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With New Validation Data, BillionToOne Boosts Commercial Prospects of Therapy Selection Assay


CHICAGO – With two new abstracts at the American Society of Clinical Oncology's annual meeting, prenatal and cancer testing firm BillionToOne aims to boost the commercial prospects of its Northstar Select comprehensive genomic profiling test for therapy selection. 

The plasma-based test was launched for research use in 2022 and utilizes the company's Quantitative Counting Template technology for genomic profiling of solid tumors. The QCT technology allows for the quantification of DNA fragments at the single-molecule level, combining the sensitivity of digital-droplet PCR with the multiplexing power of next-generation sequencing, BillionToOne Chief Product Officer Shan Riku said in an interview. 

The 84-gene genomic alteration panel covers all solid tumor alterations associated with US Food and Drug Administration-approved targeted therapies and immunotherapies, including 82 genes for single nucleotide variants and indels, 19 genes for copy number amplifications, five genes for copy number loss, and nine genes for fusions. 

In an abstract presented on Saturday, the Menlo Park, California-based firm unveiled results from a prospective validation study that included 182 patients with stage III or stage IV solid tumors from a large hospital center and six community clinics in the US. The study assessed head-to-head concordance with unnamed "widely adopted, commercially available 'comparator' liquid biopsy CGP assays," the researchers wrote in the abstract. The cohort included more than 15 cancer types, with a majority of patients having lung, breast, colorectal, or prostate cancer. 

In the study, pathogenic and likely pathogenic variants called by Northstar Select and/or the comparator assay were analyzed for concordance. Researchers found that a large number of variants were concordant between Northstar Select and the comparator assay, while the test detected 43 percent more pathogenic variants than comparators when controlling for matched coverage regions. The majority of those variants were detected below the reported limit of detection of the comparator assays, but above the limit of detection of Northstar Select, they noted. 

In addition, the proportion of patients with no pathogenic variants detected was shown to be lower by 45 percent when using Northstar Select compared to the other assays. The results "suggest that some patients with low levels of ctDNA would derive clinical benefit from testing with NS Select due to its high sensitivity," the researchers wrote. 

The researchers also analyzed circulating tumor DNA shedding and clinical actionability, estimating the ctDNA shedding level as the average variant allele fraction (VAF) of pathogenic single nucleotide variants and indels for each patient. Clinically actionable variants were defined as those associated with targeted therapy, clinical trial, or diagnostic or prognostic relevance. In a cohort with a high proportion of patients with low ctDNA shedding cancers, Northstar Select was able to detect clinically relevant results for about 70 percent of patients. 

Northstar Select also reduced the number of "negative" reports from samples — meaning reports in which no clinically actionable alterations were detected — from 20 percent with the comparator assays to 11 percent with Northstar Select. 

"If you have a report without any variants, you have no treatment options," Senior VP of Sales and Commercial Operations Nancy Johnson said. 

A separate abstract presented at ASCO on Saturday validated Northstar Select's performance specifically in central nervous system tumors. Detection of ctDNA from central nervous system tumors "is impeded by its inherently low shedding biology and poor permeability across the [blood-brain barrier]," which results in low plasma VAFs, the researchers wrote. 

For the study, 62 cases of primary central nervous system tumors were submitted commercially for assessment with Northstar Select from one clinic. Northstar Select had a detection rate of 88.7 percent in all cases, due to the test's low limit of detection of 0.13 percent to 0.16 percent VAF — below the 0.17 percent median VAF found across the tumors in the study. This allowed "for more low-abundance alterations to be detected," the researchers noted, adding the data supports the clinical utility of Northstar Select to complement imaging and tissue analyses or for use when tissue biopsies aren't available. 

The data also suggests the test could be expanded into metastatic brain disease and other tumors with low ctDNA shedding, they said. 

Northstar Select is meant to be used in conjunction with BillionToOne's response monitoring assay Northstar Response, Riku noted. Clinicians can use Northstar Select to make sure they don't miss any targetable alterations and then continue using Northstar Response to monitor the treatment. If they see a signal increase from the Response assay, that could be a sign of progression, and Northstar Select could be used again to switch therapies. 

Northstar Select competes with other liquid biopsy comprehensive genomic profiling assays for late-stage cancer from companies such as Foundation Medicine's FoundationOne Liquid CDx and Guardant Health's Guardant 360. But BillionToOne's smaller size gives it an advantage, Riku said, as it is able to be more "nimble and flexible" and adapt its tests quickly compared to other larger firms when it sees an unmet need. The firm is also able to incorporate clinician feedback more easily than a large company, such as by changing report designs or other minor alterations. 

Riku noted that the clinical version of Northstar Select was launched in January 2023 and that a second version of the test with a higher sensitivity was launched last July. 

"When we see an unmet need, it takes years for other companies to respond because of their size, because of their regulatory status, it is just a lot harder for them to innovate," Riku said. "We are in a much better position." 

Johnson echoed Riku's comments, noting that continuing to improve the sensitivity of the test has been a major focus of the company. "You don't always find all the alterations in the peripheral blood that actually exist in the tumor, so the more sensitive you can be in your liquid biopsy, the better the test you have." 

However, the firm is still working to grow its presence in the market. Johnson said that the team is hiring 25 additional sales representatives this year, with plans to double that number by the end of next year and boost its commercialization plans. 

BillionToOne also aims to enter other cancer diagnostics markets, including the development of a minimal residual disease assay that could act as a standalone or be included with Northstar Response, Riku said.