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Element Biosciences Points to First Wave of Customer Data at JP Morgan Conference

SAN FRANCISCO – Element Biosciences customers are starting to release data generated on the firm's Aviti sequencer, showcased by CEO Molly He at this week's JP Morgan Healthcare conference.

In a Wednesday afternoon talk, she highlighted data from three customers: the University of California, San Diego; Gencove; and Qiagen.

At UCSD, researchers performed whole-genome sequencing for rare disease diagnostics, publishing their results in a preprint in MedRxiv last month.

They study looked at 10 families affected by an inherited retinal degradation phenotype, including one positive control that had been sequenced on Illumina's HiSeq X10. The previously unsequenced samples were run using 2×150 bp mode. The researchers sequenced one trio, for which the parents were "sequenced at a lower coverage so that all three samples could be combined on a single flow cell," the authors wrote. "High confidence variants were identified in five of the 10 pedigrees that we sequenced, including the positive control."

"The study confirms that avidity sequencing is effective in detection of causal mutations when used for whole-genome sequencing in rare disease applications," the authors wrote.

In the study, 94 percent of bases had Q30 quality scores or above, He said. The trio was completed in less than 40 hours, and total yield per flow cell was 326.7 Gb, He said.

A collaboration with Gencove, results of which appeared in BioRxiv in December, used Element's platform for low-pass, whole-genome sequencing — often used in genotyping — and compared it with data generated on an Illumina NovaSeq 6000. 

"We observed dramatically lower duplication rates in the data deriving from the Aviti system compared to the NovaSeq 6000, resulting in higher effective coverage given a fixed number of sequenced bases, and comparable imputation accuracy performance between sequencing chemistries across ancestries," the authors wrote.

"That means you can sequence less for the same coverage," He noted.

She also showed a chart from Qiagen comparing accuracy of results from the same QIAseq xHYB actionable exome panel library analyzed on both Aviti and Illumina's NextSeq 550 sequencer. The graph showed Element's base quality peaking around Q43, almost 10 points higher than the Illumina data, He said. Element had "essentially greater than 85 percent of bases above Q40" accuracy, she said.

A Qiagen spokesperson confirmed that the data were "prepared as a joint effort between Element and Qiagen."

In November, Element also published a detailed description of its so-called "avidity-based sequencing chemistry" in BioRxiv and has submitted the manuscript for publication in a journal. Element VP of Informatics Semyon Kruglyak was a coauthor on all three preprints.

The data come as Element and other startups are jockeying for position with each other and with Illumina, which has dominated the next-generation sequencing market for years. Illumina recently released a new chemistry and line of high-throughput instruments, suggesting volume-discounted pricing as low as $2 per Gb, or around $200 for a 30X human genome.

On Wednesday, Element announced a new pricing program that would provide similar pricing of about $2 per Gb for customers that can meet certain throughput commitments. To get that pricing, a customer would need to run the equivalent of nearly 3,000 human genomes per year, Shawn Levy, Element's senior VP of applications and scientific affairs, told GenomeWeb; by corollary, that customer would probably need to have at least three Element sequencers running at 60 to 70 percent capacity. So far, the Broad Institute is the only customer that Element has revealed to possess that many.

CEO He noted that Element has seen Illumina engage in "a wide range of discounting behavior," including "significant" discounts on capital expenditure instrument purchases and "moderate" discounts on consumables.

In 2023, He said Element will focus on expanding its commercial organization not only in the US but also globally. It will also launch a 2x300 bp kit in the third quarter.

"We are continuously improving our chemistry," she added, "including innovations to make our reagents more stable and more environmentally friendly."

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