Element Biosciences, the developer of the AVITI benchtop sequencer, will be sharing details about its technology and discussing customer stories at the annual meeting of the American Society of Human Genetics (ASHG) annual meeting. Element is a silver sponsor of the meeting, which will be held November 1–5 in Washington, DC.
Element’s contributions to the ASHG program will include a workshop on higher accuracy sequencing for improved variant detection, a “platform talk,” and poster presentations. At its booth (#1223), Element will display its products and applications, and it will share details about its $200 genome program and introduce a new grant program, the AVITI Accelerator Grant, in partnership with co-sponsor AUGenomics.
The AVITI sequencer
At the heart of all of the Element-related presentations will be the AVITI sequencer, a system that incorporates optics that can simultaneously image four spectrally separated colors. Specific features of the AVITI include two parallel runs or independent operation, choice of one or two libraries per flow cell, and flexible throughput from low to full.
According to Element, AVITI uses a sequencing-by-avidity approach rather than a sequencing-by-synthesis approach. Last May, in a Nature Biotechnology article, Element scientists described avidity sequencing as “a sequencing chemistry that separately optimizes the processes of stepping along a DNA template and that of identifying each nucleotide within the template.”
“Nucleotide identification uses multivalent nucleotide ligands on dye-labeled cores to form polymerase–polymer–nucleotide complexes bound to clonal copies of DNA targets,” the article’s authors noted. “These polymer–nucleotide substrates, termed avidites, decrease the required concentration of reporting nucleotides from micromolar to nanomolar and yield negligible dissociation rates.”
For more background on the AVITI, readers should revisit an article GEN posted online last year “Old Dogs, New Tricks: Element Biosciences Launches the AVITI.” Of course, readers curious about the most recent developments will want to know what Element has in store for ASHG.
Recent applications of AVITI technology
The platform talk mentioned earlier will be delivered by Patrick Kennedy, Research Technician, Samuel A. Myers Lab at the La Jolla Institute for Immunology. The title? “Discovery of novel signaling-to-transcription networks in T cell activation coupling base editor screens with single cell multiomics.”
In a workshop talk, Keri Ramsey, the clinical co-director of the Center for Rare Childhood Disorders, Translational Genomics Research Institute (TGen), will share results from a research study that identified the likely genetic causes of neurological disorders in children who experienced developmental delay, problems with language, seizures, heart anomalies, or other difficulties. The title of this talk corresponds to the title of a recent medRxiv preprint “An efficient design for whole genome trio sequencing leads to high diagnostic yield in rare neurological disorder cases.”
TGen researchers worked with Element to sequence the genome of each child and the genomes of their parents (the trio) in nine families. After findings were clinically validated, the families were counseled about disease management, current research studies, and family planning.
“Once the sequencing data was generated, our two teams used independent informatics pipelines for variant calling and interpretation,” the preprint’s authors stated. “In five of the nine cases, both teams found a single SNV or small indel that was deemed causal pending clinical validation. In three of the nine cases, neither team had a significant finding. In the final case, an additional scan for large CNVs performed by one of the teams identified a de novo deletion and duplication in the proband which is the likely cause of the underlying disease.”
A second workshop talk will be delivered by Semyon Kruglyak, PhD, Element’s vice president of informatics. The title of the talk “Accurate human genome analysis with Element Avidity sequencing” corresponds to the title of a recent bioRxiv preprint.
“We use Element’s ability to generate paired end sequencing with longer insert sizes than typical short–read sequencing,” the preprint’s authors noted. “We show that longer insert sizes result in even higher accuracy, with long insert Element sequencing giving noticeably more accurate genome analyses at all coverages.”
Data generated on the AVITI platform will be featured in a poster by Phase Genomics on next-generation cytogenomics, where Hi-C DNA sequencing has the potential to provide data in one workflow that currently requires multiple distinct assays. This is important for labs because workflow consolidation has the potential to simplify lab operations, reduce costs, and use limited samples more efficiently.
The poster, to be presented by Phase Genomics’ vice president of R&D (Stephen Eacker, PhD), suggests that when OncoTerra, the Phase Genomics platform, is used with the AVITI, it is possible to speed turnaround time and batch fewer samples while still meeting cost targets.
Another poster will be presented by Semyon Kruglyak, PhD, Element’s vice president of informatics. Like one of the workshop talks, it will cover the “whole genome trio sequencing identifies causal variants in rare neurological disorder cases.”