Transcript 3_platform
FLEXGene Repository Platform The FLEXGene Platform Universal Scientific Excellence Access Freedom to Operate Scientific Excellence Highest quality • Gold standard • Fully sequence verified Flexibility • Genes rapidly moved to any protein expression vector • Collections of genes moved simultaneously with ease • Enables high-throughput functional experiments Diligence • World class experts have vetted the technologies • Pilot studies confirmed robustness Research and Development • Continued effort to improve vectors and gene transfer Universal Access Broad availability • Equal access to the entire community • Includes both clones and cloning methodology • Provides a level playing field Distribution strategy promotes access • Multiple reputable distributors • Third party quality control Public/private venture • Membership open to all • Garners the best experience from all sectors Freedom to Operate FLEXGene clones • No restrictions or reach through attached to clones • Assembled and distributed under NIH umbrella FLEXGene cloning methodology • Methodology available to everyone • Simple and open licensing structure • Available in perpetuity FLEXGene Repository Organizational Plan FLEXGene Organizational Structure Scientific Advisory Board (Contributing Members) Legal Committee Administrative Staff Director Operations NIH Foundation Communications and Public Relations Suppliers Informatics Clone Production Sequencing site(s) Distribution and Quality Control Director Bob Strausberg • Full time position – CGAP – MGC – FLEXGene • Responsible for: – – – – – – – Managing the project Ensuring that suppliers reach milestones Overseeing budget Enforcing standards Driving and managing all key activities & processes Communications & PR (with Harlow and LaBaer) Governance Scientific Advisory Board • One representative per member organization • One class of membership • Responsible for: – – – – Setting the scope and objectives Approving the standards Monitoring and guiding the operations Defining future projects FLEXGene Repository Scientific Plan Strategy Scope of project • • • One representative version for each human gene Project limited to producing master clones • Expression clones and proteins to be made by users Two clones per gene: with and without stop codon Clone production • FLEXGene uses MGC clones as starting template • • • • • • High quality template Fully sequenced Fewer cycles of PCR needed higher fidelity MGC has agreed to continue until all genes represented Alternate splice forms, mutant collections, etc. considered for subsequent projects, e.g., FLEXGene II Cloning system selection to be managed by independent blue ribbon panel The FLEXGene Concept-I mRNA 5’ Untranslated Coding Region 3’ Untranslated Precisely copy the coding region Add recombination sites Move to plasmid vector Master clones that populate the repository •Precise coding region •No 5’ stop codons, 5’ or 3’ regulatory sequences •Ready for expression as native protein, NH2- or COOH-terminal fusions The FLEXGene Concept-II FLEXGene master clone Move the insert by recombination to: (Now a simple automated procedure) Any expression vector (bacteria, yeast, mammalian, viral et al.) Native protein or Amino-terminal fusions or Carboxy-terminal fusions or Amino- and carboxy-terminal fusions Pilot Study Project Scope GOAL: 1. Direct comparison of cloning systems 2. Assess mutation rate during clone assembly •Used MGC clones as template for PCR •Same set of 384 genes are cloned in each system •Evaluate each system based on – Efficiency (hit rate) – Product quality (sequence) – Ease of use (for cloners and for end users) – Cost Sequence Fidelity Pilot Study 384 MGC clones converted to each of two systems Pilot completed in 3 months No significant differences between systems 768 clones have been fully sequenced: • 192 genes, 2 systems, 2 separate isolates each • Sequencing done to at least 1 in 10,000 accuracy • Average mutation rate ~1 error every 3700 bases • Concordance indicates <3% duplicates have same mutation Combining the two systems: average = 1 error in every 4-5 clones. FLEXGene Repository Legal and Intellectual Property Strategy Legal Issues Addressed Organizational structure • Under NIH umbrella • FLEXGene membership open to all • Uniform cost of membership; no special payment terms • Cloning system recommendations by independent blue ribbon panel Intellectual property • Existing gene IP • Cloning system IP • No IP overhead added by FLEXGene Intellectual Property Existing Gene IP FLEXGene will: • • • • Publish its plans broadly Operate under the NIH umbrella Not search for IP on individual genes Provide a shrink wrap MTA: it is users’ responsibility to check IP on specific genes • Attach no IP to the clones Intellectual Property Cloning System FLEXGene (through NIH) will request a contract from cloning system provider that: • Ensures that users will always be able to use technology • • • • • • • Perpetual license Methods for producing reagents will be placed in escrow Ensures that there are no limitations on the use of the clones added by cloning technology Ensures that the cost will be the same for everyone Encourages innovation by ensuring that third parties who develop new technologies can make them compatible with the system Ensures that the price will not jump as soon as the contract is signed Ensures that clones can be distributed by multiple distributors FLEXGene Repository Clone Distribution and Maintenance Strategy Maintenance and Distribution Overview • Vital issue for FLEXGene • Production Central Archive Distributors • Multiple distributors is essential • Multiple distributors ensure competitive pricing • Multiple distributors ensure better quality control • FLEXGene will not dictate price • License to distribute may be contingent upon a minimum level of quality control • Oversight board established to monitor quality control • Distributors can be commercial or non-profit • Distributors must offer all FLEXGene clones for sale • Distributors cannot provide clones to another distributor for resale Maintenance and Distribution Distributor Responsibilities Distributors must provide • • • • • Clones on a fair, equitable and confidential basis E-mail or web-based help desk Clone annotation – either locally or linked to FLEXGene E-mail or web-based complaint system with record keeping A published and accessible list of their products, services, prices, expected response times and guaranteed delivery times • A completed MTA from each customer • Feedback on aberrant clone identities to the central archive Each distributor can determine its distribution format • DNA, bacterial strain, or both Distributors can offer additional services for added value • Pre-made clone sets (cancer, kinase, etc.) • User-specified custom sets • Re-sequencing, T1 Phage testing, testing for cross-contamination Maintenance and Distribution Distribution Oversight Board The Distribution Oversight Board will: • Consist of 4-6 users • • • • Review complaints about distributors semi-annually • • • Academic, commercial and geographic representation No conflicts of interest with distributors Agree to maintain confidentiality Ensure adequate response and follow-up Ensure measures established to improve systematic problems Spot check distributors annually (Optional) • Order 100-200 clones • • • • • Monitor service quality and response times Ensure clone viability Confirm clone quality by sequencing Help to identify problems early, before complaints come in Continue to operate even after production is completed Maintenance and Distribution Distributor Qualifications Experience distributing clones on a fee basis • Evidence of quality service • Positive customer references Existing infrastructure • For clone storage • For distribution • For testing • DNA Sequencing • Contamination monitoring Ability to provide annotation • Electronically • Enclosed with shipped parcel of clones