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March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Ida Sim, MD, PhD
March 9, 2010
Division of General Internal Medicine, and Center for Clinical and Translational Informatics
UCSF
Informatics for Clinical Research
Copyright Ida Sim, 2010. All federal and state rights reserved for all original material presented in this course through any medium, including lecture or print.
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Outline
• Clinical Research Systems Overview• Clinical Research Informatics (CRI)
– sharing research meaning• UCSF clinical research information systems
– MyResearch– Integrated Data Repository– REDCap– Epic
• Summary
Big Picture of Health Informatics
Virtual Patient
Transactions
Raw data
Medical knowledge
Clinical research
transactions
Raw research
data
Dec
isio
n su
ppor
t
Med
ical
logi
c
PATIENT CARE / WELLNES RESEARCH
Workflow modeling and support, usability, cognitive support, computer-supported cooperative work (CSCW), etc.
CRMSs
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Clinic 2008
FrontDesk
Radiology
MedicalInformationBureau
Walgreens
Pharm BenefitManager
Benefits Check(RxHub)
HealthNet
B&T
UCare
Specialist
ReferralAuthorization
Internet Intranet Phone/Paper/Fax
Lab
UniLab
(HL-7)
IRB Funding Agency
Study DB
Data analysis
Results reporting
Contract R
esearch O
rganization (C
RO
)
Protocol
Trial DesignSponsorsAcademic PIs
?Site 1 Site 2 Site 3
Site Management Organization (SMO)
Clinical Research Today
• >80% on paper
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
IT Systems for Clinical Research
• Electronic IRB systems– electronic system for submission and review of
applications– e.g., ClickCommerce, home grown, iMedRIS (at UCSF)
• Clinical Trial Management System (CTMS)– web-based application to define variables, forms, sign-in
authentication, data entry, data cleaning, data analysis and
reporting, etc. – e.g, Velos, OnCore (at UCSF Cancer Center)
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
iMedRIS
• Just launched 2 weeks ago
– http://research.ucsf.edu/chr/iMedRIS/Home.asp
• Each institution can customize what information is collected– mostly administrative
data (e.g., PI name)– scientific info is all in text
(e.g., design type = RCT)
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
IT Systems for Clinical Research
• Electronic IRB systems– electronic system for submission and review of
applications– e.g., ClickCommerce, home grown, iMedRIS (at UCSF)
• Clinical Trial Management System (CTMS)– web-based application to define variables, forms, sign-in
authentication, data entry, data cleaning, data analysis and
reporting, etc. – e.g, Velos, OnCore (at UCSF Cancer Center)
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
CRMSs
• Clinical Research Management Systems are for running/managing a study– document management (protocol, case report
forms)– finances, IRB– study calendar (what to do to whom when) and
data entry– data management and analysis– reporting
• Most systems designed for supporting interventional clinical trials (CTMS)
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
EHR vs. CTMS Contents
• EHR• Patient demographics• Chart notes
– problem list• Visit and assessment• Lab and other orders• Lab and other results• Clinical decision-making• Discharge summary
• CTMS• Title, NCT #, IRB #• Protocol document
– interventions, design,
outcomes, etc.• Study assessment• Outcomes assessment• Case report forms• Data analysis• Trial reporting/publication
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
CRMS Policy at UCSF
• Currently– Cancer Center on OnCore– rest of campus on smattering of other systems
• e.g., Quesgen, Immune Tolerance Network/Stanford
• Longer term– may extend OnCore to rest of campus
• In the meantime, have a few systems providing some support – REDCap, MyResearch, IDR, etc.
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Outline
• Clinical Research Systems Overview• Clinical Research Informatics (CRI)
– sharing research meaning • UCSF clinical research information systems
– REDCap– MyResearch– Integrated Data Repository– Epic
• Summary
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Why is CRI Important?
• Clinical trials are becoming very complex– avg 460 days (2002) to 780 days (2006)– avg # of participants: 1700 to 3400 over 30 yrs– # of study procedures: 70% increase to 85 procedures, from
2000 to 2005
• Fragmented, global industry– estimated 1100 organizations involved in clinical research in
2009 in US (Sponsors, CROs, SMOs, AHCs...)
– “43% big pharma FDA trials were conducted abroad... projecting as much as 65% within 3 years” [Tufts Outlook 2008]
• Can we afford to do this all in paper??
Tufts Center for the Study of Drug Development, “Growing Protocol Design Complexity Stresses Investigators, Volunteers,” Impact Report 10, no. 1 (January/February 2008).
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Clinic 2008
FrontDesk
Radiology
MedicalInformationBureau
Walgreens
Pharm BenefitManager
Benefits Check(RxHub)
HealthNet
B&T
UCare
Specialist
ReferralAuthorization
Internet Intranet Phone/Paper/Fax
Lab
UniLab
(HL-7)
IRB
Trial Design
Protocol
Funding Agency
Site 1 Site 2 Site 3
Site Management Organization (SMO)
Study DB
Data analysis
Results reporting
Contract R
esearch Organ
ization
(CR
O)
SponsorsAcademic PIs
?
Simplifying Clin Research Management
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Need to “Interoperate”
• Can achieve through one single standard system – one end-to-end CTMS from trial inception to end– used by all PIs, industry, CROs, worldwide– like everyone using Word for word processing
• ...or through “plug and play” of multiple modular systems– define common terms, models, interchange
protocols– provide software components for assembly – provide way to “certify” compatibility of systems
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Interoperation
• Ability of two or more systems or components to exchange information and to use the information that has been exchanged [IEEE Standard Computer Dictionary, 1990]
– syntactic: grammar, composition of what is said• e.g., using an exchange protocol over networks• e.g., HL7, DICOM, XML Document Type Definition (DTD)
– semantic: meaning of what is said• e.g., using a controlled vocabulary aka dictionary• e.g., SNOMED, ICD-9
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Biomedical IT “Stacks”
Administrative Clinical Care Research
ClinicalBilling
Physical Networking
Communications Protocols (e.g., HL-7)
Standard Vocabulary
PracticeManagement
Systems
Medical BusinessData Model
ElectronicMedicalRecord
Clinical CareData Model
Clinical Res. Management
Systems
Clinical StudyData Models
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Interoperation Over the Stack
Administrative Clinical Care Research
ClinicalBilling
Physical Networking
Communications Protocols (e.g., HL-7)
Standard Vocabulary
PracticeManagement
Systems
Medical BusinessData Model
ElectronicMedicalRecord
Clinical CareData Model
Clinical Res. Management
Systems
Clinical StudyData Models
Syn
tact
icS
em
ant
ic a
nd
Wo
rkflo
w
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
MICU
FinanceResearch
QA
Clinical / ResearchData Repository
Internet
ADT Chem EHR XRay PBM Claims
• How do the machines “talk” to each other?
Networking Basics
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Internet = Network of Networks
itsa
medicine
ucsf.edu
nci.nih.gov
“the cloud”
myhome.com
Main Trunk Cables
local trunk cablethrough Berkeley
amazon.com
at homedial-in to itsa.ucsf.edu via modem
pacbell.net
aol.com
Internet Service Provider (ISP)via DSLor cable
LAN
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
• Protocol = grammar for machines talking to each other– e.g., hypertext transfer protocol http for web
• http://www.epibiostat.ucsf.edu/courses/schedule/med_informatics.html
– e.g., ftp file transfer protocol– all sit on top of basic networking protocol TCP/IP
• Health-specific protocols needed “on top of” http or TCP/IP– a “grammar” for how to exchange health-related data
What Happens Over the Cables
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Health Data Interchange Protocols• HL7, “containers” for data packages, e.g., lab
• DICOM, “containers” for radiology studies– machine used, type of study, # of images, etc.
• CCD (Continuity of Care Document) for the electronic chart– e.g., problem list, allergies, family history
• “Containers” do not address the data naming issue– e.g., Na, sodium, serum sodium -- need to standardize to a SNOMED code
MSH|…message headerPID|…patient identifier<!-OBX…observation result>OBX|1|ST|84295^NA||150|mmol/l|136-148|H||A|F|19850301<CR>
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Sharing Research Meaning
Administrative Clinical Care Research
ClinicalBilling
Physical Networking
Communications Protocols (e.g., HL-7)
Standard Vocabulary
PracticeManagement
Systems
Medical BusinessData Model
ElectronicMedicalRecord
Clinical CareData Model
Clinical Res. Management
Systems
Clinical StudyData Models
Syn
tact
icS
em
ant
ic a
nd
Wo
rkflo
w
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Computable Protocol
• Study protocol is core essence of a research study– the investigational plan, including the actions to be
undertaken, the measurements, and the analysis
procedures to be followed– is not the same as the study protocol document (i.e.,
the Word or PDF file)• If this protocol is made computable, and
standardized, then all clinical studies can be described in the same way so that clinical research systems can interoperate
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Components of a Study Protocol• Who
– participants: eligibility criteria, recruitment, followup– investigators: PI, sponsors, advisors, etc.
• What– interventions or exposures: experimental, control– study outcomes: primary, secondary, baseline
• When– dates of enrollment, timing of assessments
• Where– study sites
• Why– background, objective, hypothesis
• How– analytic approach, study monitoring, outcomes adjudication, etc.
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Computable Protocol
Administrative Clinical Care Research
ClinicalBilling
Physical Networking
Communications Protocols (e.g., HL-7)
Standard Vocabulary
PracticeManagement
Systems
Medical BusinessData Model
ElectronicMedicalRecord
Clinical CareData Model
Clinical Res. Management
Systems
Computable Protocol
Syn
tact
icS
em
ant
ic a
nd
Wo
rkflo
w
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Need Standardization To...
• Common computable study protocol– the study plan: e.g., eligibility criteria, treatment, outcomes
• CTOM, SDTM, BRIDG, OCRe, etc. etc.
• Common variables– clinicallly-agreed upon data items for research
• e.g., “menopause” defined a certain way
• Terminologies/vocabularies– base terms used to describe biomedical concepts
• e.g., SNOMED, NCI Thesaurus
• Common interchange standards– e.g., CDISC (“HL7 for clinical research”)
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Scientific Case for Standardization
• Interventional studies fundamentally done to demonstrate differences between interventions, by types of patients [Clarke M, Trials 2007]
– common eligibility criteria would facilitate cross-study comparisons and synthesis
• e.g., post-menopause, congestive heart failure– common study outcomes (phenotypes) necessary for
pooling/meta-analysis• e.g., 5-year cancer free survival, common asthma measures
• Similar argument for observational studies– e.g., comparative effectiveness research
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
NCI Approach in Cancer
• NCI caDSR (Data Standards Repository)– library of Common Data Elements (CDEs) that
others have defined– you can define new CDEs using terms from NCI
Thesaurus
• Let’s go search...– https://cdebrowser.nci.nih.gov/CDEBrowser/
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Case Report Forms (CRF)
• Why reinvent the wheel for common forms?• NCI has a Forms Builder
– “shop” for CDEs, put them into your cart– insert CDEs into your case report form
• can download as HTML, XML, Excel, Word, PDF
• NCI now building library of forms – e.g., Demographics Case Report Form built from
CDEs• PDF, Word, etc. or directly to CTMS for direct data
entry
• Grant proposals to NCI are beginning to be reviewed on use of CDEs
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Summary: Interoperation of Research Data
• Interoperation = meaningful exchange of data among computers– syntactic: how things are said, the grammar– semantic: what is said, the meaning
• Semantic standardization a greater challenge in research than clinical care– need a common computable protocol model– need to be very precise, research needs change as
knowledge grows, researchers very individualistic• Moving towards standardized, coded variables
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Outline
• Clinical Research Systems Overview• Clinical Research Informatics (CRI)
– sharing research meaning • UCSF clinical research information systems
– REDCap– MyResearch– Integrated Data Repository– Epic
• Summary
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Clinic 2008
FrontDesk
Radiology
MedicalInformationBureau
Walgreens
Pharm BenefitManager
Benefits Check(RxHub)
HealthNet
B&T
UCare
Specialist
ReferralAuthorization
Internet Intranet Phone/Paper/Fax
Lab
UniLab
(HL-7) IRB Funding Agency
MyResearch
Data analysis
Results reporting
On
cor C
RM
S?
Protocol
Trial DesignSponsorsAcademic PIs
Site 1 Site 2 Site 3
Site Management Organization (SMO)
UCSF Research Info Systems
Integrated Data Repository
REDCap
Epic
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
REDCap
• Web-based tool for building study databases and defining data entry forms– https://redcap.ucsfopenresearch.org/– https://redcap.ucsfopenresearch.org/index.php?ac
tion=training– is HIPAA-compliant (unlike Survey Monkey)
• Example web-based survey– https://redcap.ucsfopenresearch.org/surveys/index
.php?hash=c9f0f895fb98ab9159f51fd0297e236d• Now available to you for free
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Clinic 2008
FrontDesk
Radiology
MedicalInformationBureau
Walgreens
Pharm BenefitManager
Benefits Check(RxHub)
HealthNet
B&T
UCare
Specialist
ReferralAuthorization
Internet Intranet Phone/Paper/Fax
Lab
UniLab
(HL-7) IRB Funding Agency
MyResearch
Data analysis
Results reporting
On
cor C
RM
S?
Protocol
Trial DesignSponsorsAcademic PIs
Site 1 Site 2 Site 3
Site Management Organization (SMO)
Where Should REDCap Data Go?
Integrated Data Repository
REDCap
Epic
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Risks of Data Security Breach
• PIs storing Protected Health Information (PHI) data on laptops, unsecured desktops
– thefts, losses– VA, cancer registry
• New CA law: you can be fined up to $250,000 for PHI breach
• MyResearch is ultra-secure storage for your PHI data
IRB Funding Agency
MyResearch
Data analysis
Results reporting
On
cor C
RM
S?
Protocol
Trial DesignSponsorsAcademic PIs
Site 1 Site 2 Site 3
Site Management Organization (SMO)
REDCap
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
No More Lax Storage
PI #2
PI #1
MyResearch
Secure location with backup
SAS, R
Firewall
Pixels only
Secure Global Desktop
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
• PHI stored in FISMA level secure database system
• Data never physically leaves MyResearch
• Your browser is a “dumb” window onto the MyResearch computer– SAS, etc. runs on data
on MyResearch– you see pixels only, no
local caching on your
computer
MyResearch
MyResearch
Secure location with backup
SAS, R
Firewall
Pixels only
Secure Global Desktop
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Using MyResearch
• Satisfies soon-to-be required CHR criteria for secure data storage– if you don’t use MyResearch, must show you are
as secure (i.e., FISMA level, very difficult)• Works on PC, Mac with Leopard, Unix• Is brand new, still has bugs • Will cost ~$400/yr/PI starting ~July• http://oaais.ucsf.edu/OAAIS/networking/
research_data/1034-DSY.html
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Clinic 2008
FrontDesk
Radiology
MedicalInformationBureau
Walgreens
Pharm BenefitManager
Benefits Check(RxHub)
HealthNet
B&T
UCare
Specialist
ReferralAuthorization
Internet Intranet Phone/Paper/Fax
Lab
UniLab
(HL-7) IRB Funding Agency
MyResearch
Data analysis
Results reporting
On
cor C
RM
S?
Protocol
Trial DesignSponsorsAcademic PIs
Site 1 Site 2 Site 3
Site Management Organization (SMO)
UCSF Research Info Systems
Integrated Data Repository
REDCap
Epic
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
• Retrospective cohort study of outpatients• Compare 5 year rate for congestive heart failure for
diabetics treated with a glitazone vs. not– find diabetics– find whether treated with a glitazone– for these patients, find all subsequent cases of congestive
heart failure – analyze at 5 years
• adjust for age, sex, severity of diabetes, previous CHF,
other meds, etc., etc.
Outcomes Research Project
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
• Diabetes diagnosis– chart, HgbA1C, meds taken, problem list...
• Glitazone usage– orders, pharmacy
• Potential confounders– age, sex, severity, other meds, etc.
Health System Minnesota: 50 paper, 50 computer
200,000 lives, 460 physicians
Health System Minnesota: 50 paper, 50 computer
200,000 lives, 460 physicians
Types of Data Needed
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
MICU
FinanceResearch
QA
IntegratedData Repository
Internet
ADT Chem EHR XRay PBM Claims
• autofeed nightly, data stored securely with backup
Data from UCare to IDR
The IDR Is Live!
• Complete UCare Data Set– 2.7 Million patient records– 5 Million encounter records– Currently inpatient data – Beginning to get billing data– Importing Dentistry (Axium system)
• Pilot Release to Select Investigators– Slow ramp up of customers will continue– Building full support for all users– Self Service interface
43
Typical Research Query
• A typical query:
To do retrospective patient analyses using ICD-9 code searches/discharge diagnoses, e.g. a UCSF clinician is interested in looking at a patient population composed of children <21yo with heparin induced thrombocytopenia (ICD=289.84) in the last 5 years.
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
i2b2 Demo
• UCSF IDR built using the i2b2 software suite from Harvard Partners
• Demo of i2b2 query interface to over 5000 anonymized real records from Partners
– http://services.i2b2.org/webclient/#
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Changing UCSF Research Culture
• Must keep all data/analyses in MyResearch environment
• Can search IDR for non-PHI and PHI-sensitive data• Policies established on who owns what data when
and when to share under what circumstances– e.g., what if you put data in then leave UCSF?
• In 2 years, UCSF will revisit policy on IDR use– may well require all PIs to deposit final research data
into IDR for sharing• Slow uptake, many reasons
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Clinic 2008
FrontDesk
Radiology
MedicalInformationBureau
Walgreens
Pharm BenefitManager
Benefits Check(RxHub)
HealthNet
B&T
UCare
Specialist
ReferralAuthorization
Internet Intranet Phone/Paper/Fax
Lab
UniLab
(HL-7) IRB Funding Agency
MyResearch
Data analysis
Results reporting
On
cor C
RM
S?
Protocol
Trial DesignSponsorsAcademic PIs
Site 1 Site 2 Site 3
Site Management Organization (SMO)
Epic Research Functionality?
Integrated Data Repository
REDCap
Epic
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Summary• Clinical research fragmented, global, essentially
separate from clinical care• Clinical research informatics ongoing in two worlds
– most still paper, commercial CTMSs mostly document centered (PDFs) rather than data or concept-centered
– moving towards modular component approach with • standard data elements (CDEs) and case report forms (CRFs)• common computable protocol models and interchange exchange
standards (CDISC)
• UCSF offering web-based data entry and databases, secure data storage and access to UCare data via IDR
• Still very very early in design and use of clinical research information systems
March 9, 2010: I. Sim EHRs and ResearchEpi 206 — Medical Informatics
Market Facts
• In early 90s, 80% trials done in academia, now 20% – about 10% of UCSF studies are pharma-related
• Huge business– Big Pharma: $15.9 b on clinical trials [2006], out of $50.3 b total
R&D [2009 PhRMA Industry Profile]
– NIH budget $29.5 billion 2009
• Fragmented, global industry– estimated 1100 organizations involved in clinical research in
2009 in US (Sponsors, CROs, SMOs, AHCs...)– CROs $15b market in 2007– “43% big pharma FDA trials were conducted abroad...
projecting as much as 65% within 3 years” [Tufts Outlook 2008]