Crimson Project http://crimsonproject.org/

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Crimson Projecthttp//crimsonproject.org/

• Lynn Bry, M.D., Ph.D
• Department of Pathology
• Brigham Womens Hospital
• Boston, MA 02115
• lbry_at_partners.org

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The basic premise for today . . .
Crimson
i2b2
Cohort
IRB
HIV
High-throughput sample collection
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Resources

• Samples Pathology Depts/Clinical Labs
• BWH labs discard gt5000 clinical samples/day
• gt2 million/year
• Partners hospitals gt20,000 samples/day
• BWH AP gt200,000 samples/year
• LIS/APLIS Structured data/match samples.
• Basic demographic data
• Tests ordered, results
• Diagnostic codes, reports

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Crimson

• Spans Clinical -gt Research systems to acquire
  materials under an IRB.
• Developed with Daedalus Software Inc. in
  Cambridge, MA
• (1) Identify discarded materials (2) process
  submitted/consented research samples.
• Study/IRB Registration management.
• LIMS system Manage lab workflow and resulting.
• Criteria Engine Identify discarded materials.
• Billing system Recoup costs for services.
• Download of data for banking and study staff

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Cohort
IRB
Crimson
IRB
i2b2 CRC
Cohort Table
Criteria Engine
Picklist (Accessions)
LIS/APLIS data
Accessioning
Workflow Engine/LIMS
Holding Tank 7-30 day rolling window of all
clinical accessions
Honest Broker
Flat-text files Misys, Powerpath, other LIS
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Crimson
i2b2 CRC
Cohort Table
Study
Rule Set
Criteria Engine
IRB
Picklist (Accessions)
LIS/APLIS data
Query
Accessioning
Workflow Engine/LIMS
Holding Tank 7-30 day rolling window of all
clinical accessions
Honest Broker
Flat-text files Misys, Powerpath, other LIS
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Crimson
i2b2 CRC
Cohort Table
Samples Located
CMV
Criteria Engine
Picklist (Accessions)
LIS/APLIS data
Query
Accessioning
Workflow Engine/LIMS
Holding Tank 7-30 day rolling window of all
clinical accessions
Honest Broker
Flat-text files Misys, Powerpath, other LIS
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Crimson
i2b2 CRC
Cohort Table
Samples Located
CMV
Criteria Engine
Workbench Anon1 Anon2 Anon3 ..
Picklist (Accessions)
Workflow Engine/LIMS
Accessioning
Holding Tank 7-30 day rolling window of all
clinical accessions
Honest Broker
MRN (If consented)
Sample Shipments
Crimson Patient ID (Not MRN)
Subject ID (Study-specific)
Crimson Sample ID (Not Acc)
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Impact of Crimsons sample collection on the
science..
Samples/Month, BWH Specimen bank

• Go- live February 2007
• gt15,000 samples handled the first year at BWH.
• Serving gt35 studies

MW 1 2 3 4
Serum antibody
Crimson go-live Feb 2007
1.0 kb
0.5
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Impact of Crimson on Sample Throughput
Higher throughput at lower cost More for less
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Low throughput example Study1

• PI needs 40 samplescontrols to test proof of
  concept for autoantibody antigen.
• Samples not available from banks no access to
  local clinics, nor staff to perform consent.
• Given time effort to set up protocol, consent
  process, considers costs infinite

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Study 1 Crimson Collection

• Query to find appropriate discarded serum samples
  (anonymzied).
• Costs of collection 8-9/sample.
• 10 samples/month 10 controls.
• Collection completed in 2 months.
• Grant submitted to NIH on findings.

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Medium Throughput Example Study 8

• gt1000 Consented patients in study
• DNA and plasma to measure stable analytes.
• Daily samples while patients in the hospital.
• 18/sample for phlebotomyprocessing in Specimen
  Bank
• 20/Sample in study coordinator effort to
  arrange phlebotomy and processing

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Study 8 Crimson collection

• Coordinators register consented patients in
  Crimson under their study
• Crimson query identifies discarded purple tops
  from clinical labs.
• Cost 8/sample 1-2 coordinators time to
  register patients in Crimson.
• gt60 reduction in sample costs.
• Estimated 10-20 increase in productivity of
  study staff and consent rate.

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High throughput example Study 4

• Study desires 10,000 samples for epidemiologic
  analyses
• Avg. cost/sample for the study 1,200
• 12,000,000 to collect 10K samples
• Throughput of 5-10 samples/month
• 120 years to collect 10K with current process.

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Study 4 Crimson Collection

• Forwarded cohorts via i2b2
• Avg cost for collection 8-9/sample
• Costs for collection of 10K samples 85,000
• Avg throughput
• 4-600 samples/month (1 Crimson node)
• 1000 with 2 Crimson nodes operational.
• Collection of controls in lt1 year
• Experimental samples in 1.5 - 4 years.

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Crimson

• It works!
• Successful high-throughput sample collection for
  many studies.
• Significant cost-savings to investigators and
  research enterprise.
• Enabling communication with i2b2.
• Multiple Crimson nodes for collection.

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http//www.crimsonproject.org/
Acknowledgements
BWH PathIT Neil Herring, MBA Diane
Steidler Shadan Shafieha
Partners IRB Judy Scheer, R.N. Libby Hohmann,
M.D. Pearl ORourke, M.D.
Daedalus Software -US Azita Sharif, CEO Erik
Lickerman, M.D.
Daedalus Software -PK Nighat Afsheen Khurram
Naseem Annas Sheikh
BWH Specimen Bank Kristina Lefteri Ashley Grant
i2b2 MGH LOC Shawn Murphy, M.D. Vivian
Gainer Anil Dubey, M.D. Susanne Churchill,
Ph.D. Zak Kohane, M.D.
BWH Pathology Michael Gimbrone, M.D. Andy
Onderdonk, Ph.D. Milenko Tanasijevic, M.D.
Funding BWH Pathology Partners ResearchIS
Research IS (dev) Diane Keogh Leo
Braginsky Natalie Boutin Ana Holzbach Brent
Richter Allan Harris Steve Roylance
MGH Pathology Patrick Sluss, Ph.D. Chris
Loftgren Anand Dighe, M.D. John Gilbertson, M.D.