Transcript CRBM Mission - Wake Forest Clinical and Translational Science

Center for Redox Biology and Medicine
CRBM
Leslie B. Poole, PhD
Cristina M. Furdui, PhD
Department of Biochemistry
Department of Internal Medicine
Section on Molecular Medicine
Wake Forest Baptist Medical Center
Mission and Scientific Vision
CRBM Mission:
--coordinate and facilitate interdisciplinary basic, translational, and clinical
research
--goal of improving the knowledge of redox processes contributing to
diseases with underlying oxidative mechanisms of damage
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neurodegenerative diseases
cancer
diabetes
cardiovascular diseases
aging
Plans:
Seminars and workshops
Pilot grants to bring together basic and clinical scientists
T32 training grant funding
Multi-investigator grants in the area of Redox Biology & Medicine
*Only other “Redox Center” in US is the “Redox Biology Center” at U Nebraska
Wake Forest Baptist Medical Center
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CMCS and Redox Biology
Center for Molecular (Communication and) Signaling
Wake Forest Baptist Medical Center
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CMCS and Redox Biology
Center for Molecular (Communication and) Signaling
Wake Forest Baptist Medical Center
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Redox Biology
Area of strength in basic sciences
Scientifically:
1 or 2 electron transfers, relevant to
NAD(P)H chemistry, NADPH oxidases (Nox)
innate immunity, inflammation
Electron transfer through heme and flavin proteins
“Antioxidants”, battling oxidant damage
But also mediates/regulates cell signaling processes
e.g., proliferation, insulin signaling, “stemness”
Molecular targets mostly unknown
Wake Forest Baptist Medical Center
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Redox Biology and Medicine
From basic science to disease
Known cell signaling targets:
Protein tyrosine phosphatases
Kinases (e.g., ATM, Akt2, PKA)
Calcium channels
Historical areas of strength:
WFU Development of chemical probes to identify sites of protein oxidation
Oxidant defense enzymes
Vascular biology and nitric oxide, dietary nitrates
Wake Forest Baptist Medical Center
Redox Biology and Medicine
From basic science to disease
Known cell signaling targets:
Protein tyrosine phosphatases
Kinases (e.g., ATM, Akt2, PKA)
Calcium channels
Historical areas of strength:
WFU Development of chemical probes to identify sites of protein oxidation
Oxidant defense enzymes
Vascular biology and nitric oxide, dietary nitrates
Disease interests:
Head and neck cancer
Lung injury
Arthritis and chondrocyte biology
Dietary nitrates and exercise, pulmonary hypertension
Sepsis
Cardioprotection from anthracycline chemotherapy
Wake Forest Baptist Medical Center
Redox Biology and Medicine
From basic science to disease
Known cell signaling targets:
Protein tyrosine phosphatases
Kinases (e.g., ATM, Akt2, PKA)
Calcium channels
Historical areas of strength:
WFU Development of chemical probes to identify sites of protein oxidation
Oxidant defense enzymes
Vascular biology and nitric oxide, dietary nitrates
Disease interests:
Head and neck cancer
Lung injury
Arthritis and chondrocyte biology
Dietary nitrates and exercise, pulmonary hypertension
Sepsis
Cardioprotection from anthracycline chemotherapy
Wake Forest Baptist Medical Center
EXPAND!
CRBM membership
• 32 WFSM members
Internal Medicine
Cancer Biology
Biochemistry
Hypertension
Micro/Immunol
Phys/Pharm
Path/Comp Med
Biomed Eng
Anatomy
• 9 WFU members
Cardiology
Chemistry
Biology
Physics
• 6 regional members
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High Point U
NC A&T
UNC-CH
Duke
Ga Tech
• Many participating faculty will be located at
the Innovation Quarter, further increasing
opportunities for interaction and crosscampus collaborations
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Wake Forest Baptist Medical Center
CRBM membership
• 32 WFSM members
Internal Medicine
Cancer Biology
Biochemistry
Hypertension
Micro/Immunol
Phys/Pharm
Path/Comp Med
Biomed Eng
Anatomy
Cardiology
• Mostly PhDs, also 4 MD/PhDs, 2 MDs, 1 VMS
• Executive Board:
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Co-Directors Furdui and Poole
Don McClain (diabetes and metabolic disease)
Suzanne Craft (Alzheimer’s disease)
Greg Hundley (Cardiology and Vascular Biology)
Todd Lowther (Structural Biology, Cancer Center)
Gloria Muday (Director of Ctr for Molecular Signaling, WFU)
Bruce King (Associate Provost for Research, WFU)
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Wake Forest Baptist Medical Center
Mission and Scientific Vision
CRBM Mission:
--coordinate and facilitate interdisciplinary basic, translational, and
clinical research
--goal of improving the knowledge of redox processes contributing to
diseases with underlying oxidative mechanisms of damage
•
•
•
•
•
•
neurodegenerative diseases
cancer
diabetes
cardiovascular diseases
aging
etc
Plans:
Seminars and workshops
Pilot grants to bring together basic and clinical scientists
T32 training grant funding
Multi-investigator grants in the area of Redox Biology & Medicine
Wake Forest Baptist Medical Center
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Mission and Scientific Vision
CRBM Mission:
--coordinate and facilitate interdisciplinary basic, translational, and
clinical research
--goal of improving the knowledge of redox processes contributing to
diseases with underlying oxidative mechanisms of damage
•
•
•
•
•
•
neurodegenerative diseases
cancer
diabetes
cardiovascular diseases
aging
etc
Recent activities:
Symposium (Oct. 24th) with external consultant (Banerjee)
Faculty recruitment (e.g. Boothman to Cancer Biology)
RFA for Pilot grants to bring together basic and clinical scientists
(LOI, Oct. 16th, full proposal Nov. 14th)
Wake Forest Baptist Medical Center
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Clinical Informatics
Resources for the CTSI
Brian Wells, MD, PhD
Director of Clinical Informatics – CTSI
[email protected]
Data Team
• 2 Stats programmers*
– Kristin Lenoir, Kelly Kuykendall
• 2 Report writers*
– Wendell Futrell, Kerry Hauser
• 2 Clinical Informaticians
– Brian Wells, Ajay Dharod
• 2 Analyst Programmers
– Brian Ostasiewski, Michael Horvath
• 1 Operation administrator
– Lindsay Trost
• 1 Associate project manager and 2 “overflow”
– Tamosia Lea
• 1 Community Intern 20% time beginning in July *
– Elizabeth Lees
* New team members
Open Positions
• 1 Assistant Professor Clinical Informatics
Faculty position
• 1 Associate Professor Clinical Informatics
Faculty Position
• 2 Epic Programmers
• Need for additional report writers.
https://ctsi.wakehealth.edu/data-access
i2b2
i2b2
i2b2
i2b2
i2b2
i2b2
i2b2
Linking the TDW / i2b2 with External Data
Mortality Status
• Deterministic algorithm used to match patients with the NC State Center for
Health Statistics and continuously updated.
• Identified >200,000 deceased individuals.
• Uncovered hundreds of incorrect vital statuses in Epic.
• Plans to include additional states and NDI (CDC).
• Disseminate to the Carolina’s Collaborative
Socio-demographic Data
• Geocoded > 2 million addresses and address changes updated automatically.
• Patient data linked with the American Community Survey at the Block Group
Level
• 20 structured variables linked at the encounter level to the TDW. (e.g. median
household income)
• Disseminate to the Carolina’s Collaborative
Linking Internal Clinical Information
Systems with the TDW / i2b2
Structured PFT results
• PFTs prior to May 2016 stored in PDF format in OnBase.
• Text parsing used to extract continuous values from >20,000 PDF reports.
• Identified errors in the Breeze to Epic interface
• Data used to present results of respiratory navigator program on COPD
readmissions to the European Respiratory Society.
Structured Echocardiogram results
• Commonly used measurements from Xcelera database being
incorporated into i2b2.
• Drs Pu and Vasu will use data to identify patients with aortic valve areas
<1cm2 who may benefit from previously unavailable procedures.
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Linking Internal Clinical Information
Systems with the TDW / i2b2
Imaging Data
• Radiological images stored in PACS.
• Previously no request process or any mechanism for obtaining image files
for analyses.
• CTSI can now locate images in PACS and provide researchers with URL to
download raw image files.
• Plan to provide bulk extracts for multiple images.
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ITEM
STATUS
Human Imaging Data
Historically there was no way to provide direct access to
images through our health system’s
iSite PACS system and a manual chart review was needed to
find images of interest. We now have
access to provide direct URLs for the images to the
investigator. Still working on bulk imaging requests – after
PACS upgrade.
Cancer Biospecimen registry
Brian O has worked with Umit Topaloglu to integrate data
with the TDW.
Nonhuman Primate Data
Basic data received. In process of mapping to the TDW
Tobacco / Smoking
Included in the TDW ontology
Medication Ontologies
TDW / i2b2 now supports NDFRT, RxNorm, and First Data
Bank
Informatics Resources for Investigators
R-Based Program Library
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Create functions to make analysis of EHR data easier for statistical programmers.
(e.g. Charlson Comorbidity Index, GFR, active Medications, procedure and
diagnostic groups)
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Share functions via GitHub and R library on CRAN
Server based shared resources
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Unified Medical Language System to allow crosswalk between ontologies
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QGIS, R, NLP software
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Tableau – CTSI can publish datasets to ITS server
BRSA Verse “Wiki”
http://brsadata01pv.medctr.ad.wfubmc.edu/brsaverse/
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“data dictionary” defining TDW data and providing summary statistics
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User defined calculations (e.g. Length of Stay, comorbidity groupings, medication
groupings etc)
Medication Ontologies
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I2b2 now supports RxNorm, NDFRT, and First Data Bank
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Data Requests
Clinical Informatics Affinity Group
• Core group has 8
members and is
meeting bi-monthly
• Two large CI meetings
have been held.
• 7 WFSM faculty taking
CI board exam, 5
subsidized with CTSI
funds
Currently Funded Projects Supported
by Clinical Informatics Data Team
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Heart Pathway (Mahler)
MSSP (Williams)
Internal Medicine Quality Improvement Projects (Atkinson)
SEARCH (Wagenknecht)
Patient Reported Outcomes (Wagner)
Automated Heart-Health Applications for Survivors
(Weaver)
• Carolinas Collaborative (Duke Endowment – Burke)
• Critical Illness Injury Recovery and Research Center Registry
(Miller)
• Comorbidities in ESRD (Freedman)
CTSI Clinical Informatics Pilots funded
• Automated Heart – Health Applications for
cancer Survivors (Weaver)
• mPath tobacco (Miller)
• Heart Pathway (Mahler)
Unfunded Clinical Informatics
Consultations
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Endocarditis (Barnes)
GIS mapping for ID (Sanders)
ICU transfers (Christiano)
Critical Illness Common Data Model (Miller)
Sugar Sweetened Beverages (Skelton, Lewis)
Medication ontologies (Snively)
ePHIM (Bertoni)
Concussion registry (Stitzel)
Other Updates
• Carolinas Collaborative
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https://carolinascollaborative.org
2 face-face meetings
ETL and CDM process defined for sharing data via Shrine
Handling Requests any time
Wells leading methods paper
2 pilots from Wake Forest funded
• ITS has agreed to activate RDF for Red Cap to Epic interface
• ITS working on uploading Risk predictions from MSSP
project into Star / Epic
• Met with Josh Pederson from Vanderbilt about the
possibility of creating a CI fellowship at Wake Forest.