FLEXGene Repository

1. FLEXGene Repository Platform

2. Universal Access Scientific Excellence Freedom to Operate The FLEXGene Platform FLEXGene

3. Scientific Excellence Highest quality • Goldstandard • 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

4. Universal Access Broad availability • Equal access to the entire community • Includes both clones andcloning 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 bestexperience from all sectors

5. 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

6. FLEXGene Repository Organizational Plan

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

8. DirectorBob 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

9. 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

10. FLEXGene Repository Scientific Plan

11. 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

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

13. 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

14. Pilot Study Project Scope • GOAL: • Direct comparison of cloning systems • 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

15. 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.

16. FLEXGene Repository Legal and Intellectual Property Strategy

17. 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

18. Intellectual PropertyExisting 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

19. Intellectual PropertyCloning System FLEXGene (through NIH) will request a contract from cloning system provider that: • Ensures that users will always be able to usetechnology • 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

20. FLEXGene Repository Clone Distribution and Maintenance Strategy

21. Maintenance and DistributionOverview • 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

22. Maintenance and DistributionDistributor 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

23. Maintenance and DistributionDistribution 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

24. Maintenance and DistributionDistributor Qualifications Experiencedistributing 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