3 platform

FLEXGene Repository: 

FLEXGene Repository Platform

The FLEXGene Platform: 

The FLEXGene Platform

Scientific Excellence: 

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: 

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: 

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: 

FLEXGene Repository Organizational Plan

FLEXGeneOrganizational Structure: 

Scientific Advisory Board (Contributing Members) Legal Committee Communications and Public Relations Administrative Staff NIH Foundation Suppliers Sequencing site(s) Informatics Distribution and Quality Control Clone Production Director Operations FLEXGene Organizational Structure

DirectorBob Strausberg: 

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: 

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: 

FLEXGene Repository Scientific Plan

Strategy: 

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: 

The FLEXGene Concept-I mRNA 5’ Untranslated 3’ Untranslated Coding Region 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: 

The FLEXGene Concept-II Move the insert by recombination to: (Now a simple automated procedure) FLEXGene master clone Any expression vector (bacteria, yeast, mammalian, viral et al.) Amino-terminal fusions Carboxy-terminal fusions Amino- and carboxy-terminal fusions Native protein or or or

Slide14: 

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 Pilot Study Project Scope GOAL: Direct comparison of cloning systems Assess mutation rate during clone assembly

Slide15: 

Sequence Fidelity Pilot Study 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.   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:

FLEXGene Repository: 

FLEXGene Repository Legal and Intellectual Property Strategy

Legal Issues Addressed: 

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 PropertyExisting Gene IP: 

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 PropertyCloning System: 

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: 

FLEXGene Repository Clone Distribution and Maintenance Strategy

Maintenance and DistributionOverview: 

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 DistributionDistributor Responsibilities: 

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 DistributionDistribution Oversight Board: 

Maintenance and Distribution Distribution Oversight Board The Distribution Oversight Board will: Consist of 4-6 users Academic, commercial and geographic representation No conflicts of interest with distributors Agree to maintain confidentiality Review complaints about distributors semi-annually 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 DistributionDistributor Qualifications: 

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