Biotech Connector Series: Liquid Biopsies

February 21, 2021

Biotech Connector Series: Liquid Biopsies

On February 25, the Biotech Connector series from Frederick National Laboratory for Cancer Research 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.

Talk 1: Validation of a Liquid Biopsy Assay to Support NCI Clinical Studies
Presented by Chris Karlovich, PhD, associate director, Molecular Characterization Laboratory (MoCha), FNLCR

“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. In addition to being able to identify common mutations in cancer, this particular assay 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. 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 also saw additional mutations in the blood that we did not see in the tumor."

Talk 2: Incorporating Reference Materials into the Development and Evaluation of Liquid Biopsies
Speaker: Yves Konigshofer, PhD, director of technology development, LGC Clinical Diagnostics

Reference materials (RMs) enable assay development and allow for the evaluation of assay performance. Liquid biopsies can be challenging assays to develop and implement because relevant patient samples are rare, poorly characterized, and only available in limited quantities. Liquid biopsies are also moving towards single molecule detection, which requires extreme sensitivity and specificity.

This talk will discuss the development of customizable patient-like RMs for liquid biopsies as well as how RMs are indispensable for improving both the laboratory and bioinformatic elements of assays. In doing so, they increase diagnostic accuracy, allow our customers to achieve regulatory approvals, and ensure assay performance across labs, geographical boundaries, and platforms.