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Infectious Diseases Labs and LOINC Coding
Stephen Soroka, NCEZID/ODJune 25, 2014
Office of the Director
National Center for Emerging and Zoonotic Infectious Diseases
Agenda Background to OID/CGH, a systems
perspective Recent history ELIMS Current status
Understanding OID/CGH lab test orders and tests
Gaps and Challenges of LOINC coding in OID/CGH
OID/CGH Lab Organization
4 National Centers NCEZID, NCIRD, NCHHSTP, CGH
16 Divisions with Labs 32 Lab Branches 90+ Infectious Diseases Laboratories
OID/CGH Lab Organization
Every year 50-100,000 specimens received into CDC for testing
200-500,000 tests performed in Infectious Diseases (ID) laboratories Numbers vary by year Not all tests are reported
IT Systems for managing specimens, data, and tests vary widely in ID
Recent Lab History (Systems Perspective)
Early 2000s: High profile events demonstrated the need for labs to collectively organize and manage lab data. Few labs utilized anything beyond MS Excel/Access
2004: A Laboratory Information Management System was selected, STARLIMS v9 (SLv9). A lab-by-lab implementation approach was taken
2009: 40+ labs were given customized implementations into SLv9, leading to system performance issues, difficulty in data sharing, and long lab implementations
Late 2000s: Other labs have also developed systems. Siloed approaches to specimen and data management
Recent Lab History (Systems Perspective)
2010: A LIMS Blue Ribbon Panel recommended an enterprise approach to implementing LIMS within the ID labs.
2011: A strategic approach for implementing an enterprise LIMS (ELIMS) was developed. The plan calls for standardization of data management and lab workflows (management of specimen testing). This is in contrast to previous lab-by-lab custom implementations.
2012: ID selected STARLIMS v10 (SLv10) as the foundation for ELIMS.
2013: ID ELIMS development initiated.
Centralization and Standardization
Implementation of an enterprise Laboratory Information Management System (ELIMS) To support and centralize lab workflows and data Culture shift from silo to enterprise
Benefits Process Automation Systems Integration ELIMS Specimen Management Quality Improvements in data accuracy, security, and
access Establishes a common/core data model across the labs Improves data sharing with internal/external partners Allows for establishment of ETOR
ELIMS Current State 42 ID laboratories have been implemented and
are active Units in SLv9. By end of FY14, all ID labs (~93) will be
accessioning specimens into ELIMS through SLv10 Systems integration with SLv9 Establishes an Enterprise lab data model Future development work includes standard workflows,
electronic reporting, and other lab-specific functionality
Some labs still use custom developed systems Many SQL-based, Access front end systems Some systems maintained by 1 developer
Interoperability is still not on the ELIMS radar Attempts were made with SLv9 ELIMS development based on future utilization of ETOR
Enterprise Accomplishments Improved the specimen submission process
for samples submitted to CDC: new 50.34 form (an electronically fillable,
barcoded specimen submission form); online infectious diseases laboratory test
directory; new ‘one-stop shop’ website.
SLv9 laboratories have the ability to issue standardized, encrypted PDF reports electronically
Demonstrated the importance of standardized data during a recent Anthrax Lab Surge Exercise (2013) Real-time data sharing with EOC Efficient data integration with epidemiological data
Why is all of this important to know?
Without ELIMS, silo approaches to interoperability were the way forward A lack of a standardized system would mean different
lab requirements (i.e. 90+ different ETOR guides) Difficult to standardize/code data across labs Who would monitor for appropriate SNOMED/LOINC
codes? What system(s) would labs use?
Standardizing the specimen submission process and establishing ELIMS allowed CDC to create its first ID Test Directory
Test Directory for the Infectious Diseases Laboratories
Identified by SPHLs as an area of improvement
List of CDC Test Orders Required when specimens are submitted to
CDC Supplemental information supplied with orders
• Key contact information, pre-approvals• Test descriptions, turn around time, required volume• Available online and orderable through the 50.34
Form Laboratory-defined test orders
• 350+ test orders• Similar in concept to test panels
Test Directory for the Infectious Diseases Laboratories
Test Orders are flexible Not directly linked to any tests Allows labs ability to choose tests based on different
scenarios Test orders development process did not collect tests per
order
ELIMS does not link orders with tests ID Test Orders and Tests are not
LOINC coded Why?
It was new; many changes since going live Time and budget Limited SME support Should they be coded? Well…yes!
• Benefits to LOINC codes are known in this WG
Gaps and Challenges to LOINC Coding
ID Test Orders and Tests Most labs lack knowledge of
LOINC/SNOMED While many labs lack knowledge, they are the ones who
know their tests and need to review codes with those who assign them
Not all labs will care about coding
Linkage between Test Orders and actual tests performed does not currently exist
Development work needed within ELIMS Low in priority on the ELIMS roadmap Decreased budget over the past few years led to lost
interoperability resources on the ELIMS team
Gaps and Challenges to LOINC Coding
ID Test Orders and Tests LOINC coding need SNOMED coding
Capturing proper data elements for tests Result values, interpretations need coding as well ELIMS results data model in progress
Effort requires OID leadership buy-in Progress can be impeded by lack of leadership support
Potential Solutions to LOINC Coding
ID Test Orders and Tests Well-organized agency wide implementation
plan for LOINC coding ID tests is needed Coordination across CIOs is fundamentally necessary OID leadership needs buy-in and oversight Educating staff on benefits of coding and interoperability Promote and support the concept and importance of
harmonization, standardization, and collaboration
An enterprise process/guide for getting new codes or retiring codes should be established Should CDC have a central group for getting SNOMED/LOINC
codes? Do they now? The knowledge of a few shared to the whole
Establish Test Orders (i.e. LOINC panels) not directly linked to actual test performed Implementation becomes more simplified, though still not easy
Summary and Discussion Points
LOINC coding ID test orders and tests is necessary
Education for buy-in would be ideal Lab involvement is necessary
Makes for a lengthy process; • Few are fully aware of coding standards• Who to involve from the lab?
Must consider other competing factors• ELIMS implementation• QMS implementation• Routine lab work
Need a CDC-defining a coding process