Takara Bio transforms single-cell landscape with new large-scale NGS profiling system for oncology biomarker discovery

On April 2, 2024 Takara Bio USA, Inc., a wholly owned subsidiary of Takara Bio Inc., reported the launch of the Shasta Single-Cell System, an automated, high-throughput NGS solution with well-validated chemistries and intuitive bioinformatics tools that enables novel biomarker discovery for oncology research (Press release, Takara Bio, APR 2, 2024, View Source [SID1234641728]). This complete system allows researchers to mine more genomic and transcriptomic information from many more cells than possible with current technologies, while saving time and costs for research groups. Existing whole-genome amplification (WGA) technologies currently process 96–384 single cells per plate; the Shasta system increases WGA throughput to 1,500 cells per run. With its total RNA-seq application, the Shasta system detects more RNA biotypes with high sensitivity at high throughput—up to 100,000 cells per run—which is an improvement over both plate-based full-length RNA-seq and high-throughput mRNA-seq methods.

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In March, Takara Bio USA delivered instruments and NGS kits to early-access users, who have started producing results with the system. The company is accepting orders with plans to ship instruments and chemistries towards the end of Q2. "We’re very excited about this technology," said early-access user Dr. Ting Wang, Head, Department of Genetics at Washington University School of Medicine in St. Louis. "I want to expand our usage of this technology. We have two other projects in the lab where we want to do a full set of profiling of our entire model system. We’re fully committed to continue pushing the limit of the technology to do the best science."

The Shasta system has three core elements: a state-of-the-art, automated dispensing and imaging platform, a unique array of NGS library prep chemistries, and Cogent bioinformatics software for comprehensive data analysis—easy to use even for researchers and staff without bioinformatics experience.

"We have reached a new era in single-cell analysis. Researchers are no longer limited to profiling just hundreds of cells or accessing only part of a cell’s rich genetic information. Shasta technologies have broken the limits of current methods to allow the detection of events like splicing isoforms, gene fusions, long noncoding RNAs, and arm-level CNVs—without sacrificing sensitivity or scale," said Carol Lou, President & CEO of Takara Bio USA. Researchers can take advantage of three applications:

The Shasta Total RNA-Seq Kit profiles the full-length transcriptomes of up to 100,000 single cells and up to 96 samples per experiment with only two rounds of barcoding. The random-priming-based chemistry enables the discovery of novel types of biomarkers beyond mRNA, facilitating understanding of disease mechanisms and therapeutic responses.
The Shasta Whole-Genome Amplification Kit features a fully automated protocol that prepares single-cell DNA-seq libraries for up to 8 samples and 1,500 single cells per run, reducing hands-on time. This application enables researchers to scale up their WGA workflow to understand tumor heterogeneity and perform tumor subclonal analysis through copy number variation (CNV) and single nucleotide variation (SNV) profiling at a shallower sequencing depth, saving costs.
The Shasta mRNA-Seq Kit accomplishes full-length transcript coverage with outstanding sensitivity for up to 1,500 single cells per run. This application delivers the most sensitive full-length mRNA-seq data on the market, enabling the detection of low-expressed biomarkers that are missed by current 3′ end-counting technologies.
The Shasta system will be demonstrated at the upcoming American Association for Cancer Research (AACR) (Free AACR Whitepaper) Annual Meeting from April 5–10, 2024, where two posters have been accepted. Attendees of the AACR (Free AACR Whitepaper) meeting can learn more about Shasta workflows and view the system at Booth #2955. The Shasta system will also be presented at the Association of Biomolecular Resource Facilities (ABRF) Annual Meeting from April 21–24, 2024. At ABRF, attendees can engage with Takara Bio during the plenary keynote session on April 21st and again during the technology showcase at 8 am on April 23rd. Attendees can view the Shasta system at Booth #502. Researchers and other professionals wanting details can sign up to receive priority access to product and technical information.