Natera Publishes Data on Liquid Biopsy Technology for Early Cancer Detection

NEW YORK (GenomeWeb) – Natera announced today the publication of pilot study data demonstrating that its liquid biopsy technology can detect ubiquitous and heterogeneous tumor mutation variants in blood samples from patients with early-stage non-small cell lung cancer (NSCLC). 

The company is now testing its technology in a large observational clinical trial in the UK. 

Natera originally developed the technology, which combines massively multiplexed PCR and next-generation sequencing (mmPCR-NGS), for non-invasive prenatal testing applications, but the company has been adapting the system for oncology as part of a recent push into the early cancer detection space.

In the pilot study, which appeared in Annals of Oncology, investigators performed whole-exome sequencing on primary tumor samples from four early-stage NSCLC patients, followed by AmpliSeq validation. 

They selected a subset of 50 ubiquitous and heterogeneous single-nucleotide variants (SNVs) from the resulting data, which the authors wrote represented "both ubiquitous and heterogeneous mutations, as well as clinically relevant driver mutations based on the driver category classification." Due to technical reasons, the researchers ultimately chose 37 SNVs to analyze using Natera's mmPCR-NGS system.

Of these 37, 16 were detected in blood samples from all four patients, with at least two detected for each patient. Twenty-five of the SNVs were ubiquitous and 12 were heterogeneous. Notably, 94 percent of the SNVs detected were predicted tumor driver mutations.

Overall, the study investigators found good concordance between mmPCR-NGS and whole-genome sequencing plus AmpliSeq, as well as between variants detected in tumor tissue and in plasma using Natera's system, with no false positives found in plasma, they wrote in their paper.

They noted that low levels of variant DNA in cell-free DNA from three of the patients may have affected the sensitivity of the mmPCR-NGS system, but suggested that this limitation might be overcome by starting with more plasma.

Further validation of Natera's system will be required before it can be translated into clinical practice, the team added.

To that end, the company is participating in a large-scale trial — called Tracking Cancer Evolution through Therapy, or TRACERx — that is enrolling up to 842 NSCLC patients to examine the genomic landscape between primary and metastatic tumor sites, as well as to evaluate the dynamics of intratumor heterogeneity over time, by analyzing both tumor tissue and circulating tumor DNA.

TRACERx is being funded by Cancer Research UK, with additional support from the Rosetrees Foundation and University College, London. Using Natera's technology, study investigators specifically aim to examine point mutations and copy number variations in patient blood.

The company has called the trial a springboard for its plans to develop and launch cell-free DNA-based diagnostics for lung, breast, and ovarian cancer.

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