Reduce SPRI bead-based reagent costs in your NGS workflow

Part 1: How small Savings in magnetic bead-based purification add up at NGS scale.

When laboratories look for ways to reduce the cost of NGS library preparation, attention often goes to the largest expenses: sequencing reagents, library preparation kits, automation, instruments, and labor.

But one opportunity may already be hiding in a step performed repeatedly throughout the workflow:

SPRI magnetic bead-based purification.

 

SPRI bead-based reagents are routinely used for PCR cleanup, DNA purification, DNA size selection, post-ligation cleanup, post-PCR purification, and NGS library cleanup.

The cost of one cleanup reaction may appear small. Multiply that cost by several purification steps and thousands or even millions of libraries, and then the economics will look very different.

For high-throughput sequencing laboratories, genomics core facilities, and biotechnology companies, taking a closer look at magnetic bead-based reagent cost per library can reveal a surprisingly significant opportunity for savings.

 

How much is your SPRI bead-based reagent really costing?

Consider an illustrative NGS workflow that uses a total of 150 µL of magnetic bead reagent per library.

Based on the 500 mL list-price comparison evaluated:

  • The Leading SPRI bead-based reagent: approximately $2.56 per library
  • MagBio Genomics’ HighPrep PCR: approximately $1.37 per library
  • Potential savings: approximately $1.19 per library

That represents an estimated 46% reduction in SPRI bead-based reagent cost at this production-scale purchasing volume.

Saving $1.19 on a single library may not sound transformational. But, at scale, it is a different story.

Libraries Processed Approximate Reagent Savings
10,000 $11,900
50,000 $59,500
100,000 $119,000
1,000,000 $1,190,000

For a laboratory processing 100,000 libraries, the difference approaches $119,000 in potential bead reagent savings.

At one million libraries, it reaches approximately $1.19 million.

 

Why PCR Clean-up costs matter more at High Throughput?

A typical NGS library preparation workflow can contain multiple bead-based purification steps.

Depending on the protocol, these magnetic bead-based reagents may be used for:

  • PCR product cleanup
  • DNA purification
  • Post-ligation cleanup
  • Post-amplification cleanup
  • Removal of unwanted reaction components
  • DNA fragment size selection
  • Final NGS library purification

Every additional cleanup step increases total bead consumption.

That means laboratories should consider more than the price of an individual bottle. A more useful question is:

What does magnetic bead-based purification cost per library and what does that cost become at our annual throughput?

For high-volume laboratories, even relatively small differences in reagent cost can have a meaningful effect on overall NGS library preparation cost.

 

Cost optimization does not have to mean workflow redesign

Reducing NGS costs does not always require changing a sequencing platform, replacing automation, or redesigning an entire library preparation protocol.

Sometimes the opportunity lies in evaluating a frequently used consumable.

HighPrep PCR is a paramagnetic bead-based DNA purification reagent designed for efficient DNA purification, tight DNA size selection, NGS library clean-up, and Oxford Nanopore Technologies® (ONT) Library Preparation Cleanup.  For laboratories already using SPRI bead-based purification reagents, it provides an opportunity to examine whether routine cleanup steps can be performed more economically.

Of course, price is only one part of the decision.

Before changing a PCR cleanup reagent, laboratories also need to know:

  • Will DNA recovery remain consistent?
  • Will purified DNA yield be comparable?
  • Will fragment profiles change?
  • How will the reagent behave at different bead-to-sample ratios?
  • Can it support both cleanup and selective DNA size-selection conditions?

Those performance questions are just as important as cost.

 

And that brings us to the next part of the series.

Next in Part 2: Does lower cost mean lower DNA recovery?

A cost-effective alternative to the Leading SPRI Bead-Based Reagent is only valuable if it can deliver dependable purification performance.

In Part 2, we compare HighPrep PCR with the Leading SPRI bead-based reagent at 1.8x, 1.0x, 0.9x, and 0.8x bead-to-sample ratios.

We’ll look at:

  • Recovered DNA yield
  • DNA recovery rate
  • Gel-based purification profiles
  • Ratio-dependent DNA fragment selection

The objective is simple: Determine whether laboratories can reduce PCR cleanup and NGS purification costs without sacrificing the performance their workflows require.

 

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Kindly Note: Cost examples are illustrative and based on the 500 mL list-price comparison and assumed consumption of 150 µL of bead reagent per library. Actual costs and savings may vary based on workflow, pricing agreements, bead usage, and purchasing volume.