Harnessing the Power of Sound to Optimize Metagenomic Sequencing Library Prep

Written by Bioscribe on February 09, 2019

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There’s no doubt about it: Manual library preparation is tedious. It can hold up sequencing projects and contribute a great deal to their costs. Traditional liquid handlers may provide some relief in terms of labor, but they can still strain the budget due to reagent volume requirements and expensive, proprietary tips.

Enter acoustic liquid handlers. With their sub-microliter precision and automated efficiency, Echo systems from Labcyte have transformed sample preparation and transfer in a number of fields.

In order to optimize the technology for metagenomic next-generation sequencing (mNGS), scientists at the University of California San Francisco (UCSF), have developed a high-throughput protocol that leverages the small dispensing volumes of the Echo 525 Liquid Handler to provide high-fidelity, miniaturized, automated, cost- and time-efficient 384-well library preparation.

As reported in a recent bioRxiv pre-print, Joseph L. DeRisi, Eric Chow and colleagues adapted a previously described mNGS library prep protocol for RNA, testing several protocol modifications involving reduced volume of reagents using variable HeLa RNA input.

An Echo 525 Liquid Handler, used for all dispensing steps, was paired with traditional liquid handlers for magnetic bead cleaning steps. Additionally, acoustic dispensing was also used to optimize the pooling of hundreds of samples with small scale sequencing on a benchtop system. This replaced qPCR and fluorimetric methods that can otherwise be costly, tedious, and error-prone due to imprecise estimations and inaccurate pipetting.

To test the protocol, the team applied it in mNGS for pathogen detection in two clinical samples, where it successfully correlated with clinical microbiology test results.

They also found that the miniaturized, high-throughput protocol significantly reduced the cost and time associated with library prep.

The cost of materials for each library preparation using the manual protocol, including reagents and tips, was approximately $43 (~$16,648 for 384 samples). This dropped to $8 per sample (~$3,161 for 384 samples) using the miniaturized protocol, resulting in cost savings of over 80%.

In terms of time, the automated miniaturized protocol took approximately 10 hours, whereas completing the 384 samples by hand with the manual protocol would have consumed an estimated 166 hours.

“With this workflow, it is possible to prepare 384 high-quality sequencing libraries with just 10% of the regular reagent volume, at less than 20% of the cost and in less than 10% of the time compared to the regular hand-prep,” the authors wrote.

For further details, read the full paper or access the complete protocol.

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