Ten years ago it was unimaginable that a cancer patient could visit a doctor’s office, have blood drawn, and based partly on those results, receive guidance on which targeted cancer treatment course to follow. “Being able to collect, sequence, and analyze the DNA that is shed from one’s tumors has been transformative for certain types of cancer patients over this past decade,” explained Razelle Kurzrock, M.D., Associate Director, Clinical Science at UCSD.
Liquid biopsies are blood tests that can be analyzed for circulating tumor DNA (ctDNA), also known as cell free tumor DNA. The blood is analyzed with ctDNA assay kits to make targeted cancer treatment decisions or genetic biomarker correlations. Which types of cancer patients have benefited from ctDNA analysis via liquid biopsies? And are there more types of patients (or non-patients!) who will soon benefit?
Liquid biopsies for patient care
For patient care there are approximately ten different ctDNA laboratory developed tests (LDT) available for use in CLIA certified labs. Most of the kits rely on next-gen sequencing to test patients with advanced cancer for the presence or absence of a panel of 70 or so different genetic mutations (such as those in genes p53, EGFR, BRCA1, BRCA2, bRAF, KRAS) that are associated with actionable knowledge. “The core idea for panel-based ctDNA clinical kits is that it’s a one stop shop for comprehensive genomic profiling of all advanced tumors. The same kit can be used for a breast cancer patient, a lung cancer patient, or a pancreatic cancer patient because the kit tests for all the genes with known mutational correlations with treatment selections,” said Justin Odegaard, M.D., Ph.D., VP Clinical Development, Guardant.”
The most widely used ctDNA clinical-grade kits, judging by Google searches and confirmed by Dr. Kurzrock, include Roche’s FoundationOne Liquid CDx and Guardant Health’s Guardant 360 test. The first clinical-grade liquid biopsy NGS panel was Guardant 360 which was launched for patient care testing as an LDT in 2014 (and received FDA approval, which only a few companies have pursued, in August 2020). Roche’s FoundationOne Liquid CDx was also approved by the FDA in August of 2020, after it had been available as an LDT since 2018.
PCR is the technology used for the other type of ctDNA kits. They are best suited to assay for a narrower set of specific mutations. The first such kit was Roche’s cobas® EGFR Mutation Test v2 test that looks for 42 different mutations within EGFR. This was the first liquid biopsy test to be approved by the FDA—in 2016.
Dan Klass, Ph.D., Lifecycle Team Development Lead from Roche, explains that qPCR (and the newer technology digital PCR) is often more sensitive than NGS for specific biomarkers and can usually detect abnormal DNA when it is present at lower amounts than would be detected by broad NGS panels. "dPCR is less expensive, faster, and easier to use if you are only trying to detect a small number of biomarkers from a liquid biopsy. NGS is for when the goal is to in one assay, detect DNA variants in multiple genes where the area of the genome being interrogated is much larger,” continued Klass.
Though liquid biopsies are much more convenient for the patient, they haven’t completely replaced traditional tumor tissue biopsies. Kurzrock believes you need results from both types of biopsies for the most complete picture of a patient’s tumor burden. Liquid biopsies sometimes reveal mutations that may not have been in the location from where the tumor was biopsied. Liquid biopsies can also include cancer-cell origin DNA that was shed from cancer cells beyond the primary tumor. On the other hand, because the amount of tumor-specific DNA in circulation is less than in the tumor, low-level mutations may not be detectable in a liquid biopsy. Liquid biopsies though are a savior when tissue biopsy has been used up for other types of analysis, was of poor quality, or the tumor was in a location too dangerous to biopsy.
RUO applications for circulating tumor DNA assays
Some of liquid biopsies’ biggest patient-care applications are yet to come. Most in the field are excited about using liquid biopsies to monitor disease in order to reach decisions on prognosis, measure how much disease burden remains after treatment, and determine if new treatment regimens need to be tried. With liquid biopsies, serial biopsies are now possible. Taking biopsies of a patient’s tumor every few months is too expensive, cumbersome, and potentially dangerous for a patient.
However, these up-and-coming applications of liquid biopsies hinge on more knowledge becoming available about which tumor mutational changes are associated with cancer prognosis—more correlations studies are needed. That’s where ctDNA assays approved for research use only (RUO) come in. There are roughly 10 companies, including Guardant and Roche, who make RUO ctDNA assays based on NGS. Often the use of a specific ctDNA assay is funded by pharma within a clinical trial to investigate if use of the trial’s drug correlates with specific ctDNA signatures. If it is found that the drug works best when given with a specific tumor profile, that RUO kit would then become a companion diagnostic for the treatment being studied in the clinical trial.
Farther future applications of liquid biopsies
The dream application of liquid biopsies is that it can eventually be used in a person without cancer, for potential early diagnosis of cancer. “I’m hoping within 2–5 years we will be able to go the doctor and as part of a regular checkup, get a blood test to see if a cancer we don’t even know about, is there,” said Kurzrock. Such tests would be especially useful for silent cancers such a pancreatic cancer that is often not diagnosed until it is too late to treat.
Companies such as Thrive Early Detection, Grail, or Biological Dynamics (which Kurzrock consults for) are working on such tests. Frank Diehl, Ph.D., EVP of Product Solutions at Thrive, said they are working on a screening test that will be able to detect multiple types of cancer from a patient’s blood cells and plan to start a pivotal trial some time in 2021. Their liquid biopsy assay looks for biomarker correlations beyond only ctDNA. They also detect analytes such as protein expression to determine cancer correlation patterns. Kurzrock says more time is needed for the accuracy of these tests to improve because there is a very low bar for false negatives or positives when it comes to a cancer diagnosis. Diehl also cites clinical utility as a hurdle for acceptance of liquid biopsies as a cancer screening tool. One does not want to be diagnosed for a cancer if there is nothing yet that can be done about it.