Internal vs. External Genomic Reporting: What’s Right for Your Lab?
The Sequencing Isn’t the Problem. The Reporting Is.
Over the past decade, sequencing has become faster, cheaper, and more accessible than ever. But the ability to generate genomic data doesn’t guarantee that clinicians can use it or that it arrives in time to guide decisions.
What often gets overlooked is how that genomic data is processed, interpreted, and reported.
For many health systems and research centers, the default solution has been to outsource not just sequencing, but also variant interpretation and reporting. While this can offer short-term convenience, it comes with long-term tradeoffs: higher costs, longer turnaround times, and limited control over the final clinical output.
The alternative? Bringing genomic reporting in-house.
Let’s explore the pros, cons, and considerations of each approach and why more labs are rethinking what stays internal.
The Case for OUTSOURCED Genomic Reporting
Outsourcing is often the first step when standing up a genomic program. Partnering with commercial reference labs or sequencing vendors simplifies logistics and leverages existing infrastructure.
Pros:
- No internal setup or staffing required
- Access to large variant databases and prebuilt pipelines
- Easier for low-volume or research-only programs
- Often bundled with sequencing and storage services
Tradeoffs:
- Turnaround time can be slow – especially for PGx and oncology
- Little control over report format or data structure
- Interpretation logic is often opaque (black-box pipelines)
- Patient data may leave your system and be stored externally
- Custom reports or workflows are difficult to implement
- Scaling costs can balloon quickly
Outsourcing can help you get started but it’s rarely the right long-term model for programs seeking speed, standardization, and sustainability.
The Case for IN-HOUSE Genomic Reporting
In-house doesn’t mean doing everything internally. It means owning the analysis, interpretation, and reporting steps – the ones closest to patient care and clinical decision-making.
Benefits:
- Faster turnaround times, often under 24-48 hours
- Customizable report templates for PGx, oncology, hereditary risk
- EHR and LIS integration options that match institutional workflows
- Better alignment with IRB and privacy policies
- Visibility into pipelines and annotation tools
- More consistent output across test types and departments
- Lower per-sample cost at scale
With modern tools, your team doesn’t need to build the pipeline from scratch. You just need a platform that’s ready for clinical-grade deployment.
Choosing the Right Model: 4 Key Questions
Whether you’re launching a PGx program, scaling tumor profiling, or modernizing a research lab, ask these questions to evaluate your approach:
- What’s the turnaround time you need to support care decisions? If your reports are delayed by days or weeks, clinicians will lose trust and the opportunity for action may pass.
- Do you need to standardize reporting across multiple departments? In-house tools allow for consistent reporting formats between pharmacy, oncology, and primary care.
- Is data control a concern for compliance or research reuse? If so, keeping interpretation and reporting internal may reduce risk and enhance IRB alignment.
- Will you eventually scale? Outsourcing might be fine at 20 samples/month. At 200/month or more, in-house systems become dramatically more cost-effective and operationally sustainable.
How PraediGene Supports In-House Reporting
PraediGene is a clinical-grade genomic analysis and reporting platform that enables labs to internalize what matters most:
- UMI processing
- BWA/GATK-based alignment
- PharmWatch + SylVIA annotation
- Templated, clinician-ready report generation
- Output formats that match EHR, LIS, and research system needs
With report turnaround in hours, not days, PraediGene helps institutions cut their dependency on external vendors and bring genomic decision-making closer to the patient.
FINAL THOUGHT: You Don’t Need to Own Sequencing. You Need to Own the Outcome.
You can still partner with a reference lab for sequencing. But when it comes to what clinicians see and how fast they see it – internal control matters.
If you’re ready to take ownership of your genomic reporting pipeline, now’s the time to rethink your model.
WANT TO SEE HOW PRAEDIGENE SUPPORTS IN-HOUSE GENOMIC REPORTING AT SCALE?
Our team is happy to discuss how PraediGene can support your in-house genomic reporting.