NEW YORK – A little more than a month into its new life as a publicly traded company, sequencing firm Personalis updated investors this week on how customers have been receiving its recently launched comprehensive tumor and immune profiling assay ImmunoID NeXT, as well as how its efforts to develop an exome-wide liquid biopsy product are proceeding.
Launched through an early-access program that began in January, NeXT combines exome-wide analysis of DNA and RNA with interrogation of the tumor microenvironment in a single FFPE sample.
Along with more standard detection of DNA variants and gene expression, the new product identifies neoantigens and analyzes tumor mutational burden, neoantigen load, and microsatellite instability status. It also performs HLA typing, characterization of tumor infiltrating immune cells, T-cell and B-cell receptor repertoire profiling, and detection of other biomarkers of immune response and tumor escape mechanisms.
During a call discussing the company's second quarter earnings this week, Personalis CEO John West said that interest in NeXT during the early-access period has been strong. He also reiterated that the company expects to release a version of the platform that can also provide information for clinical decision-making by the end of this year.
The core exome sequencing arm of the assay has already been approved for clinical research use for some time, as was the company's neoantigen identification methodology last summer.
West said that the company isn't reporting on new customers in real time, but claimed that the feedback Personalis has received so far for NeXT has been very encouraging.
"People understand that this is ... biology that they haven't seen all together in a single platform before," he said.
"There's a period of time where [customers are] assessing and going through pilots and that kind of activity, but … we've always thought of NeXT as something that would likely drive our revenue up in 2020 [and] based on what I see today that's still likely to be the case," he added.
One early customer the firm has disclosed is RAPT Therapeutics. "This is the first year where we've worked with them … [so there is] a lot of enthusiasm in their case because they're just starting with us. They don't have prior work with the earlier versions of our platforms," West explained.
"One of the reactions we hear fairly often," he added, "is that people are finding it almost incredible that it is actually possible to get all those different elements of the biology from a single small FFPE sample."
Personalis is also working hard to "fill out the feature set" of analytics and other peripheral tools that help customers put the assay to work, West said.
On August 1, for example, the firm announced an update that adds the ability to measure HLA loss of heterozygosity, the presence or absence of seven of the most common oncogenic viruses, and the composition of the T-cell receptor alpha repertoire.
According to West, while Personalis is focused on emphasizing the NeXT approach as a united, or integrated system, different components of the service can also be run as separate assays, and the firm does see some customers who remain interested in more focused analyses.
That said, he added, the company also sees cases where customers want to build even further on the standard. "Our flagship product would include both the transcriptome as well as the exome, both being augmented with the immune repertoire and so forth … [standardly performed on] one tumor sample and one normal sample," West said. "But we do have customers who ask for us to process multiple tumor samples from the same patient, or others who have tissue samples at multiple time points."
Support is growing for more comprehensive evaluation of cancer biology and drug response in the biopharmaceutical space, and companies continue to add capabilities for immune profiling and interrogation of the microenvironment.
Some firms, like NanoString and Thermo Fisher Scientific, have focused on creating individual assays to interrogate specific immune signatures or immune system components. Others, like Cofactor Genomics, are hinging closer to Personalis in marketing more comprehensive transcriptomic and immune interrogation services.
The diagnostic-capable version of NeXT, which West said Personalis should have available before the end of the year, would provide customers with "20,000 gene-scale translational research data," but also with a more narrow clinical diagnostic report — something that the firm claims will be a first for the field.
"There will be some [need] to work with pharma on the best way to integrate that in with their clinical trial workflow," West said, "so that's all part of what we'll do working collectively with our customers."
Enthusiasm for this option and the resulting impact on Personalis' business is something that will have to be tracked over the next year, West added. "I think there's interest but it's quite early days … [These] things always take time for pharma to assess … particularly if they want to use it prospectively on a trial, that would be something that would be have to be baked into the planning."
Beyond its efforts to grow adoption of the NeXT approach, Personalis has also said that it is developing an exome-wide liquid biopsy assay, which it hopes to have finished in 2020. During the call this week, West said that the company will focus on the parallel utility of liquid and tissue.
"We see that liquid biopsy and tissue biopsy complement each other in many ways. Liquid biopsy makes it easier for us [to analyze] at multiple time points, but the tissue biopsy gives us access to RNA and it also gives us access to the immune cells that are inside the tumor and those are both pretty critical in terms of understanding what's happening in the growth and evolution of a cancer," he said.
Regarding assay development, West said the firm has "a lot of the core elements together," but analyzing the cancer genome in blood at an exome-scale is "pushing the state of the art," he argued.
"I would anticipate that once we have that running at the level that we're comfortable with internally we'll probably work early on with some initial collaborators and so forth to make sure it works well in their hands and then figure out what we are going to do in terms of a release date."
Although liquid biopsy is now being adopted into clinical oncology practice, this is largely limited to narrower panels of immediately actionable genes. According to West, a liquid biopsy exome will likely remain attractive mainly to biopharmaceutical customers for some time. "Looking at 20,000 genes [is] tremendous from a translational medicine research standpoint, [but] clinical utility … is probably a little bit further out," he said.
Despite that, the company already faces a competitor in the arena, with Natera having announced this April that it would begin offering whole-genome sequencing of liquid biopsy samples for research customers.
How Personalis' approach may differ from potential competitors remains to be seen. But prior research has shown that it can be challenging to glean a whole exome's worth of data from the blood, especially in cancer cases that shed little DNA into circulation.