PacBio Brings Genomics and a Grammy Winner to ASHG This Year

By Julianna LeMieux, PhD

When GEN spoke with Christian Henry, CEO of PacBio, before last year’s American Society of Human Genetics (ASHG) conference being held in Los Angeles, his excitement was palpable. The company was about to announce what Henry described as “the biggest jump forward in the company’s history.”

During that meeting, PacBio launched not one, but two, new sequencing instruments. First, the short-read instrument “Onso,” sparked by their acquisition of Omniome’s short-read, sequencing by binding (SBB), technology. And, a new long-read platform, Revio, designed to replace their workhorse instrument—the Sequel IIe.

PacBio’s plans are not as grand going into this year’s ASHG meeting. However, Henry’s enthusiasm has not waned. “It’s been a whirlwind year,” he told GEN. “The Revio system has already generated more data than our entire history of the entire Sequel IIe install base in six months.” (Although PacBio does not reveal the total number of Revio instruments sold, they note that their install base is currently over 150.)

The increased throughput is particularly exciting to Henry because this has been one of PacBio’s ongoing challenge. Their instruments have not had enough throughput to create the large data sets necessary to do big science. Now, they are entering into conversations for very large-scale projects—with tens of thousands of whole genomes—which they never would have considered before. Revio has changed everything, he adds, by creating access to long read sequencing and putting PacBio on a “whole new trajectory.”

Later this week, in DC

At ASHG this year, Henry is excited about a few new areas for PacBio. The first is Revio’s role in diagnostics. This comes in the wake of an announcement earlier this month that Children’s Mercy Kansas City is the first health care system to adopt HiFi sequencing as a first line diagnostic test for rare disease.

In addition, Henry expects to focus on multiomics. Recent work by Andrew Stergachis, MD, PhD, and Mitchell Vollger, PhD, both at the University of Washington, posted as a preprint on bioRxiv, describes generating four haplotype-resolved ‘omes—the genome, CpG methylome, chromatin epigenome, and transcriptome—from a single Revio run.

PacBio will have other news being released in press releases throughout the week (they were still under embargo at the time of the writing of this article.) Henry says that, taken together, the news will illustrate that they are becoming more complete as a company—focused on more than instruments but also informatics, workflow, and making their instruments easier to use.

New technology

PacBio may be synonymous with long reads, but its most recent moves bring them squarely into the short-read world. The company recently launched Onso—a mid-throughput short-read instrument. But the company has their sights set on more. To facilitate that growth, PacBIo acquired the sequencing company Apton, this past August, for their instrument. The plan is take the SBB chemistry from Omniome, put it into Apton’s box, and bring it to market. If Onso is like NextSeq, Henry says, then this Apton/SBB system will be like NovaSeqX—with an anticipated billions of reads in one run.

Choices already exist for customers wanted short reads at scale, including Illumina’s NovaSeqX and Ultima’s UG 100. So, why try to make inroads here? Henry says that he gest this question from just about everyone. His justification lies in the growth of the genomics market, which he anticipates will be about $14 billion by 2026. PacBio predicts that roughly half that market will be served by long reads and the other will be served by short reads. By offering both, they move beyond selling a technology into an overarching strategy—with software and informatics capabilities—that allows the integration of long read data and short read data.

Henry is also betting on accuracy. Yes, the short-read market is very competitive, he says. But SBB technology is highly differentiated, he asserts. It is, he says, “much more accurate than the UG 100, much more accurate than NovaSeq X, and much more accurate than what Element is doing. That accuracy, I think, gives us the ability to, to capture some market share.”

They have no expectations to capture a large amount of the market. But Henry notes, even if they capture 2, 3, 4, 5% of the market on the short-read side, “it’s still a material amount of revenue that’s coming to the company.” And Henry has his sights set beyond these three platforms; he says that they need five platforms. They are, Henry says, throwing all of their chips into the middle of the pot and making big bets on how the market is going to work. And, he adds, “we’re going against formidable competitors.” But, “we were going against them anyway,” he notes.

Competition

PacBio is building the company in the shadow of Illumina’s the 800-pound gorilla and several smaller, emerging companies. “It’s super interesting, and it’s hard, and it’s super competitive, but it’s really fun,” notes Henry.

Three years ago, PacBio was “on the brink of destruction,” notes Henry. Back then, he says, PacBio was a sleepy company. Now, he says, they are a dynamic company making major progress.

Another way that PacBio has moved away from being a “sleepy company” is to deliver some of the best entertainment. Last year at ASHG, it sponsored a concert by Maroon 5. At AGBT, it was a Flo Rida concert. Naturally, I asked Henry to reveal who might be performing later this week. And naturally, he declined.

He mentioned that I am not the first to ask to reveal the secret. In fact, he told me, the company recently gathered their top customers, and shared a lot of confidential information, including a future product roadmap and other info that, he adds, Illumina would not have shared in a million years. But none of that compared to who would be performing at ASHG.  It was “almost the number one thing” that people wanted to know. He did let me know two things: it’s not Maroon 5 and it is “going to be cool.”

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