The MutaDATABASE project Wim Van Criekinge, BIOBIX, Univ Ghent, Belgium Sherri Bale, GENEDX, Gaithersburg, USA Frederik Decouttere, GENOHM, Ghent, Belgium Heidi Rehm, PhD, Harvard Medical Schoool, Boston, USA Bob Nussbaum, Dept Human Genetics, UCSF, USA Johan Den Dunnen, Leiden University, the Netherlands Patrick Willems, GENDIA, Antwerp, Belgium
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The MutaDATABASE project
Wim Van Criekinge, BIOBIX, Univ Ghent, Belgium
Sherri Bale, GENEDX, Gaithersburg, USA
Frederik Decouttere, GENOHM, Ghent, Belgium
Heidi Rehm, PhD, Harvard Medical Schoool, Boston, USA
Bob Nussbaum, Dept Human Genetics, UCSF, USA
Johan Den Dunnen, Leiden University, the Netherlands
Patrick Willems, GENDIA, Antwerp, Belgium
The Problem
Novel mutations are not being made public through publication or database entry
Many remain unclassified variants which is a challenge for genetic counseling
4. Provides figures of :• Cytogenetic localization• Physical map • Genomic structure• Mutations listed as observations in single patients together with clinical info
5. Allows easy submission of molecular and clinical info
MutaDATABASE - LOVD
MutaDATABASE and LOVD
are collaborating
through Johan Den Dunnen
MutaCURATORS
• Control gene databases in MutaDATABASE
• Review all info submitted to MutaDATABASE
• Supervise MutaCIRCLES
• Write gene reviews for MutaREVIEWS
MutaADMINISTRATORS
• Travel to large test labs to put info into MutaDATABASE
• Contact small test labs to put info into MutaDATABASE
• Teach labs how to put information into MutaDATABASE
MutaCIRCLES
• Labs that work on the same gene form a gene circle
• The exchanged info is available on the website
• Questions automatically go to all members of the circle
• The lab circles joinedly write the gene reviews for the Journal
• The lab circles joinedly write the gene reviews for the Website
meaning variants will be named according to user preference
• Submits novel variations to MutaCURATORS
who evaluates before accepting variation into MutaDATABASE
• Generates the correct nomenclature for the variation
(HGVS, BIG, …)
Offered as a “Software as a Service” or SaaS Centrally managed on mutareporter servers, configured
on a high-availability linux cluster Fine-grained security model: public – curator – circle – lab Client requirement: every web browser with flash support built with java and flex (adobe) technologies Supports simultaneous login & real-time variant updates
within 1 lab and/or MutaCIRCLE: easy collaboration amongst your colleagues
Open data access (nightly database exports) Import/export functions for other popular databases like
LOVD, …
MutaREPORTER Technical background
MutaREPORTER Final goal
• Recording variants directly from sequencer
• Interpretation variants using algorithm
• Ranking variants in order of importance
• Issuying result report
• Input info into MutaDATABASE
Early Adopter program (EAP)
• Early Adopter program (EAP) for MutaREPORTER
• Proof-of-principle for MutaREPORTER, MutaCIRCLES and MutaDATABASE
• This will also facilitate grant applications to NIH and EU/EBI
• The EAP program could be presented to +/- 10 labs for +/- 10 heterogenic diseases for +/- 50 genes
• The choice of labs and genes-diseases is based upon the amount of variants expected (Large US labs, labs doing next generation sequencing)
MutaCURATORS
Patients
MutaDATABASE
CliniciansLabs
MutaREPORTER
Input Mutation information
MutaADMINISTRATORS
Charter The MutaDATABASE Charter on Intellectual Property
Pertaining to DNA Variants and the Information Embedded Therein
We, the undersigned participants in and supporters of the MutaDATABASE, take the position that variants in human DNA are the ultimate open-source resource: they should be freely available for scientists to study, clinicians to test, and patients (and everyone) to derive health and/or other benefits from. Our view is that human DNA and human DNA information are res publicae [1]. As such, there can be no abiding claims on these data, not by clinical testing laboratories, research laboratories, universities, commercial sequencing and/or genomic interpretation enterprises, gene curators, informaticians, insurers, the state, multinational governance organizations, database proprietors, or persons from whom these data are derived. Maximization of benefits from genomic variant data will require successful interactions among all of these entities with as few barriers in place as possible. Accordingly, MutaDATABASE will be completely "Open Access." There will be no restrictions and no usage fees. Each participating laboratory and investigator agrees to these terms and agrees to place no strings whatsoever on any data they deposit into MutaDATABASE. Variants in MutaDATABASE are governed by a Creative Commons CC0 license [2]. Specifically, MutaDATABASE depositors waive all copyrights, intellectual property rights, and related or neighboring rights, such as their moral rights (to the extent waivable), their publicity or privacy rights, rights they have protecting against unfair competition, and database rights and rights protecting the extraction, dissemination and reuse of any and all data deposited into MutaDATABASE.
1. Ossorio, P.N., The human genome as common heritage: Common sense or legal nonsense? J Law Med Ethics, 2007. 35 (3): 425-439.2. http://creativecommons.org/choose/zero/