Crimson Project
http://crimsonproject.org/
Lynn Bry, M.D., Ph.D
Department of Pathology
Brigham & Women’s Hospital
Boston, MA 02115
lbry@partners.org
The basic premise for today . . .
i2b2
IRB#
Cohort
Crimson
HIV
High-throughput
sample collection
Resources
• Samples: Pathology Depts/Clinical Labs
• BWH labs discard >5000 clinical samples/day
• >2 million/year
• Partners hospitals: >20,000 samples/day
• BWH AP >200,000 samples/year
• LIS/APLIS: Structured data/match samples.
• Basic demographic data
• Tests ordered, results
• Diagnostic codes, reports
Crimson
• Spans Clinical -> 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.
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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
Cohort
IRB#
IRB#
Cohort Table
Crimson
i2b2 CRC
Criteria Engine
Picklist
(Accession#s)
LIS/APLIS data
Holding Tank:
7-30 day rolling window of
all clinical accessions
Flat-text files: Misys,
Powerpath, other LIS
Workflow
Engine/LIMS
Accessioning
Honest Broker
i2b2 CRC
Cohort Table
Crimson
Rule Set
Study
IRB#
Criteria Engine
Picklist
(Accession#s)
LIS/APLIS data
Query
Holding Tank:
7-30 day rolling window of
all clinical accessions
Flat-text files: Misys,
Powerpath, other LIS
Workflow
Engine/LIMS
Accessioning
Honest Broker
Cohort Table
Crimson
i2b2 CRC
Samples Located
CMV
Criteria Engine
Picklist
(Accession#s)
LIS/APLIS data
Query
Holding Tank:
7-30 day rolling window of
all clinical accessions
Flat-text files: Misys,
Powerpath, other LIS
Workflow
Engine/LIMS
Accessioning
Honest Broker
Cohort Table
Crimson
i2b2 CRC
Workbench
Samples Located
CMV
Criteria Engine
Anon1
Anon2
Anon3
[..]
Picklist
(Accession#s)
Holding Tank:
7-30 day rolling window of
all clinical accessions
Sample
Shipments
Workflow
Engine/LIMS
Accessioning
Honest Broker
MRN
(If consented)
Subject ID
(Study-specific)
Crimson Patient ID Crimson Sample ID
(Not MRN#)
(Not Acc#)
Impact of Crimson’s sample
collection on the science..
Samples/Month, BWH Specimen bank
• Go- live February 2007
• >15,000 samples handled
the first year at BWH.
• Serving >35 studies
MW
1
2
Crimson go-live
Feb 2007
1.0 kb
0.5
3
4
Serum antibody
Impact of Crimson on Sample Throughput
Higher throughput at lower cost: “More for less”
Low throughput example: Study1
• PI needs ~40 samples+controls 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”
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.
Medium Throughput Example: Study 8
• >1000 Consented patients in study
• DNA and plasma to measure stable analytes.
• Daily samples while patients in the hospital.
• $18/sample for phlebotomy+processing in
Specimen Bank
• + $20+/Sample in study coordinator effort to
arrange phlebotomy and processing
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 coordinator’s time to
register patients in Crimson.
• >60% reduction in sample costs.
• Estimated 10-20% increase in productivity of
study staff and consent rate.
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.
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 <1 year
• Experimental samples in 1.5 - 4 years.
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.
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 O’Rourke, M.D.
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.
MGH Pathology
Patrick Sluss, Ph.D.
Chris Loftgren
Anand Dighe, M.D.
John Gilbertson, M.D.
Research IS (dev)
Diane Keogh
Leo Braginsky
Natalie Boutin
Ana Holzbach
Brent Richter
Allan Harris
Steve Roylance
Daedalus Software -US
Azita Sharif, CEO
Erik Lickerman, M.D.
Daedalus Software -PK
Nighat Afsheen
Khurram Naseem
Annas Sheikh
Funding
BWH Pathology
Partners ResearchIS