Genomic results often reach clinicians as reports that decision support cannot read. Agnotic Technologies builds the integration that brings structured variant and pharmacogenomic results from your lab partners into the EHR, with consent, access controls and audit logging designed in from the first sprint.
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Precision medicine data integration moves genomic test results, from variants to pharmacogenomic findings, out of lab systems and into the EHR as structured data that clinicians and decision support can use. Agnotic Technologies builds it for you on the HL7 FHIR Genomics Reporting implementation guide, with consent and access rules for sensitive genetic data.
The hard part is not the transport. It is keeping each variant, its interpretation and its link to the signed report intact as data moves between lab partners, your platform and the EHR.
This page covers the data integration. Sequencing, variant calling and diagnostic models stay with your lab partners and data science teams.
Data path
Three layers. We build the middle one and the connections on each side.
FHIR Genomics Reporting
The HL7 FHIR Genomics Reporting guide (v3.0.0, STU 3, on FHIR R4) defines these profiles. They build on DiagnosticReport and Observation, so systems without genomics support still keep the data.
| Code | Name | Typical use |
|---|---|---|
| Genomic Report | Derived from DiagnosticReport | The container clinicians open, linked to the signed report and each finding. |
| Variant | A genomic finding | A detected variant, described with standard notation such as HGVS. |
| Genotype | A genomic finding | A genotype call, often the input to pharmacogenomic rules. |
| Haplotype | A genomic finding | A set of variants reported together. |
| Diagnostic Implication | A genomic implication | The lab's interpretation of a finding for a condition. |
| Therapeutic Implication | A genomic implication | Medication relevance of a finding, which decision support acts on. |
| Molecular Consequence | A genomic implication | The predicted effect of a variant on the gene product. |
| Genomic Study | Derived from Procedure | What was tested and how, so results can be read in context. |
Decision table
Most programs use more than one format. This is how we decide which carries what.
| Delivery format | What the clinician gets | What decision support can use | When we choose it |
|---|---|---|---|
| Signed PDF report | The full narrative report attached to the chart | Nothing discrete; rules cannot read a PDF | Always, as the signed record, but never as the only feed |
| HL7 v2 result message | The report plus discrete results the lab codes | Coded values the lab sends as discrete results | When the lab and EHR already run HL7 v2 result interfaces |
| FHIR Genomics Reporting bundle | A genomic report with each variant and interpretation as its own Observation | Every variant, genotype and implication can be queried | When the lab can produce it, or we convert to it in the integration layer |
| SMART on FHIR genomics app | A dedicated genomic view launched from the chart | Whatever the app reads from the genomic repository | When the detail is too much for the EHR's own result screens |
Each module is scoped on its own, so a first release can be one of them.
Orders out and results in for each genomic lab, over HL7 v2, FHIR or both, with one internal model behind them.
Variants, genotypes and implications stored to the Genomics Reporting profiles, linked to the signed report.
CDS Hooks services that check genotype results when a clinician orders a drug and return a card in the workflow.
A SMART on FHIR app that shows the full genomic picture, launched from the patient's chart.
Consent capture, sensitivity labels and role-based access applied to genetic results before they are shown.
De-identified or consented extracts for research programs, kept separate from clinical data paths.
Failure points
These fail quietly, and a quiet failure in genomics can mean a wrong prescription.
Challenge
Variants lose their interpretation in transit
Agnotic approach
Each variant and implication is its own Observation linked to the report, as the Genomics Reporting guide recommends.
Challenge
A variant is reclassified after the report
Agnotic approach
The guide leaves amendment workflow to implementers, so we keep versioned interpretations and a notification path to the ordering clinician.
Challenge
Results filed to the wrong patient
Agnotic approach
Patient matching runs before anything is filed, with a review queue for uncertain matches and no silent merges.
Challenge
Pharmacogenomic alerts nobody acts on
Agnotic approach
Alerts fire at ordering through CDS Hooks for the drug and gene pairs your clinicians agree, not on every chart open.
Challenge
Genetic data shared beyond its purpose
Agnotic approach
Sensitivity labels and purpose checks travel with the data, and payer-facing feeds exclude genetic results unless a lawful purpose is documented.
Challenge
Every lab sends a different format
Agnotic approach
A per-lab adapter maps each partner's format to one internal model, so a new lab does not change the EHR side.
Genetic results are protected health information under HIPAA. We treat that as design input, not a policy note.
Agnotic signs a BAA before any PHI is shared. Development uses synthetic genomic data, never real patients.
Consent is captured and stored with the data it covers, and each downstream use is checked against its purpose.
Genetic results are visible only to roles that need them, with stricter rules for research and payer-facing feeds.
Every view and export of a genetic result is logged with user, patient, purpose and time.
Who needs it
Programs where genomic results have to reach clinicians as data, not documents.
Germline and somatic results from several labs, filed consistently to one EHR.
Tumor profiling results with therapeutic implications for treatment planning.
Genotype results that drive prescribing alerts at the point of ordering.
Labs that need to deliver structured results into client EHRs.
Products that interpret or act on genomic data and need it from labs and EHRs.
Consented or de-identified genomic data kept apart from clinical feeds.
Scope drivers
We do not quote a price before scoping. These factors move the effort most.
Each lab brings its own formats, codes and testing, so effort grows with every partner.
Labs that already send structured results need mapping. PDF-only labs need a conversion plan or a different contract.
A few agreed drug and gene pairs is a contained build. A broad pharmacogenomics program needs clinical governance alongside.
Filing discrete results to the chart and building a SMART app are separate pieces of work.
Simple clinical consent is quick to support. Research consent and data sharing agreements add rules and review.
New programs need the genomic data model designed with the integration. Established programs mostly need connections.
Four steps, with a fixed first release agreed before build starts.
We list your lab partners, their formats, the EHR you file to and the clinical decisions the data must support.
We design the genomic data model on the Genomics Reporting profiles and map one lab partner's results to it with synthetic data.
One lab, results filed to the chart, consent and audit in place, tested with your clinical and lab teams.
More lab partners, pharmacogenomic CDS and the clinician app follow, each as its own release.
Health Insurance Portability and Accountability Act
Protect PHI with privacy-first architecture, encrypted storage and transmission, strict access controls, and traceable audit logs.
General Data Protection Regulation
Implement lawful consent flows, data minimization, retention controls, and secure processing for sensitive health data.
Fast Healthcare Interoperability Resources
Enable standardized health data exchange across apps, care teams, and systems through standards-based FHIR APIs.
Health Level Seven International
Support enterprise-grade interoperability with HL7-based integrations for records, events, and clinical messaging workflows.
Health Information Trust Alliance
Align security programs to healthcare-specific control and risk management practices trusted by providers and ecosystem partners.
Health Information Technology for Economic and Clinical Health Act
Design with breach notification readiness, digital record safeguards, and operational controls that support regulated care programs.
FDA Software as a Medical Device
Plan software quality, traceability, and documentation pathways for products that may require SaMD review and submission.
Medical Device Regulation (European Union)
Prepare EU market-ready processes for risk classification, evidence tracking, and lifecycle governance under MDR expectations.
Substance Abuse and Mental Health Services Administration
Apply confidentiality controls and consent-aware sharing models for behavioral and mental health data experiences.
Standards in scope
Short facts we design around, each linked to its primary source.
The HL7 FHIR Genomics Reporting implementation guide (v3.0.0, STU 3, based on FHIR R4) defines how to structure genomic reports and variants. It covers data structures only, not how reports are ordered, routed, delivered or amended.
Source: HL7 International, Genomics Reporting Implementation GuideUnder HIPAA, health information includes genetic information, so individually identifiable genetic test results held by a covered entity or business associate are protected health information.
Source: 45 CFR 160.103 (eCFR)The HIPAA Privacy Rule prohibits health plans, other than issuers of certain long-term care policies, from using or disclosing protected health information that is genetic information for underwriting.
Source: 45 CFR 164.502(a)(5)(i) (eCFR)CLIA requires a laboratory to have systems that send test results accurately and reliably from data entry to the final report destination, including results reported electronically to interfaced systems.
Source: 42 CFR 493.1291 (eCFR)CDS Hooks is an HL7 specification that lets an EHR call an external decision support service at points in the clinician's workflow, such as opening a chart or signing an order.
Source: HL7 International (CDS Hooks)
