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Personalis Highlights Use Cases for NeXT Platform as Company Seeks Greater Adoption


NEW YORK – Although the majority of its revenue is currently coming from from its population sequencing work for the US Department of Veterans Affairs, cancer genomics firm Personalis said this week that it is hoping to see increased adoption of its comprehensive cancer testing platform, ImmunoID NeXT, by pharmaceutical customers over the next year.

The company also shared some of the first data from studies conducted using the platform in a set of posters at last week's annual meeting of the Society for Immunotherapy of Cancer (SITC), offering a look at early uses of the technology and the kinds of use cases that might attract future adopters.

During a call discussing the company's third-quarter earnings on Wednesday, Personalis CEO John West said that the company continues to be "really pleased" with reception for ImmunoID NeXT, and has been heartened at how rapidly understanding seems to be growing in the cancer research community regarding the value of comprehensive paired genomic and transcriptomic approaches that can provide information on both cancer cells and the body's immune or microenvironment processes from a single sample.

West also addressed some concerns from investors around variability that the company is seeing in its pharma services revenues, noting that new orders from customers during Q3 reflect a wave of "strong interest" from existing clients in converting to the new NeXT platform, as well as a continuing flow of new adoptees.

Specifically, West said the company is in "advanced discussions" with four multinational biopharma companies who would be new gets for the firm, not having been customers in the prior year.

CFO Aaron Tachibana added that although revenue from NeXT specifically is currently minimal, Personalis now has 10 new orders on the books for studies using the platform.

In the meantime, presentations at the SITC meeting last week provided a glimpse of some of the ways Personalis has already applied NeXT platform — the kinds of studies that new and future adopters might hope to extend or mirror.

In one abstract, researchers described an integrated pipeline for neoepitope discovery that couples comprehensive profiling of putative neoantigens using ImmunoID NeXT, with prediction of major histocompatibility complex, or MHC presentations of such neoantigens. Using this method, the authors wrote that they could more effectively generate neoepitopes that are critical for developing personalized cancer vaccines.

Another poster presented at the meeting described Personalis' use of NeXT to characterize immungenomic profiles and assess potential response biomarkers in 52 unresectable stage III and IV melanoma patients treated with anti-PD1 immunotherapy.

Getting a combined read on tumor genetics, tumor microenvironment, and immune system factors, the authors wrote, allowed them to see that several factors were associated with response including elevated pretreatment neoantigen burden — which was not only predictive of response, but also significantly associated with progression-free survival — and elevated pretreatment T-cell receptor clonality. 

"Patients with high neoantigen burden and TCR clonality that failed to achieve complete response [also showed specific] potential resistance mechanisms to anti-PD-1 therapy," the group added. This included two patients with high expression of IDO1 or CTLA4, which the authors wrote may facilitate PD-1-independent immune escape. 

Two other patients had antigen presentation machinery (APM) mutations, which suggest reduced neoantigen presentation and are probable mechanism for tumor escape. 

Perhaps most importantly, the investigators reported that an integrated predictor — combining neoantigen burden, HLA-loss of heterozygosity, and APM mutational data — increased the predictive strength over neoantigen levels alone.

And a third presentation described reproducibility and accuracy tests of ImmunoID NeXT, as well as the use of the platform to analyze the clonal diversity of pre-treatment tumor samples in immunotherapy-treated melanoma patients and to profile the clonal diversity across more than 100 solid tumor samples.

So far, the application of the platform by pharma customers would have to have been limited to retrospective studies, but during the earnings call this week West said that Personalis is currently completing its validation of a clinical version of NeXT, which will allow its use prospectively in clinical trials. The company expects to launch that product before the end of this year. 

Further down the line, the firm also plans to extend its reach with a whole-exome liquid biopsy addition. According to West, this remains on track for launch in 2020.

"Interest in the use of liquid biopsies to complement data from tissue biopsies continues to grow and our conversations with customers about our initial product are positive," he said.

The process is a complicated one, though, considering that the test Personalis says it will be releasing will far outstrip the breadth of current blood-based cancer tests, the largest of which currently profile around 500 genes.

"The thing we're trying to do … [is] pretty unprecedented, [analyzing] 20,000 genes off of what can be tiny amounts of DNA that come out of a plasma sample," West said during the firm's earnings call. 

"We're working to make sure that with the variability of samples that that can come from patients, that we're satisfied with the results we can get before we go out to customers," he added.