Two advances in sequencing prep

PLEASANTON & SOUTH SAN FRANCISCO, Calif.—This summer saw Roche sign a definitive asset purchase agreement with Lumora for products associated with the Heat Elution technology for nucleic acid purification of multiple sample types. The technology is intended to work not just with straightforward samples but also with challenging formalin-fixed paraffin-embedded (FFPE) tumor samples.

The purpose for the deal: Roche wants to explore integration of this technology into its sequencing workflow solution, noting that “Today, nucleic acid purification technology from specimens including formalin-fixed tissues can be cumbersome and inefficient. Lumora’s highly differentiated proprietary methodology will enable simple and automated nucleic acid isolation in minutes instead of hours.”

In addition, the technology is reportedly environmentally friendly and can be applied to process a wide variety of sample types that include whole blood, fecal matter, sputum, FFPE tissue and buccal swabs. The Heat Elution technology is currently for research use only, not for use in diagnostic procedures.

“Lumora’s Heat Elution technology can be integrated to an automated sequencing workflow, which makes it an ideal fit for Roche’s sequencing vision of a sample-in/results-out workflow,” said Dan Zabrowski, head of Roche Tissue Diagnostics and the Roche Sequencing Unit in Pleasanton, Calif.

“An important bottleneck in sequencing workflow is nucleic acid extraction. Heat Elution technology significantly simplifies extraction and is simple to automate. The acquisition of this technology may offer Roche a unique position in fully integrated sequencing devices,” said Laurence Tisi, CEO of Lumora.

Meanwhile, around the same time as the Roche-Lumora deal was being inked, in another part of California (South San Francisco, to be precise), Fluidigm Corp. announced commercial availability of a new high-throughput single-cell mRNA sequencing workflow for its C1 system to enable large-scale studies to characterize heterogeneous samples.

The company notes that this validated workflow includes “a new advanced integrated fluidic circuit (IFC) and reagent kit that significantly increases throughput and ease of use, while simultaneously decreasing the cost of preparation and sequencing (by maximizing sequencer capacity) on a per-cell basis. The C1 mRNA Seq HT application is the first and only commercial product to address large single-cell studies and is available today.”

Researchers reportedly can apply the new HT workflow to explore heterogeneity in fields such as cancer, neuroscience, stem cell biology and immunology to understand how the underlying cellular mechanisms impact biological processes or disease progression. This new offering is a complete solution that enables scientists to deeply explore the diversity of cell subpopulations, quickly discover novel or rare cell types and increase the statistical sample size to better estimate biological variation between similar cell types.

The C1 mRNA Seq HT IFC is said to capture up to 800 cells at a time, and employs a new protocol to facilitate two runs—1,600 cells total—a day. Additionally, the IFC features two-cell loading inlets to facilitate case-versus-controls studies, allowing users more flexibility in their experimental design. The assay protocol enables on-IFC multiplexing and cell pooling that provides users with a streamlined workflow. According to Fluidigm, the complete workflow reduces customer library preparation costs by approximately 85 percent when compared to the original C1 mRNA Seq IFC costs, while maintaining the automation and reproducibility of the C1 platform, and Fluidigm maintains that it is the only single-cell workflow that also allows automated staining to visualize the isolation and viability of individual cells.

“Our knowledge of cell populations is largely limited by our ability to precisely study many cells at a transcriptome level,” said Gajus Worthington, Fluidigm’s president and CEO. “The C1 mRNA Seq HT application substantially alleviates this challenge—our customers can now process 1,600 cells per day for transcriptome sequencing. Unlike error-prone, expensive and laborious manual methods such as FACS with plate-based workflows, the C1 mRNA Seq HT workflow provides a high-throughput, easy-to-implement, reliable and low-cost solution not previously available to single-cell researchers exploring cell heterogeneity.”