Download Common Data Model Clinical Data Tables: Laboratory Test Results

Common Data Model Clinical
Data Tables: Laboratory Test
Results as an Example
Marsha A. Raebel, PharmD
Senior Investigator, Kaiser Permanente
Colorado
[email protected]
December 11, 2014
Development Principles of the Mini-Sentinel and
HMO Research Network Laboratory Results
Tables (LRT)
 Transparency
 Maximize use of existing data resources
 Stay as close to source data as possible
 Recognize disparities in electronic clinical data sources
 Leverage lab results reporting standards (e.g., LOINC) when feasible
 Seek guidance from those with expertise
– Investigators with clinical database and lab test result interpretation knowledge
– Project managers with experience managing multiple sites
– Data partners representatives with knowledge of site-specific source data
– Programmers/analysts with clinical results table and lab test expertise
 Structure facilitates adding additional test types
2
Laboratory Test Results in the MiniSentinel LRT (9/13)
3
Laboratory Test Results in the Mini-Sentinel
LRT (11/14)
 12 Data Partners participating
Date Range
2006 - 2014
4
Unique Lab Test
Results
730,361,167
Unique Patient IDs
32,352,924
Development and Implementation of the MiniSentinel LRT
Detailed information:
Raebel MA, Haynes K, Woodworth TS, et al. Electronic Clinical
Laboratory Test Results Data Tables: Lessons from Mini- Sentinel.
Pharmacoepidemiol Drug Saf. 2014;23(6):609-18.
Current Mini-Sentinel LRT data dictionary:
http://www.mini-sentinel.org/data_activities/distributed_db_and_data/details.aspx?ID=105
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Laboratory Procedures (administrative
data) vs. Results (clinical data) Tables
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Laboratory Test Procedure
Tables
Laboratory Test Results
Tables
 Administrative data (e.g., CPT
code; test done)
 Clinical data (e.g., test result
values)
 Developed for billing
 Developed for patient care
 Use standardized nomenclature
and coding
 Lack standardized
nomenclature and coding
 Not useful in defining cohorts,
assessing outcomes, or
adjusting for confounders
 Useful for cohort identification,
outcomes, confounder
adjustment
Information in Source Data used to Extract Lab
Results across 12 Mini-Sentinel Data Partners
Extraction Source
Test name/test substring search
LOINC
Component codes
Test-specific CPT codes
Site-specific codes
Test name & specimen type combination
Other
Battery/panel codes
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No Data Partner uses just one source
Number of Data
Partners Using Source
8
7
6
5
4
2
2
0
Challenges in Developing Laboratory
Results Data into a Common Data Model
 Lab test results obtained during routine healthcare delivery
– No uniform coding or standard documentation. Use of standards (e.g., LOINC) is
variable and inconsistent
– Vary across organizations and within an organization over time
 Tests change over time
– Identifiers
– Result units
– Repeated re-evaluation necessary to ensure current and comprehensive
incorporation of source and transformed data
 Result units
– Multiple (e.g., mmol/L, IU/L, mg/dl) for a single test require conversion to a
standard unit
– Incomplete (e.g., number with no unit volume [no denominator])
 Reference ranges
– Unique for every test type
– Variations within a single test type (e.g., male vs. female, adult vs. pediatric)
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9 March 25, 2015
Characterization, Harmonization, and
Quality Checking the Mini-Sentinel LRT
 Transformed results data evaluated initially (e.g., upon
loading) and with each refresh
 Assessments for each variable separately for each lab test
type include completeness, consistency, content, alignment
with specifications, patterns, and trends
 Data distributions examined over time within and between
Mini-Sentinel Distributed Database refreshes
 Feedback given to data partners with expectation that
anomalies be investigated, corrected, or otherwise
addressed
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Examples of Variations in Platelet (Quantitative)
Result Units in Source Data
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Examples of
Variations in
(Qualitative)
Pregnancy Result
Units in Source
Data (aka, how
many ways can you
spell negative?)
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NEGATIVE
POSITIVE
UNDETERMINED
BORDERLINE
BORDERLI
NEG
NONE DET
POS
COMMENT:
160.8
0.5
1.2
1000
122
14
140
15
2
2
2.1
203
252.3
278
28
3178.2
345
38.1
400
5 Int
5272.4
642.2
670
697.7
DETECTED
INDETERM
N
NOT DETE
Neg
Negative
Negatvie
P
Positive
SPRCS
TNP
n
neg
negative
.
820
840
1615
ABNORMAL
BOARDERL
BODERLIN
CANCELLE
DUPLICAT
EQIVOCAL
EQUIVOCA
HIRABAYA
NE-CHECK
NEAGTIVE
NEG (-)
NEGA
NEGA T I
NEGA TIV
NEGAT IV
NEGATAIV
NEGATIAV
NEGATIBE
NEGATIE
NEGATRIV
NEGATTVE
NEGATVIE
NEGAVTIV
NEGITIVE
NEGTIVE
NETGATIV
NORM
NORMAL
POA
POPSITIV
POSIITIV
POSITIFV
POSITTVE
POSITVE
POSOTIVE
POSTIVE
PSOITIVE
REPEAT
STAT
URINE
Missingness/Completeness: Serum Creatinine
(sCR) Procedure Codes vs. Lab Result Values
 Modular program query of Mini-Sentinel LRT
 sCr laboratory test results and procedures (CPT) codes
 Entire Mini-Sentinel Distributed Database population
– Lab results for 90% - 100% of enrollees in integrated healthcare delivery
systems
– Lab results for ~ 30% of enrollees in large national insurers
 Inform further assessment of missing LRT values
 Crudely estimate numbers and proportions of sCr test results with
and without corresponding coded procedures
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Serum Creatinine Procedure Codes vs. Lab
Result Values
 >=55% of CPT codes from any care setting did not have lab
result values
 ~ 10% of lab result values from outpatient settings did not
have CPT codes
 ~ 75% of lab result values from inpatient settings did not
have CPT codes
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Key Points about Developing and Implementing
a Multi-Site LRT into a CDM
Unique Challenges
 Multiple source
databases
 Engage experts
 No uniform coding
 Stay as close as possible to
source data
 Few documentation
standards
 Decisions can be necessary
on test-by-test basis
 Inter- and intraorganization variation
 Characterize data
 Every lab test has its
own considerations
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Systematic Approach
 Harmonize data
Ongoing Oversight
 Continuous
monitoring and
management to keep
valid and useful
 Identifies emerging
themes and issues
 Facilitates updates
 Quality check
 Apply systematic
approach
 Provide feedback to sites
 Repeat