Diagnostic-Lab Focus | HL7 v2 / FHIR R4 | Epic, Cerner, LabWare, STARLIMS | Mirth Connect Engineering
LIS and LIMS Integration Services for Diagnostic Laboratories
Where LIS, LIMS, and EHR Integration Breaks Down
These problems show up across every lab type, and they compound. A lab rarely has just one of them.
Manual Re-Entry Between Systems
Staff re-key orders or results between the LIS/LIMS and the EHR because no interface connects them, creating duplicate-entry errors and no single source of truth for a given case.
Orders Not Reflected in the EHR in Real Time
A lab order placed in the EHR does not show up in the LIMS until someone checks a fax, portal, or inbox, so accessioning starts late and turnaround time erodes before testing even begins.
Broken or Missing Bidirectional Sync
An interface exists but only pushes one direction, so results have to be matched back to the originating order manually, and messages silently drop during high-volume periods without anyone noticing.
Billing Disconnected From the Lab Workflow
CPT and ICD-10 codes get mapped manually from the same order data the LIMS already has, driving up claim denial rates and keeping the RCM system blind to a result the moment it posts.
How We Build LIMS EHR Integration
Nothing moves to production until it has run in parallel with what you have today. Our Mirth Connect integration work follows the same stages on every engagement.
Systems and Protocol Assessment
We map every system in the loop, the LIS, LIMS, EHR, billing platform, and lab instruments, and the protocol each one already speaks: HL7 v2 (ADT, ORM, ORU), FHIR R4, ASTM/LIS2-A for instrument interfaces, or nothing standardized at all. This sets the real scope; a lab on a 15-year-old LIMS with no API needs a different plan than one already exposing FHIR R4.
Mirth Connect Channel Architecture
We design the interface-engine channels that sit between each system pair: source connectors, JavaScript transformer scripts, and destination connectors (REST, database, TCP/IP, SFTP) so no two systems ever talk to each other directly. Every order and result moves through this lab order interface engine, and any one channel can be rebuilt without touching the others.
Bidirectional HL7 v2 to FHIR R4 Mapping
We build the actual field-level mapping. ADT and ORM/ORU segments translate to FHIR R4 resources (ServiceRequest, Observation, DiagnosticReport, Specimen) through a translation layer, so a lab running HL7 v2 today can add FHIR R4 endpoints without ripping out its existing interfaces. Every result travels from LIMS to EHR through this same HL7-to-FHIR pipeline.
Order Validation and Deduplication
A rules engine checks every incoming order for completeness and the lab's own business rules before it reaches the LIMS, and flags duplicate submissions from EHR retries before they create a second accession, using the same validation pattern behind our Intergenix platform.
Parallel-Run Testing Against Live Data
New interfaces run alongside the lab's existing process, whether that is an older interface or a manual export. Output is diffed field by field against the existing interface against agreed match criteria.
Go-Live and Interface Monitoring
Cutover happens in the same phased, zero-downtime pattern as our lab platform modernization work, with a real-time dashboard tracking interface health so a broken connection gets caught before it becomes a missed result.
Systems We Integrate: Epic, Cerner, LabWare, STARLIMS
Each of the following systems already has a production integration layer, not just theoretical compatibility.
Epic-Showroom (Interconnect, App Orchard, Beacon, Willow), Cerner, Oracle Health (Millennium, PowerChart, Ignite APIs), Athenahealth, eClinicalWorks
HL7 v2 (ADT, ORM, ORU) and FHIR R4
LabWare, STARLIMS, LabVantage
Bidirectional data exchange
Illumina, Thermo Fisher, IDEXX, Roche
ASTM / LIS2-A
Quadex, Salesforce, CareViso
Automated CPT/ICD-10 mapping, eligibility verification
Run a different LIS, LIMS, or EHR platform? The systems and protocol assessment stage confirms what's possible with your specific stack before anything gets scoped.
Confirm Your Platforms Are SupportedWhich Diagnostic Labs Need LIS/LIMS Integration Services
Every lab type runs into these problems. Where you start depends on what's already installed and how many systems are actually in the loop.
- Molecular diagnostics and genetic-testing labs: order intake tightly coupled to sequencing pipelines, where integration has to trigger pipeline execution automatically, not just move data between systems.
- Clinical chemistry, toxicology, and pathology labs: instrument-heavy environments where ASTM/LIS2-A interfaces to analyzers matter as much as the EHR connection.
- Reference laboratories and multi-site networks: platforms that need to sync more than one EHR and more than one billing system at once.
- Labs on a named legacy platform: teams running LabWare, STARLIMS, or LabVantage installations where the existing interfaces were built years apart by different vendors and no longer agree with each other.
Genomics and molecular labs have a narrower problem: genetic test orders, duplicate detection across test versions, and routing a structured requisition from Epic or Cerner straight into a sequencing pipeline. We have a dedicated breakdown of exactly that.
Frequently Asked Questions
What is the difference between LIS integration and LIMS integration?
Should a lab use HL7 v2 or FHIR R4 for LIMS integration?
How do you handle real-time result delivery to the EHR?
How long does LIMS EHR integration typically take to implement?
Can you integrate LIMS and EHR systems without disrupting live lab operations?
Which LIS and LIMS platforms do you have production integration experience with?
What happens to lab instrument interfaces during a LIMS integration project?
Ready to Connect Your LIS, LIMS, and EHR?
A scoping call is a working conversation about your specific systems, not a sales pitch. Tell us which EHR, LIMS, and billing platform you run, and where the manual re-entry is happening today.
Book a Scoping Call