On February 25, the Biotech Connector series will highlight exciting research on liquid biopsies with two talks by local investigators. Liquid biopsies are highly sensitive blood tests that can detect fragments of tumor DNA, also known as circulating tumor DNA (ctDNA), in the blood—providing critical information about the tumor without an invasive tumor biopsy.
“Liquid biopsies have enormous potential and a wide range of applications,” explained Chris Karlovich, PhD, who will be presenting at the event. Karlovich is the Associate Director of the Molecular Characterization Laboratory (MoCha), part of the Frederick National Laboratory for Cancer Research. The most widely used application today is for the identification of clinically actionable, tumor-derived mutations in the blood. If such a mutation is identified, patients with cancer can be directed to a therapy that specifically targets the mutation. MoCha has recently validated its own assay for liquid biopsies.
Other emerging applications for liquid biopsies include screening and disease monitoring. Karlovich described screening to detect early stage cancer as the “Holy Grail” for liquid biopsies. However, the field has not yet achieved the “exquisitely sensitive and exquisitely specific” assay required to detect the minute amounts of tumor DNA in the blood in people will little disease without giving false positives. When used for disease monitoring, liquid biopsies could detect when a tumor is starting to regrow following treatment.
MoCha’s liquid biopsy assay
“It has been known for decades that tumors shed DNA into the blood,” Karlovich explained. “But we didn’t have the tools to identify those fragments of tumor-derived DNA with the sensitivity that we needed.”
Those tools are now here. MoCha’s 523-gene panel, the MoCha ctDNA assay, is based on Illumina’s TruSight Oncology 500 (TSO500). It can detect mutations in important cancer-related genes for any solid tumor.
Karlovich explained that, in addition to being able to identify common mutations in cancer, this particular assay is that it can identify gene fusion events—where two genes, typically a cancer-driver gene and another gene, fuse together. This type of mutation is difficult to identify, but if correctly identified, the disease can often be effectively treated with a targeted therapy.
However, before this assay could serve patients, it needed to be extensively validated.
“The last thing we want to do is use an assay for the clinical management of patients that doesn’t have good performance characteristics,” Karlovich said. “If you report back a false positive result, the patient will be put on a drug that they will not benefit from.”
Therefore, MoCha collaborated with Illumina to validate the assay to understand the performance characteristics. This effort took a year and involved testing 350 samples. First, MoCha tested 100 samples from 32 healthy donors to validate its specificity. Of the 100 samples, there were just two potentially false positive results, meaning it is highly specific. MoCha then conducted a limit of detection study and found that the assay can detect the equivalent of one molecule with a mutation in a sea of 400 normal molecules. This capability is critical, because most DNA in the blood comes from normal white blood cells, not tumors. He compared it to trying to find the proverbial needle in a haystack, and the validation showed the assay was adept at finding the needle—and without misidentifying pieces of hay as needles.
In a third study, MoCha sequenced 25 pairs of matched tumor biopsies and blood samples using the MoCha ctDNA assay and compared the results.
“Eighty-seven percent of the mutations that we found in the tumor, we also found in the blood,” Karlovich said. “That’s remarkable; we were able to identify almost all the mutations that were present in the tumor.”
However, that is not all the MoCha team found.
“We also saw additional mutations in the blood that we did not see in the tumor,” he added. He explained that this is because tumors are heterogenous, so a small biopsy will not necessarily reveal all the tumor’s mutations. The blood, on the other hand, “is acting as a reservoir, collecting mutations from all parts of the tumor, so when you test the blood, you can comprehensively assess the molecular landscape of the tumor.”
Starting in a few months, MoCha will use the assay to support National Cancer Institute (NCI)-sponsored studies, including testing patients at the NCI Developmental Therapeutics Clinic and assigning them treatments based on the results. MoCha will also test blood samples from 4,200 participants of the NCI-MATCH Trial and compare the blood results to their previously sequenced tumor biopsy results. Because many participants in MATCH had rare cancers, this will provide valuable data on these rare diseases.
At the upcoming Biotech Connector, Karlovich will present further results from the validation study. The event will also feature a scientist working in the industry, Yves Konigshofer, Ph.D., director of technology development at LGC Clinical Diagnostics Division. Konigshofer will discuss the incorporation of reference materials in the development and evaluation of liquid biopsies. The Biotech Connector is held in collaboration with the Frederick Chamber of Commerce.