In 2025, genomic DNA extraction continues to be the foundation of clinical diagnostics. But the landscape is shifting - faster tests, higher sample volumes, and greater sample diversity are now the norm. Clinical labs are under pressure to deliver more results, with less time and fewer people.

Let’s break down what’s driving this change and what the best labs are doing about it.

1. The Sample Types Are Getting More Diverse

In recent years, clinical labs have seen a sharp increase in the diversity of sample types other than blood like plasma, FFPE tissue, saliva, and even low-input single-cell material largely because diagnostic technologies and clinical practices have evolved.

Non-invasive methods like liquid biopsies and NIPT have become standard, driving demand for cfDNA extraction from plasma and serum. Advances in precision medicine have made archived FFPE samples more valuable for retrospective genomic profiling, due to improved extraction chemistries. Meanwhile, swabs and saliva, normalized during the pandemic, are now common in infectious disease and genetic testing due to their ease of collection and growing assay validation. The rise of highly sensitive downstream tools, like NGS and digital PCR, has made it possible to derive clinically meaningful data even from minimal or degraded inputs shifting the DNA extraction challenge from high-yield to high-fidelity and consistency across diverse sample types.

Each of these sample types presents different challenges: degraded nucleic acids, low yields, PCR inhibitors, or variability in input volume. Labs are expected to handle all of them — often in the same day — with equally reliable output. This has placed pressure on extraction protocols to be more versatile and robust. 

2. Turnaround Times Are Shorter, but Quality Standards Are Higher

Turnaround time is now a clinical KPI. Whether it's a STAT oncology panel or a prenatal screen, labs are expected to process samples quickly — often within 24–48 hours — and with minimal error.

This speed requirement coexists with increasing downstream sensitivity. NGS, digital PCR, and single-cell technologies don’t just need DNA — they need clean, intact, inhibitor-free DNA. And unlike older assays, they’re less forgiving of even small errors in extraction.

The implication: extraction must be both fast and precise. The conventional manual protocols are vulnerable to variability — from pipetting errors to inconsistent wash steps — especially when run under time pressure or by overburdened staff.

3. Batching Is Becoming Less Feasible and Less Efficient

Traditionally, labs have relied on batching to justify the time and reagent cost of extractions. But in 2025, many labs are moving toward continuous or semi-continuous sample intake. Waiting to hit a batch size of 24 or 96 samples before processing introduces delays and ties up downstream workflows.

In diagnostic contexts like cancer panels, prenatal tests, and transplant monitoring, batching is increasingly at odds with the clinical need for faster, more responsive processing.

Labs are starting to rethink batching entirely not just to reduce turnaround, but to avoid waste from partial runs and idle reagents.

4. The Margin for Error Has Shrunk

In older workflows, if an extraction failed, you could sometimes rerun the assay without major clinical consequence. That’s no longer the case.

With FFPE tissue, for example, you may only get one shot at extraction before the sample is exhausted. With NGS-based tests, failed libraries don’t just delay results — they also cost real money in terms of reagents, instrument time, and wasted sequencing capacity.

As the cost of a failed run increases, labs are becoming more focused on standardizing extraction quality. They want predictability — not just in yield, but also in purity, inhibitor removal, and sample recovery.

Automation Is Stepping In as an Infrastructure Upgrade

In response to these evolving needs, many labs are turning to automation. But not in the traditional sense of replacing staff or running massive batch systems. Instead, automation is being adopted to:

• Improve reproducibility across operators and shifts

• Enable flexible run sizes without increasing waste

• Handle diverse sample types using validated protocols

• Reduce hands-on time and potential for error

• Integrate better with downstream workflows (e.g., direct transfer into PCR or NGS prep)

Automation is not being deployed to speed things up arbitrarily. It’s being used to stabilize workflows, standardize output, and adapt to increasingly heterogeneous sample loads.

Manta, our automation extraction device, is designed around these evolving needs. It allows labs to run even a single sample on-demand—without batching, buffer wastage, or unnecessary plastic use. Whether you're handling 5 samples or 50, the workflow remains consistent, clean, and scalable.

Learn more here.