Discoveries at the Margins: How iconPCR™ with AutoNorm™ is Transforming Amplicon and Microbiome Workflows at Penn State

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What happens when you hand a cutting-edge PCR thermocycler to a genomics technologist who lives for optimizing every cycle? At the Penn State Genomics Core Facility, Kerry Hair and her team have been putting the icon96™, utilizing iconPCR technology with AutoNorm through its paces—and the results are shaking up how we think about amplicon workflows, metagenomics, and even those pesky NGS indexes. As Kerry mentions below, "The use of the iconPCR has opened my eyes to the different ways that these reactions behave... It was a paradigm shift."

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Amplicon Workflows: Less is More

Amplicon sequencing is the bread and butter for many genomics labs, especially when it comes to microbiome projects. But as Kerry points out, over-amplification can hide the true diversity in your samples—masking the very signals you’re trying to uncover. "When we learned about the iconPCR we were very excited about using it to really target the optimum number for each of our amplicon customers individually".

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With iconPCR and AutoNorm, the Penn State team was able to:

  • Target the optimal cycle number for each sample, not just each project
  • Minimize over-amplification, preserving rare species and fine details
  • Reduce QC steps (goodbye, extra gels and bead normalization plates!)
  • Cut library prep costs by ~50%—yes, you read that right!

"By incorporating the iconPCR, we can remove several of the QC steps that are pretty expensive... We estimate that once we fully incorporate this procedure, we will have reduced our overall [library] costs by about 50% for an amplicon project."

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Microbiome Projects: Seeing the Unseen

Penn State's One Health Microbiome group is at the forefront of metagenomics and spatial transcriptomics. For them, every cycle counts—especially when discovering new species or understanding subtle shifts in microbial communities.

"...the iconPCR creates these opportunities to really fundamentally rethink how we process these samples and what our options are to see these microbiome communities in particular."

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iconPCR enabled the team to:

  • Optimize PCR for each sample, rescuing borderline or low-abundance samples
  • Uncover hidden diversity that standard protocols might miss
  • Rethink traditional workflows—because sometimes, the best discoveries happen at the margins

"Scientific discoveries are frequently made at the margins... the iconPCR shines because it has finally become easier to optimize those reactions and capture those details that might be missing in over-amplified samples."

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Indexes: Not All Are Created Equal

Kerry didn’t stop at samples—she and the n6 team dove deep into index performance (see the technical note she co-authored). Here’s what they found:

  • Index primers vary in amplification efficiency, GC content, and dimerization risk
  • Some indexes can cause biased representation or even premature reaction termination
  • AutoNorm on iconPCR can normalize libraries in real time, bringing all samples to equivalent levels and minimizing index-induced bias

Key findings from the tech note:

  • Indexes with high dimerization or concentration issues can be identified and avoided
  • Adjusting primer concentration and annealing temperature can restore normal amplification profiles
  • AutoNorm allows for sample-by-sample optimization, not just one-size-fits-all cycling

The Takeaway: Optimize Everything, Discover More

Whether you’re working on amplicons, microbiome samples, or even RNA-Seq libraries, the message is clear: the details matter. iconPCR and AutoNorm empower researchers to optimize every step, save time and money, and—most importantly—unlock discoveries hiding at the margins.

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Scientific discoveries happen at the margins — and with AutoNorm and iconPCR  now available in two formats, icon96 and icon16, there's never been a better time to find out what you might be missing. Whatever your throughput or budget, AutoNorm has you covered.

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