ngs testing: choosing a provider by panel and validation rather than by price, and reading a report that states its own limits

Choosing a provider

1. Panel design against your genes of interest. A targeted panel sequences a defined gene set very deeply and cheaply, and it sees nothing outside that set. Check the panel's content against your genes and, importantly, against the specific regions within them, since coverage within a gene is rarely uniform.
2. Validation and the limit of detection. Ask what the laboratory validated, on what sample types, and at what lowest detectable variant fraction. A detection claim without a stated validation is a capability statement rather than a specification you can rely on.
3. Accreditation appropriate to the use. Research testing and testing that informs a clinical decision sit under different regimes, and in the United States clinical testing requires a laboratory operating under the clinical laboratory improvement regime. A research result cannot be repurposed for a clinical decision because it was technically good.
4. Sample type and input requirement. Fresh tissue, fixed tissue, blood and cell-free material each have different input requirements and different achievable quality. Declare the sample type at quoting, since fixed material in particular constrains what is possible.
5. Turnaround, repeat policy and failures. Establish the turnaround, what happens when a sample fails quality control, whether a repeat is included and whether you are charged. Sample failures are routine in this field and the policy matters.

Reading the report

A good report states the regions covered and the regions that failed coverage, the variants detected with their fractions, the limit of detection applied, and explicitly what the test does not cover. A report that lists findings without stating its own limits is incomplete, because absence of a finding is meaningless without knowing what could have been found.

Ask for the underlying data as well as the report. Re-analysis with an updated annotation is common and impossible without the aligned reads.

Where this hub stops

This page is about an organisation choosing a testing provider: panels, validation, accreditation and reports. It is not medical advice and does not interpret any individual result.

Where a result could inform a clinical decision, that interpretation belongs with a clinician and a laboratory operating under the appropriate clinical regime, not with a research testing provider or with this site.

Common questions

What should I check before choosing an NGS testing provider?

The panel content against your genes and the regions within them, the validated limit of detection and the sample types it was validated on, the accreditation appropriate to your use, and the policy on sample failures.

What is the difference between research and clinical NGS testing?

They operate under different regimes. In the United States, testing that informs a clinical decision must come from a laboratory under the clinical laboratory improvement regime; a research result cannot be repurposed however good it is technically.

What should an NGS report contain?

The regions covered and those that failed coverage, variants with their fractions, the limit of detection applied, and an explicit statement of what the test does not cover. Absence of a finding means nothing without that.

Can fixed tissue be used?

Usually, with constraints. Fixation fragments and chemically damages nucleic acid, so yields are lower and some approaches are unavailable. Declare the sample type at quoting rather than at the laboratory.

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