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 Solution

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

Specimen Submission Form

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