Genetic Alliance BioBank

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Genetic Alliance BioBank

• Liz Horn, Ph.D., M.B.I.
• Board member, Genetic Alliance BioBank
• LizHorn.consulting_at_gmail.com

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Genetic Alliance BioBankOur Vision
Individuals and Advocacy Organizations
Partnering with Researchers Industry to drive
Translational Research Leading to New Safe and
Effective Treatments.
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ProblemWell annotated samples needed to catalyze
and focus research

• Solution build new nonprofit designed to meet
  the needs of multiple advocacy organizations,
  providing infrastructure to collect biological
  and clinical data samples

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Genetic Alliance BioBank

• Advocacy owned repository for biological samples
  and clinical data.
• Centralized, standardized collection and
  archiving
• Highest biorepository and participant protection
  standards
• Open access for all organization approved
  researchers
• Advocacy organization control

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Founded October, 2003 Board members Sharon F.
Terry, Genetic Alliance and PXE
International Joan Scott, Center for Genetics and
Public Policy Patrick F. Terry, International
Genetic Alliance and PXE International Claire
Driscoll, National Human Genome Research
Institute Liz Horn, PhD, MBI, International
Psoriasis Council Owen Johnson, CEO, Inflammatory
Breast Cancer Research Foundation
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GA BioBank functions as a cooperative

• The Board, representing the members, configures
  the best possible infrastructure, and continually
  improves the options available to the members as
  science and technology improve
• As the number of members of the BioBank
  increases the BioBank has more resources and is
  able to offer more and more options

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Phase I Biological Sample Repository
Completed October 2003

• DNA/RNA Self-reported Data
• Cell Lines Medical Records
• Tissue / Organs

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www.biobank.org
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Genetic Alliance BioBank

• Centralized, standardized collection and
  archiving
• Maintains the integrity of advocacys
  organizations collections data
• Enable IRB approved investigator research that
  otherwise would not happen
• Ensure appropriate use of samples data
  patients advocacy organization
• Enable ethical re-contact and follow-up for
  phenotype/genotype correlations, natural history
  and longitudinal studies
• Regular communications to key constituents
• Advocacy organization control benefit sharing
  with the advocacy organization

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GA BioBank members receive

• Training/mentoring
• Templates for all necessary documents, including
  membership agreement, consent documents, material
  transfer templates, protocols
• IRB review of all documents approval
• Biological Samples Collection/Processing/Archiving
  and Distribution System
• Clinical Data Collection System
• Availability of multiple other genomic services

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www.biobank.org
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Successes

• The gene discovery for PXE and CFC have both come
  about as a result of advocacy group BioBanks.
• For CFC, this seems to be quickly leading to a
  drug treatment.

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GX TRIMS Tissue Repository Information
Management System
Phase II Clinical Data Repository Launched
November 2006

• Vendor
• Gene Logic

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Gene Logic
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Gene Logic Genomics Core Competencies - a la cart
for BioBank

• Genomics Production
• Expression
• qRT-PCR
• SNP Genotyping

• Tissue, cells, blood, RNA, DNA, sections
• Extensive clinical data collected for each sample
• Rigorous QC and in-house pathology review
• Residual samples for future analysis (qRT-PCR,
  LCM, SNP, IHC)

• Largest commercial Affymetrix data production
  facility
• Over 175,000 arrays processed
• Stringent QC SOPs
• Proprietary process tracking system
• Over eight years experience
• New LIMS implementation

• Data Mining Tools
• Query Tools
• Pathway Mapping
• Gene Family Analysis
• Fold-Change Analysis
• Electronic Northern
• Third Party Tool APIs
• dB Management Development
• Data analysis
• Data integration

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Gene Logics biorepository

• 8 years in the making
• 120,000 samples accessioned
• International network of clinical and academic
  centers
• IRB approval and Gene Logic training
• Covers all major disease areas
• Extensive clinical data
• Rigorous QC collection procedures
• In-house board-certified pathology review
• Residual sample stored and available for LCM,
  proteomics, IHC, PCR, SNP
• Resource for clinical samples and proprietary
  studies

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Biorepository services

• Bio-banking
• Clinical Protocol Development
• Source Clinical and Animal model samples on
  specification
• Support Genomics Services
• Sample shipping, handling and storage
• Assist in protocol design/execution
• IRB protocols
• Training (site, protocol, sample collection)
• Clinical data capture
• Communication with client
• Support Genomic Information Business
• ensure consistency and quality in sample handling
  and storage
• establish and maintain accrual programs for
  biosamples and clinical data
• maintain integrity, quality and consistency of
  sample data
• maintain physical inventory and storage

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Clinical information services

• Clinical questionnaire
• Action request portal
• TRIMS system
• Tissue Repository Information Management System
• Industry-grade registry
• Web-interface to enter data is in development

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GX TRIMS - Tissue Repository Information
Management System

• GX TRIMS is Gene Logics primary system for
• Data entry and secure storage of information
• sample annotations
• source and handling information
• processing and QA information
• clinical data
• Inventory and process flow data
• Managing physical inventory and storage
• Interfacing with production and release
• Providing reports and data in multiple formats.

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GX TRIMS major components

• Data entry interface (TRIMS Client)
• Robust Oracle database back-end
• Freezer management
• Workflow processing
• Web based query and reporting
• Role-based security
• Administrative interfaces
• Transaction logging

Ad Hoc Inquiry Portal Based Reports
Sample Data Entry, Inventory Management, Release
Management
Data Storage, Security, Administration
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Clinical data

• Over 1000 clinical data fields captured in TRIMS
• Demographics
• Health Risk Factors
• OB/GYN History
• Medical History
• Family History
• Diagnostic Tests
• Required vs. Disease-specific
• Medical records and imaging data storage
• Customized for each member organization

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Data update workflow

• Numerous screens allow exacting input of clinical
  data.
• Interface allows definition of new clinical
  categories, areas, panels, and measurements.

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GX TRIMS maintenance

• GX TRIMS includes strong control vocabulary to
  ensure accurate data capture.
• SNOMED is used as the key vocabulary for
  pathology, morphology, disease, and medication.
• Numerous proprietary control vocabulary used for
  gender, race, measurement units, etc.
• Some CVs are easily modified through
  administrative screens by a key user.
• Other CVs require a system administrator to make
  modifications, in order to ensure referential
  integrity.

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GX TRIMS other features

• GX TRIMS provides many other capabilities
• Bulk import / export utilities
• Various fixed and ad hoc reports
• Transaction logging
• Authentication and user management
• System Administration tools

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GX TRIMS - reports

• The following standard reports are accessed via a
  Web portal
• Accrual by year
• Inventory by site
• Inventory by tissue
• Pathology diagnosis by organ
• Shipment by date
• Biosample release report
• Consolidation report
• Inventory report
• Donor report
• Sample workflow status report
• Site Manager Release Status Report
• Sample by owner and owner group

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GX TRIMS security and authentication

• GX TRIMS includes a fine-grained hierarchical
  system of authentication with users, groups,
  permissions and roles
• Information in GX TRIMS has an owner and a
  permission object
• a users privileges are checked prior to
  displaying, or changing a data
• A site administrator creates users and groups,
  and establishes roles
• Authentication logs are maintained to show
  changes to permissions and access

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Typical BioBank costs

• Within a year, the Autism Genetic Resource
  Exchange had DNA from 100 families -- more than
  any of the research teams. The collection has
  since grown to more than 400 families and cost
  more than 6 million in private donations to
  build. - 2003 Los Angeles Times
• For these studies, 1,000 Motor Neuron Disease
  cases and equal numbers of controls are needed.
  The NHMRC has recently awarded the Bank a 5-year
  750,000 grant to enable these extra cases to be
  collected. - Australia National Health Medical
  Research Center
• Creating and managing the 1,000 sample repository
  will cost 2.5 million over the next 18 months,
  with additional funding needed to meet the 10,000
  sample goal. - Accelerated Cure Project for
  Multiple Sclerosis

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GA BioBank Costs

• Initial joining fee (payment plan available)
  20,000
• Pays for initial investment in developing
  infrastructure IRB approvals
• Annual fee (billed quarterly) 20,000
• Pays for use of biological and data collection
  systems, templates, website, administration of
  BioBank
• Customization of data structure for TRIMS -
  negotiated dependent on the complexity

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The Cost for one kit
Kits (to collect whole blood and cheek
cells) 15 DNA Isolation from blood
40 Sample storage 3/year
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Costs - Volume Dependent
Kits (to collect whole blood and cheek cells)
15 DNA Isolation from blood 40 DNA
Isolation from tissue (dependent on difficulty)
40 - 100 RNA Isolation from tissue, blood or
cells 100 Expression (plus array) 585 SNP
(plus array) 585 Sample accessioning (bring
in already stored samples) 10/sample Sample
storage 3/sample/year Sampl
e pull (distribute) 1 to 20 samples 7/sample
21 to 100 samples 6/sample 101
samples 5/sample
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Other services

• Import previously collected clinical data
  1/sample (record)
• Gene Logic enters clinical data 150/sample
  (record)

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Example Costs for One Year

• Assume Organization collects 100 tissue samples
  and 100 blood samples for the year
• Annual fee 20,000
• 100 kits 1500 (one time)
• 100 DNA extractions 4000 (one time)
• 200 samples stored 600 (annual)
• Send out 100 samples 700 (in small lots)
• Total 27,000
• First year would include an additional 20,000
  joining fee

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• Seldom is it that ordinary people like myself get
  to participate at any level in extraordinary
  events. I see donating blood to the BioBank as
  one of those events.
• ---Genetic Alliance BioBank Participant

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Appendix

• Making it happen key considerations for
  starting your BioBank

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What is a BioBank?

• Collection of Biological Samples
• Blood for DNA extraction
• Buccal swab
• Tissue
• Cell Lines
• Collection of Clinical Information/ Data
• Medical Records
• Imaging
• Donor interview or questionnaire
• Data is organized into a computerized database
  that allows for queries

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Why start a BioBank?

• Leverage scarce resources
• Donors only have to give once
• Dont have to rely on researchers to share
• More research money goes to actual research
• With Genetic Alliance BioBank, possibility for
  cross-disease research

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BioBank collection structure what will you
collect?

• No one correct answer
• Advice from experts in the field
• Scientific Advisory Board/ Medical Advisory Board
• Researchers who will use samples
• Advice from experienced advocacy organizations
• Collection goal will determine resources and
  funding needed for project
• Samples and data

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BioBank organizational structure who will help
you collect it?

• Principal Investigator
• Advisors
• Scientific Advisory Board
• Medical Board/ BioBank Oversight Committee
• Genetic Alliance BioBank
• Day-to-day operations
• Staff
• Volunteers

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GA BioBank Process how will you collect it?

• Regulatory documentation (IRB)
• Template documents at www.biobank.org
• Sample collection
• Develop system to screen participants
• Gene Logic action request system to request kits
• Clinical information collection
• Clinical questionnaire
• TRIMS system

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Marketing materials what materials can you
develop?

• Web site
• Brochures (marketing and medical professional)
• Features in newsletter/ magazine
• Direct mail pieces
• Incentive materials (stickers, pens, note cards,
  post its)

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Recruitment strategy how will you recruit
participants?

• Web site
• Member communications
• Outreach events
• Medical professionals
• Media (press releases and NAPS release)

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Retention strategy how will you retain
participants?

• Incentive mailings
• Thank you card
• Birthday card
• New Years card
• Timely updates (member communications and
  quarterly updates)

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Making collection available to researchers

• BioBank oversight committee
• Process to make collection available
• Marketing strategy to make collection available
• Announcements to research community
• Announcements to advocacy community