iCHAV1); rs16886397 (iCHAV2a); and rs17432750 (iCHAV3). Chromatin immunoprecipitation analysis revealed diminished GATA3 binding to the minor (cancer protective) allele of rs17432750...

Fine scale mapping of the 5q11.2 breast cancer locus reveals at least three independent risk variants regulating MAP3K1.

Glubb, Dylan M.; Maranian, Mel J.; Michailidou, Kyriaki; Pooley, Karen A.; Meyer, Kerstin B.; Kar, Siddhartha; Carlebur, Saskia; O'Reilly, Martin; Betts, Joshua A.; Hillman, Kristine M.; Kaufmann, Susanne; Beesley, Jonathan; Canisius, Sander; Hopper, John
Fonte: Universidade de Cambridge Publicador: Universidade de Cambridge
Tipo: Article; accepted version
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; Manuscript writing group: DMG, MJM, KM, KAP, KBM, AMD, JDF. Locus SNP selection: MG, ED, AMD. iCOGS genotyping, calling and QC: MJM, SEB, SFN, AG-N, MRA, DH, JB, DCT, DV, FB, FR, SA, CL, CB, DC, JC, JD, CSH, JS, AMD, GC-T, DFE. Imputation: KM, DFE. Statistical analyses and programming: KM, KAP, DB, ED, JT, SK, DFE. Functional analysis and bioinformatics: DMG, SLE, KBM, SC, MO, MJM JAB, KMH, SK, JB and JDF. COGS coordination: PH, DFE, JB, AMD, BCAC coordination: DFE, GC-T, PDP. BCAC data management: MKB, QW. All other authors provided participant samples and phenotype information, and read and approved the manuscript. BCAC thanks all the individuals who took part in these studies and all the researchers, clinicians, technicians and administrative staff who have enabled this work to be carried out. BCAC is funded by Cancer Research UK [C1287/A10118, C1287/A12014] and by the European Community?s Seventh Framework Programme under grant agreement number 223175 (grant number HEALTH-F2-2009-223175) (COGS). Meetings of the BCAC have been funded by the European Union COST programme (BM0606). This study would not have been possible without the contributions of the following: Andrew Berchuck (OCAC), Rosalind A. Eeles, Ali Amin Al Olama...

Curation at the NCBI: Genomes, Genes, & Sequence Standards

Garth Brown; Catherine Farrell; Jennifer Hart; Melissa Landrum; Donna Maglott; Bonnie Maidak; Michael Murphy; Terence Murphy; Bhanu Rajput; Kim D. Pruitt; Lillian Riddick; David Webb; Janet Weber; Wendy Wu
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
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The National Center for Biotechnology Information (NCBI) provides curation support for many genomes, and disseminates information in several resources including Entrez Gene, reference sequences (RefSeq), the Consensus CDS (CCDS) database, and the Genome Reference Consortium (GRC). These projects are supported by several collaborations to provide:1) support to the international consortium maintaining the assemblies for human and mouse (GRC); 2) sequence standards for chromosomes, genes, transcripts and proteins (RefSeq); 3) reports of integrated information including nomenclature, publications, phenotypes and diseases, sequences, ontologies, interactions (Gene); and 4) identification of proteins that are consistently annotated on the human and mouse reference genomes, and consistently updated by collaborating members (CCDS). NCBI curation of any one data type (e.g., a gene) is closely integrated with evaluation of the genome assembly, and determining annotation by way of RefSeq transcript and protein sequences. Database and work-flow infrastructure is designed to support reporting and tracking issues with the assembly, gene, or evidence data to collaborating groups, and to support collaborative review and discussions of issues that arise. Curation depends on publicly available information to represent the gene extent...

Creating a Translational Medicine Ontology

Christine Denney; Colin Batchelor; Olivier Bodenreider; Sam Cheng; John Hart; John Hill; John Madden; Mark Musen; Elgar Pichler; Matthias Samwald; Sándor Szalma; Lynn Schriml; David Sedlock; Larisa Soldatova; Koji Sonoda; David Statham; Holger Sten
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
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*Abstract* We, participants in the Translational Medicine Ontology activity of the World Wide Web Consortium’s Health Care and Life Sciences Interest Group ("http://esw.w3.org/topic/HCLSIG":http://esw.w3.org/topic/HCLSIG) and members of the National Center for Biomedical Ontology ("http://bioontology.org/":http://bioontology.org/), are developing a high-level, patient-centric ontology for translational medicine which will draw on existing domain ontologies and allow the integration of data throughout the drug development process. *Introduction* The pharmaceutical industry has historically focused on the development of novel blockbuster drugs. There is now an increasing focus on personalized medicines, requiring the right patients to receive the right drug at the right dose. In order to develop a tailored drug, manufacturers need to identify biomarkers that will indicate how a given patient will respond to a particular treatment. Biomarkers can also be used to demonstrate the comparative effectiveness of drugs, which is increasingly required by payers. Such translational medicine strategies require that traditionally separate data sets from early drug discovery through to patients in the clinical setting be integrated...