Updated: July 1, 2024
All you have is a sequencer? No problem! Alternative routes to scRNA-seq are being developed by pioneering companies around the globe.
Long reads in Rosario
In the middle of the COVID-19 pandemic, a group of scientists in Argentina decided to share their thoughts about the future of single-cell technology. Their first prediction, recalls Elizabeth Tapia, PhD, co-founder and CSO of ArgenTAG, was that the scarcity and inability to access single-cell instruments in South America would persist. Their second prediction was that long reads would gain traction in transcriptomics.
In 2020, ArgenTag was founded by Tapia along with Pilar Bulacio, PhD, Joaquin Ezpeleta, Sofía Lavista Llanos, PhD, and Leandro Ciappina. Today, Bulacio, Ezpeleta, Lavista Llanos, and Ciappina serve the company as CTO, Director of Engineering, Director of Process Development, and CEO, respectively. ArgenTAG has an R&D facility in Rosario, Argentina, and an office in the United States. The company is currently in early access mode and expects to launch its first kit in early 2025.
Leandro Ciappina, the co-founder and CEO of ArgenTAG, spoke at IndieBio NY Class 4 Demo Day, an event held by venture capital firm SOSV in 2022. In his talk, he differentiated ArgenTAG’s technology, which utilizes long-read DNA sequencers, from technologies that utilize short-read, next-generation sequencers.
ArgenTAG introduced its core technology in Scientific Reports in May 2022, in a paper titled, “Robust and scalable barcoding for massively parallel long-read sequencing.” The paper’s authors reported that the technology is designed to enable multiplex long-read sequencing. They also presented evidence that they used the technology to sequence almost 4,000 barcodes simultaneously on Oxford Nanopore Technology’s MinION platform, achieving a high recovery rate and low crosstalk.
“We took the worst-case scenario of long-read accuracy and improved the accuracy until it became comparable to that for an Illumina sequencer,” Ciappina notes. Then they started deploying barcodes in the cells for a single-cell solution.
Why focus on long reads? “When you do short reads, you’re not getting all the information,” Lavista Llanos tells GEN. “You’re just getting a tip of the information.” She adds that short reads provide just a snapshot.
Lavista Llanos has a background in embryogenesis, a discipline in which isoforms are expressed over hours or even minutes. The ability to collect those data to further explore developmental biology is also important in other disciplines. Indeed, according to Lavista Llanos, the folks at ArgenTAG believe that it is the future of single-cell technology. “Our technology makes sense today,” she remarks, “but it will make a lot more sense in five years.”
ArgenTAG’s workflow uses chip-based technology for partitioning and barcoding. Essentially, the chip’s microwells partition the cells and contain beads that carry the barcodes. This technology differs from competing technologies by performing sequencing on an Oxford Nanopore or PacBio instrument instead of an Illumina instrument.
“Our vision is to decentralize single cell today,” Ciappina declares. “10x Genomics has 5,000 instruments installed, but there is a bigger opportunity—100,000 labs that can benefit from single-cell sequencing but cannot today because of the price.”
By Julianna LeMieux, Ph.D.
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