Everyone has just been wowed and amazed by the Echo, and wish they had known about it earlier.

Eric Chow

Director, University of California San Francisco (UCSF)Center for Advanced Technology (CAT)

Echo Acoustic Liquid Handler Cuts Costs at UCSF Center for Advanced Technology


As the costs of sequencing continue to come down, we have finally achieved the dream of the $1,000 genome. But preparing the samples to be sequenced remains in the realm of nightmares, with expensive reagents limiting the amount of work most labs can afford to do.

Library prep costs now surpass sequencing costs for the vast majority of applications, says Eric Chow, Director at UCSF CAT.

One way to cut these costs is miniaturization; by using smaller sample volumes, less reagent is required. The addition of an Echo 525 Liquid Handler in Chow’s shared resource center has enabled scientists across UCSF to benefit from miniaturization when setting up their samples, resulting in significant savings of both time and money.

“Everyone has just been wowed and amazed by the Echo, and wish they had known about it earlier,” Chow said.

Hundreds of academic and commercial scientists use the CAT facility, which houses standard research equipment such as qPCR machines and plate readers as well more advanced equipment such as next-generation sequencing systems, digital PCR, and liquid handling robots.

Prior to acquiring the Echo system in 2016, library preparation was either done by hand, or by using traditional tip-based liquid handlers. These libraries were subject to human variability and needless waste due to limitations of manual pipetting volumes, and it became apparent to Chow, who became director in 2013, that a quicker, more efficient system was needed in order to handle high-throughput applications.

The Echo technology was attractive because of its high-precision, high-speed capabilities. Ease of use was also a consideration, as the facility is open access, with most users operating the equipment themselves after short training sessions.

Echo - 80% Savings in materials and reagents

The center’s users are varied, as are their uses of the Echo system, from qPCR to cloning to small-scale drug screening and synthetic biology applications. For most of them, a quick 15-minute session on the system is all they need to get started on the Echo Liquid Handler.

"They end up saving quite a bit of money on labor costs alone," Chow said.

In his own test of the system, Chow found that combining the Echo 525 Liquid Handler and the iSeq and NovaSeq Illumina sequencing platforms to miniaturize and automate metagenomic next generation sequencing (mNGS) library preparation significantly reduced the cost and the time required to prepare samples.

As reported in a recent bioRxiv pre-print, Chow and colleagues used External RNA Controls Consortium (ERCC) spike-in RNAs, to demonstrate the fidelity of the miniaturized preparation.

"Reduction of reaction volumes, combined with sub-microliter automated dispensing of reagents without consumable pipette tips, has the potential to provide significant advantages” Chow said.

For 384-well mNGS library preparations, we achieved a savings of over 80% in materials and reagents alone, and increased throughput ten-fold compared to manual approaches, without compromising quality or representation within the library.