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  • HVP3: Implementation and Integration | HVP Biennial Meetings | HVP Meetings & Events | biennial-meetings - Human Variome Project
    are currently working on the necessary components and the development of the systems relevant to the task including those working on pilot systems Individuals include bioinformaticians clinical geneticists researchers counsellors database curators diagnostic laboratory heads common disease variation experts genome sequencers support groups and will address and include topics impacting on clinical data collection genetic data collection distributed databasing country and gene specific country specific collection key pilot current projects central databasing transfer to central databases incentives for databasing ethics of databasing and funding We are looking for anyone interested in collaborating in this area to attend the meeting and abstracts are invited Presentations will be chosen from those who have or are planning systems which are relevant to the collection and display of all mutations in all genes from all countries Chairs will be asked to document projects currently underway and to nominate new collaborative projects and where possible nominate the collaborators Chairs will also be asked to develop projects leading to standards which can be developed and accepted Space is limited to 200 so please register early to be assured of a place You might also like to attend one of the concurrent satellite meetings being held on the 10th May in the same venue Satellite Meetings Professor Richard Cotton Convenor Human Variome Project Conference PlanOverall Goal Continue to increase awareness of the importance of the aims of the Human Variome Project and the further development of protocols and systems to collect curate and make available information on all human genetic variation in all genes from all countries affecting human health and its funding Objectives To ensure progression of the objectives of the Human Variome Project to collect variation causing disease mutations in all genes world wide To gather experts and leaders in the strategies and systems required

    Original URL path: http://www.humanvariomeproject.org/meetings/biennial/hvp3.html (2016-02-10)
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  • HVP4: The 4th Biennial Meeting of the Human Variome Project Consortium | HVP Biennial Meetings | HVP Meetings & Events | biennial-meetings - Human Variome Project
    The 4th Human Variome Project meeting continued the theme of the previous meetings and addressed issues of implementation in this unique project HVP4 presented the strategic plan for the Project over the next five years as expressed in Project Roadmap 2012 2016 The meeting was structured around four key themes that underpin all the activities of the Human Variome Project Consortium setting normative function behaving ethically sharing knowledge and building capacity Meeting Objectives The meeting brought together researchers database curators clinical geneticists and other healthcare professionals To present the Project s strategic plan for the next five years To ensure progression of the objective of the Human Variome Project to embed the collection and sharing of genetic variation information into routine clinical practice To present activities underway or planned towards the Human Variome Project objective To integrate current activities where possible To establish collaborations and activities were the need exists To gather experts in the strategies and software required together with those responsible for generating data To gather those who are already collecting mutations within their counties together with those who wish to establish a system especially those from developing countries Meeting Outcomes Meeting outcomes are reported in Kohonen Corish

    Original URL path: http://www.humanvariomeproject.org/meetings/biennial/hvp4.html (2016-02-10)
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  • HVP5: 5th Biennial Meeting of the Human Variome Project Consortium | HVP Biennial Meetings | HVP Meetings & Events | biennial-meetings - Human Variome Project
    manner is an on going issue There are various aspects to the problem and solutions require active participation from the full range of those directly involved in generating data as well as using it Many example were shared of how to upgrade search interfaces enhance linkages between linkage to multiple datasets using appropriately de identified case matching and how to integrate a genome wide database using LOVD3 The major questions of utility quality control and sustainability of genetic variation databases is of concern to many in different parts of the world Sharing knowledge on what works needs to be followed closely by more proactive efforts at networking and harmonizing activities Working hand in hand with the local national or regional Human Genetics Society through a mechanism like an HVP Country Node can assist Recently three NIH funded efforts were aligned with the National Center for Biotechnology Information s NCBI ClinVar database under the collaborative Clinical Genome Resource Program ClinGen ClinGen is developing interconnected resources for the community to improve our understanding of genomic variation and optimize its use in genomic medicine A unique aspect of ClinGen is that it represents a strong public academic private partnership that relies on the collaboration between NIH academic and commercial genetic testing laboratories The project includes the development of standards for variant interpretation as well as data submission and sharing ClinVar launched in April 2013 is a cornerstone of the project as it serves as the primary site for deposition and retrieval of variant data and annotations As of February 1 st 2014 ClinVar contains 73 487 submissions across 18 702 genes 66 956 unique variants with interpretations from OMIM GeneReviews 60 laboratories and 23 locus specific databases LSDBs The dataset includes 5454 variant submissions 2095 unique variants from the Sharing Clinical Reports Project SCRP on BRCA1 2 and 4100 copy number variants from the International Standards for Cytogenomic Arrays ISCA Consortium New policies and data structures are being considered to support controlled access to patient level data ClinGen is currently working with many laboratories and LSDBs to support robust mechanisms to share their data in an ongoing manner and increase the content of structured data and supporting evidence Other parts of the project include computational and machine learning approaches for identifying clinically relevant variants and the development of expert working groups across many clinical domains to support consensus driven evidence based curation of genes disease associations and genomic variant interpretations Groups have already been formed in the areas of cardiovascular disease hereditary cancer metabolic disease rasopathies congenital muscular dystrophy and developmental delay The project is also interfacing with a large and diverse community of stakeholders including professional organizations patient advocacy groups regulatory agencies research consortia and other projects from both national and international sites which is facilitated by working with the existing International Collaboration for Clinical Genomics ICCG Thousands of new variants are being identified as a result of rapid advances in sequencing technologies However much of the data are stored in separate and sometimes private databases and so may be difficult to use in the evaluation of the clinical significance of variants This is especially the case with rare variants To improve access to this type of data ClinVar LINK SLIDES maintains a freely available public archive of human variation and its relationship to disease The data can be used through a several means interactively on the web a monthly full release in XML format and weekly summary files of genes and variants are also available for incorporation into analysis pipelines Submissions include variants identified by direct testing in clinical or research labs as well as reviewed variant phenotype relationships from expert groups such as InSiGHT and CFTR2 and professional societies such as the American College of Medical Genetics and Genomics In addition to the variant and phenotype individual submissions may also provide a clinical assertion and evidence for that interpretation The data model is flexible for many data elements such that a variant may be defined by sequence or cytogenetic nomenclature the phenotype may be a diagnostic term or features of a disease and evidence for the interpretation may be structured as counts or provided as free text For submitters who maintain their own website for variants such as LSDBs ClinVar links to the submitter s site for each submitted variant allowing users who start at ClinVar an awareness of the LSDB s curated variants and access to more information on the variant that may be available at the LSDB Each individual submission is accessioned and versioned in the format SCV000000000 1 to allow the submitter to update their record as the interpretation of the variant is re evaluated over time ClinVar uses standard terminologies such as those for variant nomenclature phenotypes and pathogenicity to avoid data ambiguity and to promote comparison of information from multiple sources ClinVar also adds related variant data such as allele frequencies and HGVS expressions mapped across molecule types While ClinVar staff members provide some curation of variants and phenotypes represented in ClinVar clinical significance values are provided by submitters As part of the submission process ClinVar provides feedback to submitters This feedback includes invalid HGVS expressions and submissions that conflict in clinical significance with an existing record for the same variant and phenotype which may warrant further curation Submissions for the same variant phenotype pair from different submitters are aggregated into a record that is accessioned and versioned in the format RCV000000000 1 Aggregation allows ClinVar to indicate when multiple submitters agree or conflict in the clinical interpretation of the variant which can help clinical labs and curation groups to identify high confidence interpretations as well as those that should be prioritized for curation efforts The International Society for Gastrointestinal Hereditary Tumors InSIGHT has established a committee Variant Interpretation Committee VIC for the interpretation of sequence variants in the mismatch repair MMR genes associated with Lynch syndrome LS One of the major steps involved in this process has been the establishment of qualitative specific classification

    Original URL path: http://www.humanvariomeproject.org/meetings/biennial/hvp5.html (2016-02-10)
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  • Johan T. den Dunnen - Human Variome Project
    Pearson Leiden University and became involved in the search for the gene causing Duchenne and Becker muscular dystrophy He is currently employed at the Center for Human and Clinical Genetics head Prof dr GJB van Ommen Leiden University Medical Center Leiden Nederland studying genetic disease in general and neuromuscular disorders DMD BMD LGMD in particular As professor in Medical Genome Technology he focuses on the use of new high throughput genome technology in research and diagnosis of genetic disease in particular the development and innovation of mutation detection technologies and the application of next generation sequencing To spread the laboratories knowledge on hereditary muscle disease he initiated the Leiden Muscular Dystrophy pages http www DMD nl As part of these efforts he currently curates over 50 gene sequence variant databases His group developed the freely available LSDB in a Box software package LOVD the Mutalyzer tool HGVS mutation nomenclature description and he participates in the EU FP7 Gen2Phen project WP leader for LSDBs Shortly after its start Johan joined the HUGO Mutation Database Initiative and he is a board member of the Human Genome Variation Society since its initiation in 2002 He gradually became involved in the society s activities

    Original URL path: http://www.humanvariomeproject.org/isac-members/johan-t.-den-dunnen.html (2016-02-10)
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  • Human Variome Project Networking Event @ ASHG | Special HVP Meetings | HVP Meetings & Events | meetings - Human Variome Project
    in Baltimore Great So is the Human Variome Project Come along to the Potomac Room of the Sheraton Inner Harbour Hotel at 7pm local time 11pm UTC GMT on Thursday 8 October to meet other Human Variome Project Consortium members in a fun and social environment And who can say no to free food and drinks RSVP online Navigate Home About Activities Solutions Resources Meetings Blog Donate Members Login More

    Original URL path: http://www.humanvariomeproject.org/meetings/special/human-variome-project-networking-event-ashg.html (2016-02-10)
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  • ISAC Meeting - August 2014 | ISAC Meetings | Committee & Council Meetings | meetings - Human Variome Project
    Fora Project wide Initiatives Home Meetings ISAC Meeting October 2015 ISAC Meeting August 2014 ISAC Meetings Thursday August 28 2014 12 00 13 00 Navigate Home About Activities Solutions Resources Meetings Blog Donate Members Login More Sitemap Privacy Policy Search Login Contact Us Contact the International Coordinating Office Human Variome Project International Ltd Level 1 200 Berkeley Street University of Melbourne Victoria Australia P 61 3 9035 9519 E info

    Original URL path: http://www.humanvariomeproject.org/meetings/isac/isac-meeting-august-2014.html (2016-02-10)
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  • ISAC Meeting - September 2014 | ISAC Meetings | Committee & Council Meetings | meetings - Human Variome Project
    Fora Project wide Initiatives Home Meetings ISAC Meeting October 2015 ISAC Meeting September 2014 ISAC Meetings Thursday September 18 2014 12 00 13 00 Navigate Home About Activities Solutions Resources Meetings Blog Donate Members Login More Sitemap Privacy Policy Search Login Contact Us Contact the International Coordinating Office Human Variome Project International Ltd Level 1 200 Berkeley Street University of Melbourne Victoria Australia P 61 3 9035 9519 E info

    Original URL path: http://www.humanvariomeproject.org/meetings/isac/isac-meeting-september-2014.html (2016-02-10)
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  • ISAC Meeting - October 2014 | ISAC Meetings | Committee & Council Meetings | meetings - Human Variome Project
    Fora Project wide Initiatives Home Meetings ISAC Meeting October 2015 ISAC Meeting October 2014 ISAC Meetings Sunday October 19 2014 19 00 20 30 Navigate Home About Activities Solutions Resources Meetings Blog Donate Members Login More Sitemap Privacy Policy Search Login Contact Us Contact the International Coordinating Office Human Variome Project International Ltd Level 1 200 Berkeley Street University of Melbourne Victoria Australia P 61 3 9035 9519 E info

    Original URL path: http://www.humanvariomeproject.org/meetings/isac/isac-meeting-october-2014.html (2016-02-10)
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