NEW YORK – Precision oncology company Lucence recently published an analytical and clinical validation study of its flagship LiquidHallmark circulating tumor DNA (ctDNA) next-generation sequencing (NGS) assay, demonstrating high sensitivity and specificity for a variety of genetic lesions and oncogenic viruses.
The Palo Alto, California-based company is preparing to ramp up commercialization of the assay in the US on the back of these results, while simultaneously developing its new circulating tumor RNA (ctRNA) version of LiquidHallmark.
In the validation study, published in PLOS One in late April, the ctDNA-based LiquidHallmark demonstrated a sensitivity of 99.38 percent for point mutations and 95.83 percent for insertions/deletions (indels) at 0.1 percent variant allele frequency (VAF), and a sensitivity of 91.67 percent for gene fusions at 0.5 percent VAF, using reference genetic materials.
The assay demonstrated a 74.8 percent detection rate among 1,592 patients and identified clinically actionable mutations in 50 percent of ctDNA-positive cancer samples.
Clinical accuracy for point mutations and indels was evaluated in 355 lung cancer specimens, delivering a positive percent agreement (analogous to sensitivity when compared to non-reference standards) of 95.49 percent.
LiquidHallmark furthermore showed an overall 84 percent concordance with Roche's real-time PCR-based cobas EGFR Mutation Test v2 in detecting EGFR mutations.
LiquidHallmark's low limit of detection of 0.1 percent VAF makes the assay applicable to both early cancer detection and minimal residual disease (MRD) monitoring, essentially covering the breadth of the cancer patient journey. The company has a study underway with the Palo Alto Veterans Administration, for instance, evaluating the assay's use in cancer screening, and presented data at last year's ASCO conference, highlighting its performance in detecting and guiding treatment for late-stage cancers.
One weakness inherent in ctDNA-based cancer biopsies, to which LiquidHallmark is not immune, is a drop in sensitivity related to detecting gene fusions.
"Some fusions are just impossible to detect by DNA because of the large introns [involved]," said Han Tan, founder and CEO of Lucence.
The company recently announced an expansion of LiquidHallmark into the ctRNA space. Secreted into circulation through apoptosis and necrosis, ctRNA can reflect the systemic response to growing tumors and provide information about tissue of origin and cancer type.
The combined panel features 27 actionable and emerging gene fusions detectable by ctRNA, in addition to the 80-gene panel used for ctDNA profiling.
Han pointed out that ctRNA concentrations can be a hundredfold lower than those of ctDNA and that ctRNA tends to be even more fragmented, placing a premium on being able to detect signals at the lowest possible level.
"[Our] amplicon chemistry really shines in this ultra, ultra low-level challenge," Tan said.
The company will present more data on this chemistry and on the ctRNA profiling component of the assay at the upcoming American Society of Clinical Oncology conference in June.
Lucence will not be alone in presenting ctRNA-based cancer screening methods at ASCO.
Similar to Lucence, Predicine is developing a combined ctDNA and ctRNA NGS assay. The company presented data on this assay as a poster at the AACR conference in 2020 and, according to Predicine Founder and CEO Shidong Jia, the company is going to launch its early cancer screening technology with "very exciting" data at the upcoming ASCO meeting.
The use of RNA as a biomarker in cancer screening has lagged behind that of DNA, Jia said, largely because of the decreased stability of RNA relative to DNA in solution. Nonetheless, he said, the use of ctRNA "is a matter of time and data accumulation."
Those factors appear nearer than ever, with a number of companies now entering the field.
University of California at San Francisco spinout Exai Bio is seeking to commercialize an RNA-based cancer screening test, although through the analysis of actively secreted small noncoding RNAs.
Across the Atlantic, Spanish liquid biopsy startup Flomics recently raised €1 million ($1.05 million) in seed funding to develop its own NGS-based cell-free RNA assay for cancer and other diseases.
While Lucence continues to generate data for the ctRNA version of LiquidHallmark, it remains focused on growing its US business for the ctDNA version in the wake of the validation study.
"We are currently able to receive samples from 49 states and Washington, D.C.," said Jack Challis, senior VP of US operations. The firm currently lacks licensure in New York state but is hiring sales staff to expand within the jurisdictions where LiquidHallmark can be commercialized.
"Our goal is to grow the commercial team to cover the continental United States," Tan said.
LiquidHallmark is currently a lab-developed test. While Tan mentioned that the firm is considering a future application as a kit sold for a point-of-care setting, demonstrating its utility and providing a strong service in the US takes priority for now.
The company's most important current goal, Challis said, "is to work on Medicare reimbursement for LiquidHallmark and to develop evidence in support of that reimbursement."
The firm is beginning its Liquik study aimed at benchmarking the assay's performance versus tissue biopsy testing in non-small cell lung carcinoma and is actively considering other cancers where LiquidHallmark might substantially improve the status quo of cancer diagnostics.
Current National Comprehensive Cancer Network guidelines concerning cancer diagnostics remain hesitant on the widespread inclusion of liquid biopsies, citing concerns for reduced sensitivity.
With a demonstrated sensitivity above 90 percent, Tan sees the LiquidHallmark validation study as one step toward advancing the goal of guideline inclusion.
"The use of liquid biopsy tests like ours is already making a lot of inroads in conventional care," Tan said. "Liquid biopsy can occasionally detect variants that are outside of what can be detected in tissue, and I think the guideline process is recognizing this. We're optimistic this will continue to progress."