Progenics Labs works at the intersection of microbiology, clinical genomics, and personalised healthcare. Led by Dr. Swapnil, the team focuses heavily on the human gut microbiome - studying how microbial communities influence health, disease, and therapeutic response.

To support this work, the lab runs Oxford Nanopore MinION workflows for long-read microbiome sequencing alongside Illumina-based clinical genomics and chromosomal microarray studies.

But one challenge repeatedly surfaced at the front of the sequencing workflow: stool DNA cleanup.

Stool is one of the most difficult sample types in genomics. DNA quality varies significantly between donors. Inhibitor levels fluctuate unpredictably. Even after extraction, samples often contain short DNA fragments, contaminants, and background material that interfere with downstream sequencing performance.

For long-read Oxford Nanopore workflows, this becomes especially critical. Sequencing performance depends heavily on clean, high-molecular-weight DNA. Short fragments and residual contaminants can reduce read quality, affect library efficiency, and compromise microbiome profiling accuracy.

“Since stool samples are very inconsistent in quality, sometimes we get very little DNA,” explains Dr. Swapnil. “Inconsistent quality, more inhibitors sometimes, less inhibitors other times - reproducibility becomes very important.”

Beyond cleanup, Progenics had another requirement. The team needed to selectively remove shorter DNA fragments before library preparation while preserving longer fragments required for ONT sequencing. Conventional cleanup methods offered limited control over fragment selection and often compromised recovery in the process.

To solve this, Progenics adopted CamSelect NGS - a magnetic bead–based nucleic acid cleanup and size selection system designed for flexible sequencing workflows.

The team used CamSelect NGS upstream of library preparation to perform precise size selection directly on stool-extracted DNA. By tuning bead-to-sample ratios, they established a defined fragment cutoff that removed shorter background fragments while enriching for longer DNA more suitable for Nanopore sequencing.

The results were immediate.

“We got very good recovery and very good quality,” says Dr. Swapnil. “Purity was also improved.”

Gel electrophoresis profiles showed visibly cleaner DNA populations with reduced low-molecular-weight smearing and background carryover. The workflow produced more defined high-molecular-weight DNA suitable for long-read sequencing without sacrificing recovery.

More importantly, the cleanup became predictable across highly variable stool samples.

The ability to tune fragment selection ratios gave the team significantly greater control over sequencing input quality. Instead of treating cleanup as a passive purification step, Progenics could actively shape the DNA population entering the ONT workflow.

That consistency made a measurable operational difference. With cleaner and more uniform input DNA, downstream sequencing became more reliable, reducing QC failures and minimizing repeat sample processing.

For a microbiome programme handling complex donor-derived samples, that reproducibility matters.

CamSelect NGS has now become a standard part of Progenics’ pre-sequencing workflow. The product not only improved cleanup performance, but also enabled a level of size-selection flexibility that aligned closely with the demands of long-read microbiome sequencing.

As Progenics continues expanding its microbiome and clinical genomics programmes, CamSelect NGS remains a critical upstream step - helping the team generate cleaner input material, improve sequencing consistency, and maintain confidence across highly variable sample types.

CamSelect NGS is a magnetic bead–based nucleic acid purification product manufactured under ISO 13485, designed for PCR clean-up, size selection, and pre-library purification across Illumina, ONT, and other sequencing platforms.

Get more information here.