Genetic Alliance BioBank

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Genetic Alliance BioBank
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Genetic Alliance BioBank

• Vision and structure
• Clinical information services
• Biorepository
• Web Reporting Portal
• Costs

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Genetic Alliance BioBankOur Vision
We revolutionize access to information and
resources to enable translation of research into
services and individualized decision making.
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The Need

• Access to well annotated samples
• Ability to dynamically consent/reconsent
• Longitudinal clinical data collection
• Clinical health information registry
• Medical record collection
• Interoperability with EMR/PHR
• Archival exchange with dbGaP

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Founded October 14, 2003 BioBank Advisory
Committee 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, NIH Liz Horn, PhD,
MBI, International Psoriasis Council Owen
Johnson, CEO, Inflammatory Breast Cancer Research
Foundation
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www.biobank.org
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Biological Samples and Data Repository

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

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Genetic Alliance BioBank

• Advocacy owned repository for clinical data and
  biological samples.
• Centralized, standardized (and customizable)
  collection and archiving for data
• Highest participant protection and biorepository
  standards
• Open access to the degree determined by managing
  organization
• Advocacy organization stewardship

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Phased Development
Phase I Biological Sample Repository Launched
October 2003
Phase II Clinical Data Repository Launched
November 2006
Phase III Online web questionnaire Launched
February 2008
Phase IV Clinical Trials Recruitment Medical
Records Management Projected September 2008
Phase V Interoperability with dbGaP Projected
November 2008
Phase VI Interoperability with Major PHR/EMR
Projected November 2009
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Genetic Alliance BioBank
Disease Specific Organization Data and Sample
Management
Clinical Information
Barcoded Samples
Patient Enrollment
Sample and Clinical Banking
Informed Consent Demographic Data Sample
Collection Tracking Data Management Electronic
Paper Records
Internet

• No Additional Hardware Requirements
• Standard Web-Browser Software

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Genetic Alliance BioBank
Clinical Records
Bank Management
Genetic Alliance BioBank
Data and Sample Import Single and Batch Upload
Research
Self-reported questionnaires
Data and Sample Query Data Management Request
Inventory Management Security Access Control
Sample Bank
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Translational Research System
Formatted Datasets for Analysis
Data and Sample Set for New Study
Query Interface, Request Management, Data Sharing
Fencing, Inventory Control, Privacy Policy
Informed Consent Compliance, Access Control
User Authentication, Audit Trail
Clinical Data Repository
Sample Repository
Genomic Data Repository
Privacy Policy Informed Consent Repository
BioData Sample Bank
Study Management
Banks Other Sources
Data and Sample Import
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Genetic Alliance Banking Platform From Study Bank
to Network
GX Study 001
GX Study 001
Study 001
Cohort Number 1
Disease Specific Org Study Management
Data and Samples
Clinical ResearchNetworks
To other diseases
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Genetic Alliance BioBank

• Centralizes standardized collection and archiving
  of both clinical information and biological
  samples
• Maintains the integrity of advocacy
  organizations collections data
• Enables IRB approved investigator research
• Ensures appropriate use of data samples
• Enables ethical re-contact and follow-up for
  phenotype/genotype correlations, natural history
  and longitudinal studies
• Allows regular communications to key constituents
• Facilitates advocacy organization stewardship
  benefit sharing

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GA BioBank Cooperative

• The Advisory Board, representing the
  organizational 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
• Members bring skills and resources to the
  collective

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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
• Clinical Data Collection System including web
  interface
• Biological Samples Collection/Processing/Archiving
  and Distribution System
• Availability of multiple other genomic services

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Example Successes

• The gene discovery for PXE and CFC have both come
  about as a result of advocacy group BioBanks.
• PXE has also licensed the diagnostic and is
  proceeding to genomic and biochemical studies.
• CFC has subsequently begun drug development.
• HAE Association will join and use structure for
  adverse drug reporting in FDA approval

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GX TRIMS Tissue Repository Information
Management System

• Vendor
• Gene Logic

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Registry Clinical information services

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

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Action Request Portal

• Through the online Action Request Portal
• Enter demographic data
• Request Kits
• Generate Reports
• Donor Report
• Donor Accession Report
• Site Inventory Report
• Kit Status Report

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Online Questionnaires Administrative Portal

• Manage registry
• Give patients ID numbers and password
• Automate email invitations to registry portal
  (online questionnaire)
• Review status of
• open questionnaires
• Review completed
• questionnaires
• Release data
• to TRIMS
• (backend database)

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Online Questionnaires

• Member organizations receive clinical data from
  either online questionnaire responses (with admin
  approval step required) or direct administrator
  input

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Online Questionnaires

• Each registry respondent accesses a personal
  account to respond to their individual
  questionnaire
• They can complete sections of the questionnaire
  one at a time or from start to finish

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Online Questionnaires

• Questions are customizable
• Advocacy organization reviews each questionnaire
  prior to its upload into GX TRIMS

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GX TRIMS - Tissue Repository Information
Management System

• Data entry and secure storage of information
• clinical data
• medical history
• signs symptoms
• medications
• surgeries
• sample annotations
• source and handling information
• processing and QA information
• 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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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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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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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 controled 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 - 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
• Sample 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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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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Gene Logic Genomics Core Competencies - a la cart
for BioBank

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

• 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

• 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)

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Gene Logics Biorepository

• 9 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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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 (includes data and physical
samples)

• 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 data collection systems,
  templates, website, administration of all the
  services of the BioBank
• Customization of data structure for TRIMS -
  negotiated dependent on the complexity

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Clinical data costs
Unlimited use of TRIMS database annual
fee Import previously collected clinical data
1/record Gene Logic enters clinical data
150/record
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All Biological Sample Costs
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 10/fragment Sample storage
3/fragment/year FTA Card
storage 1/card/year Sample Splitting (into
5ug DNA aliquots) 25 Sample pull (distribute) 1
to 20 samples 7/fragment 21 to 100
samples 6/fragment 101 samples 5/fragment
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• Examples of Some Other Services
• Cell Lines
• Cell line establishment 411
• Cell line re-initiation and shipping 40.25
• Annual cell line storage 7/year
• RNA Isolation 100
• Microarray Data Generation 500 700
• Many other services available

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Example of gathering a sample from one person

• Kits (to collect whole blood and cheek cells) 15
• Sample Accessioning 10
• DNA Isolation from blood 40
• Sample storage (3 Fragments)
  9/year
• (3/fragment/year)
• Total 74/sample
• 9/each year after
• Fragment - any aliquot of DNA, at present two
  vials of blood and one cheek swab kit become 3
  fragments

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Example BioBank Charges for One Year

• Assume Organization collects 1000
  questionnaires, 100 tissue samples and 100 blood
  samples for the year
• Annual fee 20,000
• Unlimited questionnaires 0
• 100 blood kits 1500 (one time)
• 100 kits accessioned 1000 (one time)
• 100 DNA extractions from blood 4000 (one time)
• 100 tissue samples accessioned 1000 (one time)
• 100 DNA from tissue 10,000 (for very hard
  samples)
• 400 samples (fragments) stored 1200 (annual)
• Send out 100 samples 700 (in small lots)
• Total 39,400 (compare to costs on slide 34)
• First year includes 20,000 joining fee

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Becoming a Member of the GA BioBank

• Potential members complete an application to
  membership designed to ensure organizational
  health and support when entering this co-op model
• The application is reviewed and approved by a
  committee of the BioBank Board

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Membership Application Requirements

• Completion of the application
• Organizational documentation
• Documentation of 501 (c) (3) status, most recent
  990, most recent Independent Auditors Report,
  copy of your DO insurance binder, voided check
• Board rosters
• Board of directors roster and professional
  advisory board roster
• Letters of support
• 2 letters of commitment and 2 letters of
  recommendation

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Application Approval

• Once the application is approved, the member
  organization is part of the Genetic Alliance
  BioBank
• Each organization must obtain IRB approval prior
  to collecting samples

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IRB Approval

• Member organizations use customizable template
  documents for all regulatory approvals from the
  time of consent through sending samples to
  researchers
• Documents include IRB protocol, consent form,
  child assent form, sample collection protocols,
  material transfer agreement (MTA), sample
  application form for researchers, and others
• Completed documents are reviewed and approved by
  the Genetic Alliance BioBank IRB

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Beginning Sample Collection

• Once the member organization has IRB approval,
  they begin sample collection
• Each new organization works with the Genetic
  Alliance BioBank and Gene Logic to implement the
  procedures for the clinical questionnaire and
  biological sample collection (see appendices)

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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