FLEXGene Repository

Platform

The FLEXGene Platform

Scientific Excellence

Freedom to Operate

Universal Access

Scientific ExcellenceHighest 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

Scientific Advisory Board(Contributing Members)

Legal CommitteeCommunications and Public

RelationsAdministrative

Staff

NIH Foundation

Suppliers

Sequencing site(s)InformaticsDistribution and Quality

ControlClone Production

Director

Operations

FLEXGeneOrganizational Structure

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

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

mRNA5’ Untranslated 3’ UntranslatedCoding Region

Precisely copy the coding region

Add recombination sites

Move to plasmid vector

Master clonesthat populatethe 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

Move the insert by recombination to:(Now a simple automated procedure)

FLEXGenemaster 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

•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 ScopeGOAL:

1. Direct comparison of cloning systems

2. Assess mutation rate during clone assembly

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 systemsPilot completed in 3 monthsNo significant differences between systems768 clones have been fully sequenced:

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 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

Intellectual PropertyCloning 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 ResponsibilitiesDistributors 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 BoardThe 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 Distribution

Distributor QualificationsExperience 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