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IRBW2009 workshop presentation Babat
Posted Mon, 08/06/2009 - 12:33 by
Gudmundur A Thorisson
Brief decription of this document
Bharati Babat, University of Toronto - InSiGHT and HVP
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InSiGHT and HVP Initiative
IRBW Meeting 2009
Bharati Bapat, PhD Mount Sinai Hospital, University of Toronto on behalf of InSiGHT (Dr. F. Macrae) Human Variome Project (Dr. R. Cotton)
The Human Variome Project
The global initiative to collect and curate all genetic variation affecting human health.
Website – www.humanvariomeproject.org Aims to:
Improve health by unification of data Support collection and use data Worldwide inclusive project Initiated June 2006 in Melbourne, Australia Planning Meeting held May 2008
DNA and its variations
DNA has 3 billion units/bases (A, T, G, C) Each might have a story – many cause disease One day:- Click on each for its story So far 2,000 of 20,000 genes have 101000 mutations each 10% of all diseases have directly inherited component Human Variome Project – focuses on those causing disease Remainder collected by SNP, HapMap, 1000 Genome Consortia
For proper and efficient genetic health care and research, instant access is needed to up-to-date and accurate lists of mutations/variations in genes affecting human health
The Problem: - No such system for this collection currently
exists - Not all currently available variation information is complete, up-to-date and freely accessible - No systems currently exist for countries to easily share their information
The way forward
The Human Variome Project was formed to address these issues and to:
Provide a voice for the global community Support the creation of
Gene specific collection Disease specific collections Country specific collections Standards
Mutation Flow Needed
Countries
LSDBs
Central Databases and Browsers (NCBI, EBI, GEN2PHEN, UCSC, HGMD, OMIM)
Ideal mutation Flow phenotype Patient
Patient genotype Pathology Patient profile Clinic file LSDB Publication
Central database browsers
(NCBI, EBI, GEN2PHEN, UCSC, HGMD, OMIM)
1) Patient supplies clinical information
Closed system, accessible to a controlled set of users
Clinician
6) Record UID issued to Clinic 2) Clinician orders test providing clinical data
PubMed Potential National Genetic Test Ordering Web Application
3) Lab provides genetic data to clinician
8) Waystation facilitates acquisition of PubMed ID
4) Lab submits combined data Diagnostic Labs 5) Record UID issued to Lab
Australian Diagnosti c Database
HVP Waystatio n
LSDB
NCBI/EBI etc.
Viewer
7) De-identified data sent to LSDBs via Waystation
9) LSDBs contribute data to central databases
Data can be used to inform Lab processes
Clinical data Genetic data Combined data
De-identified core data LSDB determined core data Record identifiers
InSiGHT / HVP Pilot Studies
HVP/InSiGHT pilot to develop systems applicable genome and worldwide
HVP country specific pilot – Australian Node – this system is being developed with global input to create a system that
Can be adapted for all countries Integrates with other systems i.e.: NCBI, EBI, LSDBs Has ease of access
What is InSiGHT?
The International Society for Gastrointestinal Hereditary Tumours formed with the merger of the Leeds Castle Polyposis Group and ICG HNPCC in 2005 Maintains a database of Mismatch Repair (MMR) DNA variants through its website Chair: Gabriela Moeslein (Dusseldorf) Secretariat: Hans Vasen, M Velthuizen (Leiden), R Phillips, K Neale (London). Secretary and HVP Liaison: F Macrae
www.insight-group.org
InSiGHT and the Human Variome Project
InSiGHT formed a collaboration with HVP at its meeting in Yokohama, March 2007. Approved by InSiGHT Council and the HVP Planning Committee InSiGHT is developing a Bioinformatics Pilot Project to meet common goals of InSiGHT and HVP
InSiGHT/HVP collaboration
Establishment of a DNA variant committee, for governance of the InSiGHT MMR gene database Three related databases have merged and interacted through the InSiGHT database: The InSiGHT, Newfoundland, and the Dutch MMR missense database LOVD (Leiden Open Variant Database) www.insight-group.org www.med.mun/ca/MMRvariants/ www.mmruv.info
Current Plans
Beta testing of the phenotype database at Clinic level after InSIGHT endorsement in June (Australia, Sweden, Germany, Israel, others welcome) Software development for integration of disparate strands of data (Australian BioGrid, grant application to NCI National node interconnectivity development (NeAT grant in Australia, April 2009) Communication strategies with NCBI and
Countries represented in the InSiGHT/HVP
Europe: Finland, Sweden, Germany, UK, Italy, Holland, Denmark, France, Spain, Portugal, Poland Middle East: Israel Africa: South Africa America: USA, Canada, Brazil Oceania and Asia: Australia, Japan, New Zealand, Hong Kong, China, Korea
The US National Institutes of Health Colon Family Register (CFR)
http://epi.grants.cancer.gov/CFR/about_c olon.html
InSiGHT, NIH CFR and the Human Variome Project:
A collaboration
US NIH CFR Steering Committee Meeting April 2008
Advantages for the NIH CFR
Awareness of the federated databases Promotion of NIH CFR activity Facility for deposition of open information Support of Human Variome Project Attribution of source for CV etc through procedures being developed by Nature Genetics and Human Mutation Capacity for grading access to NIH CFR data at a field level.
Advantages for InSiGHT/HVP
More complete access to important MMR information for the community of MMR researchers and clinicians worldwide Opportunity to integrate the strengths of the NIH CFR data (eg population based, and epidemiology) with the detail and clinical utility of the InSiGHT databases
InSiGHT/HVP acknowledgements: Databases and curation
DNA Variant Curation: M Woods, P Peltomaaki, Phenotype: F Macrae (Chair) , R Scott, S Clarke, C Burke, T Weber, P Watson, A Lindblom, P Rozen, G Moeslein Virtual Histology: H Morreau, E Brazowski Missense: R Sijmons (Chair), R Hofstra, M Lahti, Interpretation: M Genuardi (Chair), J Utsunomiya, R Ramesar, J Burn, M Greenblatt, P Peltomaaki, R Hofstra, R Sijmons, R Scott, M Corish, D Golgar, B
Human Variome Project
Richard Cotton L. Hardiman, R. Horaitis, H. Howard, T. Smith, E. Webb, S Forster Human Variome Project Planning Committee
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© 2009
GEN2PHEN Project
.
The
GEN2PHEN Knowledge Centre
has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013)
under grant agreement number 200754 - the GEN2PHEN project.
