Element Biosciences Launches Benchtop Sequencer
By Bio-IT World Staff
March 15, 2022 | Element Biosciences yesterday launched the Element AVITI System, a benchtop sequencer offering an unrivaled combination of performance, cost, and flexibility. Element’s proprietary Avidity short-read sequencing chemistry enables exceptional accuracy and cost efficiency that is unmatched by other benchtop systems, according to the company. To announce this release, Element held a virtual “Be In Your Element” event where innovations were highlighted.
The AVITI System operates two random access flow cells that enable independent run start flexibility of each flow cell, and the AVITI operating software features tunable read throughput control for additional run time flexibility.
At yesterday’s launch event, Michael Previte, CTO, spoke about how Element pursued improvement with a focus on maximizing the contrast-noise ratio: maximizing the signal while minimizing the background. This involved the developments of a new low-binding surface and proprietary DNA amplification and a new Avidity sequencing chemistry that he says reduces reagent consumption 100-fold or greater by providing multiple binding sites. He also highlighted the flexibility the two random access flow cells provide, saying “It’s essentially having two sequencing systems in one box… you can start one flow cell on one side, and come back later and start the other.” Previte also says the system shows low optical duplicates and undetectable index hopping.
The launch of the AVITI System is the latest in a series of announcements that have highlighted Element’s key partnerships with established and emerging leaders in the NGS Library Prep and Bioinformatics segments, each of whom demonstrate powerful use cases for the AVITI System. These partners include, in alphabetical order: Agilent Technologies, Dovetail Genomics, Fabric Genomics, Genoox, Google DeepVariant, Jumpcode Genomics, New England Biolabs (NEB), QIAGEN, Roche, Sentieon, 10x Genomics, and Watchmaker Genomics. There is an incentive for early customers who AVITI refers to as innovation partners—they will receive 2 free reagent kits and one additional year of warranty.
“With the launch of our AVITI System, Element is delivering on its vision to dramatically expand access to high quality, low cost, easy-to-use genomics tools,” said Molly He, Ph.D., CEO and co-founder of Element Biosciences. “And with the recent Loop Genomics acquisition, we will offer both short and long-read capabilities on a single platform. AVITI will bring the ultimate freedom and flexibility for users.”
Tuval Ben-Yehezkel, formerly of Loop Genomics, highlighted how short-read sequencers can be used to achieve long-read sequencing to address the phasing problem—knowing which variants are associated on the same nucleic acid strand by barcoding samples with unique molecular identifiers. These sequences are amplified, and then a unique distribution step is performed that copies and pastes the barcode intramolecularly and randomly throughout the nucleic acid sequence. Short reads can then be obtained and re-assembled through software to infer the original long sequence: “synthetic long reads”.
“In beta testing both the library compatibility and sequencing performance proved to be as straightforward and impressive as we’d hoped. Users will feel very confident with adopting the AVITI System in terms of both workflow and data quality,” said Shawn Levy, who just joined Element as Senior Vice President of Applications and Scientific Affairs. Levy was an AVITI System beta tester in his previous role at Hudson Alpha.
Levy received one set of data provided by AVITI for validation comprised of RNAseq and whole genome sequencing data. He then ran phase two testing in his own laboratory with his own samples and compared the performance to Illumina sequencing of Genome in a Bottle samples. Levy found library conversion very straightforward and successful on all library types that were double-stranded with full-length P5 and P7 sequences.
“Data analysis shows strong equivalence in most metrics and supportive of strong compatibility between platforms,” he said. “Trends indicate slight improvement of indel [insertion/deletion] performance and lower duplication rates following alignment.”
Levy further suggested that though, validation studies are still pending, “the different error model and quality of the AVITI data suggests that the same library run on a production sequencer and topped up on an AVITI may be an effective strategy”
Element has released seven application and technology notes along with five sequencing datasets for download that cover human whole genome, bacterial whole genome, and RNA-Seq assays using the Element AVITI System, and is now accepting orders for the AVITI System, with shipments expected to begin in Q2 2022.
The Element AVITI System
The AVITI System consists of a benchtop NGS instrument and associated consumables that feature:
- Proprietary Chemistries: Deliver exceptional sequencing accuracy while dramatically lowering operating costs and eliminating index misassignments due to amplification
- State of the Art Performance: Accuracy and output metrics that enable a comprehensive range of demanding NGS applications
- Random Access Dual Flow Cells: Scalable output and batch control features; equivalent to having two sequencing systems in one
- Simple NGS Library Prep Compatibility: Easy PCR-free workflow that allows you to start immediately with your library prep of choice
- Open Informatics: FASTQ file output without proprietary requirements for analysis
Key Operating Specifications
The Element AVITI System is based on a single flow cell and sequencing reagent cartridge design that offers up to 300 cycles and tunable read throughput control for each of two independently operated flow cells. This allows the user complete run control timing and scalability while being unburdened from the order and inventory complexity of multiple kit sizes. The AVITI System’s operating specifications include:
- 2 x 150 paired end read length
- > 90% Q30 at 2x150 read length
- 800M+ paired end reads per flow cell
- 240Gb of data output per flow cell
- 2 random access flow cells for 480Gb combined output
- 13-48 hour run time
- $5-$7 per Gb run cost (determined by flow cell output, which can exceed 1000M paired-end reads per run)
- AVITI Instrument Pricing: $289,000, though Molly He, CEO, stated during a panel discussion that bulk pricing may be available. “We want to incentivize quick learning. We are considering a volume-based discount. That’s going to be transparent.”