EMR lab integration for molecular genetics & pathology labs.
The workflow layer that connects your hospital EMR and LIS to the bench — HL7, FHIR, REST and CSV — without replacing either. Built around your lab's protocols.
The short answer
A molecular lab usually integrates with the hospital EMR through a middleware layer, not by extending the EMR itself. The EMR sends orders and patient data in; the middleware runs the lab-specific workflow — cases, samples, runs, variant curation and sign-out — and sends structured results back. That layer is where CassianLab lives.
Between your EMR and your bench
Clinical systems
Hospital EMR, LIS/LIMS, patient records, lab orders
CassianLab
Cases, samples, panels, runs, variant curation, sign-out — the workflow layer
The bench
Sequencers & instruments, variant analysis tools, ClinVar / gnomAD
Data flows both ways — orders and demographics in, structured results back out.
Integrations, scoped to what you actually run
Hospital EMR
HL7 / FHIREpic, Cerner Millennium and other EMRs — order intake, patient demographics and referral data in; structured results back to the record.
LIS / LIMS
HL7 / RESTAccessioning, specimen identifiers and billing hand-off, without replacing the LIS you already run.
Sequencers & instruments
Files / CSVRun data, coverage and QC metrics captured against the right case and batch.
Variant databases
REST APIClinVar and gnomAD lookups surfaced inside the curation workflow.
Legacy data
CSV / Excel importMigrate case history off spreadsheets and REDCap without losing the record.
Custom connectors
Built as neededWhere a system has no standard interface, we build the connector around it.
Integration is the start, not the point.
Connecting the EMR to the lab is necessary, but it doesn't run the lab. The value is in the workflow the middleware holds on top of the integration — the case, panel, run and variant tracking that off-the-shelf systems handle poorly for molecular work.
Read: why EMR integration isn't enoughMap it to your stack.
Tell us what EMR, LIS and instruments you run, and we'll show you exactly where CassianLab would sit and what it would connect to.
EMR lab integration: common questions
How does a molecular pathology lab integrate with the hospital EMR?
Most molecular genetics and pathology labs integrate with the hospital EMR through a middleware layer rather than by extending the EMR itself. The EMR sends order and patient data (typically via HL7 or FHIR); the middleware manages the lab-specific workflow — case tracking, sample handling, sequencing runs, variant curation and sign-out — and sends structured results back to the EMR. CassianLab is that middleware layer: it sits between the EMR/LIS and the bench and is configured around how the lab actually works.
What is EMR-to-lab middleware?
EMR-to-lab middleware is the software layer that connects a hospital EMR (and LIS) to the laboratory bench and its instruments. It translates and routes data between systems that were never designed to talk to each other, and it holds the lab-specific workflow the EMR does not model — for molecular labs, that means cases, panels, sequencing runs, variants and family relationships. It lets the lab modernise its workflow without ripping out the EMR or LIS.
Does CassianLab replace our EMR or LIS?
No. CassianLab is designed to sit between your existing EMR/LIS and the bench, not to replace them. The EMR keeps doing order entry, the patient record and billing; the LIS keeps doing what it does well; CassianLab adds the molecular case management, sample tracking, variant curation and sign-out workflow those systems handle poorly — and integrates back to them.
What integration standards does CassianLab support?
CassianLab supports HL7 and FHIR for healthcare data exchange, REST APIs for modern systems, and CSV/Excel import for legacy data and instrument files. Where a system has no standard interface, we build a custom connector. Because each deployment is built for the lab, the integration is scoped to the systems you actually run rather than a fixed list.