NGS Updates from ASHG: What’s New in Sequencing?

As expected, the NGS companies were sharing their news, out in full force, at the annual American Society for Human Genetics (ASHG) meeting last week in Washington, DC. Whether the updates came from the expo booths showcasing instruments, or users sharing data in the lecture halls, each company had progress to share. Here, we note some of the key highlights we noticed from the meeting.

Long reads are coming out strong

When Gordon Sanghera, PhD, co-founder, and CEO of Oxford Nanopore Technologies (ONT) sat down with me in the ONT booth to offer an update, he primed their more recent news news today by going back 18 months. Since ONT launched their new chemistry in March 2022, they have “pushed the envelope on accuracy to a point where we are equivalent to short-read sequencing.” When this happened, he continued, “we could finally give you everything you get from short reads. But because 8% of the genome is unmapped, which means that 25% of all disease-causing variation is hidden, we can give you that as well. And that was a significant moment because people started to realize that they can get everything they want from short reads.”

Now, at ASHG, “our customers are not talking about accuracy. They are talking about applications.”

What ONT has noticed more recently, over the past six months, is a lot of inbound interest in crossing the chasm to applied sequencing—using ONT in clinical and industrial applications. Sanghera highlights that it has to do with their unique form factors: from the high throughput, high-density PromethION, to a handheld minION, and everything in between. This range, he notes, offers an opportunity to move from the research setting (where users sequence everything) to applied tests. Looking out over the next 12–18 months, ONT is excited to move their technology into applied markets.

When I caught up with Christian Henry, PacBio’s CEO, before the conference, he shared what he was looking forward to this year. Because PacBio chose ASHG 2022 to launch their two new instruments—a moment Henry described as “the biggest jump forward in the company’s history”—I was curious what they would be talking about one year later. Although PacBio’s plans were not as grand going into this year’s ASHG meeting, Henry’s enthusiasm was still running at full speed. “It’s been a whirlwind year,” he told GEN.

Henry told me that he is excited about a few new areas for PacBio. The first—in a vein similar to Sanghera—was moving into diagnostics. This comes in the wake of an announcement last month that Children’s Mercy Kansas City is the first healthcare system to adopt HiFi sequencing as a first-line diagnostic test for rare disease. In addition, Henry was looking forward to discussions on multiomics at ASHG.

PacBio also released other news in press releases throughout the week. First, the company has begun taking orders for their Kinnex RNA kits, which increase throughput for full-length RNA, single-cell RNA, and 16S rRNA sequencing on PacBio’s sequencing systems. It also announced the addition of two tertiary analysis partners to PacBio Compatible—Geneyx and Golden Helix—which will enable customers to leverage HiFi data for disease research. Lastly, the company announced the creation of the HiFi Solves consortium—a global consortium that brings together researchers from 15 genomics research institutions across 11 countries to study the value HiFi-based human genome sequencing may have in clinical research applications and to further our understanding of genetic diseases.

Chance meeting

Gilad Almogy, PhD, CEO of Ultima Genomics, and I have a way of bumping into each other at conferences. Earlier this year, at AGBT, we caught up on an elevator ride. This time, it was at the coffee station (which is saying something, given the 8,000 attendees at the meeting) which quickly turned into an update on the company.

I hadn’t planned to meet with Almogy because I recently visited the company’s production facility in Fremont, CA, immersing myself in their technology and asking Almogy about the company’s plans. Despite that recent deep dive, Almogy did have news to share when we caught up at ASHG. He confirmed that the timing to launch their instrument, the UG 100, by the end of this year, is on track. The second was a release of new data that, he says, highlights their accuracy. At AGBT 2022, when the company first appeared on the scene, the indel accuracy was roughly 96%. Now, given the newly released dataset, they are just over 99%. The data also shows 99.85 SNP F1 accuracy. Other than that, Ultima was quiet. But Almogy says he is looking forward to next February, when the company will be the gold sponsor of the AGBT meeting in Florida. I’m not sure where or when I will catch up with Almogy there, but I look forward to hearing their updates.

Short reads

The short-read sequencing companies were front and center, with messages that they are not only here, but they are also not going anywhere.

In Singular Genomics’ large booth, the company highlighted new additions to their current offerings. One was the compatibility of PIPseq single cell RNA sequencing with their G4 platform. PIPseq, from Fluent Biosciences, provides library prep for RNA seq. The other note from the company was the ability to do ultra-low diversity sequencing on the G4 without the need for a PhiX spike or extensive workflow modifications. And, although their newest flow cell, the F3, was announced earlier this year, the company reports that they are now shipping them to customers.

I caught up with Rob Tarbox, Complete Genomics’ vice president of product and marketing, who told me that their goal at ASHG was to educate people about their instruments and for people to “get to know them.” Tarbox made two other important points in our conversation. The first was that Complete is the only sequencing company that offers everything that a user needs, including their own robotics, for the front end of sequencing. Complete is, he told me, “the only place to go to start a lab from scratch. There is no one else that can do the entire workflow.” The other point was that they are offering a “try it before you buy it program” where, he says, people can give their instruments a test run before making a purchase.

At Illumina’s booth, representatives were showcasing the new P4 flow cell for the NextSeq 1000 and 2000 systems. The company released new data from the just-released 25B flow cell on NovaSeq X, as well as updated Q40 data on high-throughput and mid-throughput machines. And the company was busy with multiple talks and presentations. One was a fireside chat with Catherine Tcheandjieu, DVM, PhD, an assistant investigator at Gladstone Institutes and Melissa Dempsey, market development manager for rare disease testing at Illumina. The topic was the importance of diversity and inclusion in the genomics space. An industry education session by Carole Ober, PhD, chair of the department of human genetics at the University of Chicago, showcased studies characterizing the features of CpGs that most likely contribute to common disease risk and the development of a custom array for studying asthma and allergic diseases.

Element Biosciences presented new data from customers in oncology and immunology to highlight the role of their instrument, AVITI, in the rare and undiagnosed genetic disease space. A poster by Stephen Eacker, PhD, vice president of research and development at Phase Genomics, titled, “Next-generation cytogenomics using proximity ligation technology on the AVITI genome sequencing platform,” underscored where Hi-C DNA sequencing has the potential to provide data in one workflow that currently requires multiple distinct assays.

Element also hosted a talk by Patrick Kennedy, a research technician in the lab of Sam Myers, PhD, assistant professor at the La Jolla Institute for Immunology, titled, “Discovery of novel signaling-to-transcription networks in T cell activation coupling base editor screens with single cell multiomics.” Lastly, a lunch workshop included a presentation from Keri Ramsey, clinical co-director of the Center for Rare Childhood Disorders, at TGen, titled “An efficient design for whole genome trio sequencing leads to high diagnostic yield in rare neurological disorder cases,” that presented findings recently posted to medRxiv that identified the likely genetic causes of neurological disorders in children.

Taken together, the NGS companies—both veterans and recent entrants alike—were going strong at ASHG. Although this year was not full of big announcements or new instrument launches, the companies are moving forward. Most of the companies I spoke with shared that they will have more to say at AGBT in February. And we’ll be there to cover it all.

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