Top 5 reasons to go custom with Pillar Biosciences in graphic font

5 reasons to go custom with your next sequencing panel

Off-the-shelf next-generation sequencing (NGS) panels save on sequencing costs by targeting specific genes, and the smaller resulting datasets are easier to analyze. The catch is, panels are limited to a defined set of genetic targets. This one-size-fits all approach is not well-suited to the cancer research community’s rapid pace of discovery.

Custom panels, on the other hand, let you personalize your sequencing needs, focusing only on those genes that are pertinent for your research. At Pillar Biosciences, we have five good reasons you should go custom, and a host of tools to help you make the most of your custom NGS panel.

1 – Automated primer-design makes going custom easy
Pillar Biosciences’ ampPD intelligent primer design platform automates the design of primers for multiplexing hundreds or thousands of amplicons in a single tube. By masking regions where primers cannot bind and accounting for primer dimers, ampPD identifies optimal primers for sequencing target regions in a custom library.

Target preparation

  • Perform tunable masking for multi-copy regions, repeats and variants.
  • Delineate regions of interest (ROI) and collapse proximal ROIs.
graphic showing masking of unprimable regions

Primer drafting and tiling

  • Exhaustively calculate all primer tiling solutions for each ROI.
  • Select primers that are optimized for FFPE samples.
Amplicons around the region of interest

Primer screening and pooling

  • Calculate potential amplifiable dimer pairs via cluster-based computing.
  • Compute single pool with the lowest dimer potential.
Network graphic

Primer-primer interaction map 

2 – Pay only for the sequencing reads you need

Going custom allows you to take the benefits of NGS panels one step further by explicitly limiting sequencing coverage only to your specific target regions of interest. Pillar’s SLIMamp technology helps you stretch your sequencing coverage even further by eliminating unwanted amplicons, improving coverage uniformity, and enabling multiplexing.

3 – Make the most of limited samples

By creating one custom panel for all of your sequencing targets, you can limit the need for reflex testing and additional send-outs. Additionally, our SLIMamp technology enables sequencing from only 2.5ng of input DNA.

SLIMamp multiplex PCR uses a stem loop structure during amplification and gives you the ability to tile amplions across genomic regions of interest

4 – Simplify your bioinformatics workflow

Custom NGS panels exclude all unwanted amplicons, streamlining the necessary bioinformatics even more than standard panels. Pillar’s software package PiVAT further optimizes analysis by filtering reads without the proper amplicon structure in order to call variants with as low as 1% frequency.

5 – Beyond genes: defining your target areas

While off-the-shelf panels are typically designed around gene “hot spots,” many studies can benefit from sequencing non-coding regions or entire coding sequences. Custom panels allow for specification of amplicon size and target regions beyond genes that are typically found in commercial panels. Pillar’s ampPD primer-design platform makes planning these highly customized options simple.

Pillar Biosciences provides an end-to-end comprehensive NGS solution with ampPD, SLIMamp, sequencing, and PiVAT

We think our customizable technology is great, but don’t take our word for it. In this webinar, Dr. Helen Fernandes explains why her lab at the Columbia University Medical Center has made a Pillar custom panel with SLIMamp technology their new tumor diagnostic go-to.

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