ctDNA Tumor Fraction Matters When Interpreting Liquid Biopsy Test Results

Comprehensive genomic profiling helps oncologists select therapies, helps patients access therapies, helps pharmaceutical companies enroll patients in clinical trials, and helps accelerate drug development. While oncologists increasingly use liquid biopsies for genomic testing, many still have concerns that a negative result from liquid biopsy may not be meaningful enough to direct clinical decision making. This concern can be mitigated by Foundation Medicine’s new circulating tumor (ctDNA) tumor fraction which improves confidence in the meaning of a negative result from liquid biopsies. Lincoln Pasquina, PhD, Director of Clinical Development at Foundation Medicine, explains how physicians can leverage Foundation Medicine’s ctDNA tumor fraction to improve clinical care.

Liquid Biopsies Increasingly Common

It is becoming increasingly common, especially when tissue biopsies aren’t available or are difficult to obtain, for oncologists to use liquid biopsies for genomic analysis. This approach is successful because some fraction of the extracellular DNA (cell free DNA or cfDNA) in the blood is shed from tumor tissue (circulating tumor DNA or ctDNA). However, not all cfDNA is ctDNA. There is also cfDNA that is derived from healthy cells. This means that the blood contains DNA released from both healthy and cancerous tissues in the body. “Within a liquid biopsy sample, you're always going to get DNA,” says Dr. Pasquina. “There's always cell-free DNA, but that's not necessarily helpful. If you're only measuring healthy normal cells, then you're not actually testing what you want to know.” Liquid biopsies aim to detect alterations and other complex biomarkers in the ctDNA released by the tumor cells.

Historically, oncologists have had confidence that positive results from liquid biopsy tests were successfully identifying oncogenic drivers. Such positive results were particularly valuable when they matched with a specific therapy. Unfortunately, up until now, there has been a general haze of uncertainty around negative results from liquid biopsies. “Oncologists wonder if they don't get anything back that's targetable, what should they do next?” says Dr. Pasquina. Absent a targetable result, should they treat the patient with immunotherapy or a non-targeted agent? Alternatively, should they wait on therapy and instead perform an invasive procedure to obtain a tissue sample that may confirm the negative result or potentially unearth the oncogenic driver in the tissue?

Biomarker Threshold Lowered from 10% to 1%

Before the incorporation of Foundation Medicine’s ctDNA tumor fraction, FoundationOne Liquid CDx used a threshold of 10% tumor fraction in the total cell-free DNA to estimate the amount of ctDNA in any given sample. This historical threshold was based on observed aneuploidy in the sample. In order to calculate this aneuploidy, FoundationOne Liquid CDx profiled not only 300 plus genes, but also 30,000 single nucleotide polymorphisms (SNPs) across the entire genome.

Foundation Medicine’s ctDNA tumor fraction is a determination of the amount of circulating tumor DNA as a fraction of total cell free DNA in a blood sample that accounts for aneuploidy, variant allele frequency, fragment length information, clonal hematopoiesis predictions and known tumor associated alterations. ctDNA tumor fraction represents a key differentiator for FoundationOne Liquid CDx as it makes it easier for physicians to interpret and have more confidence in a driver-negative FoundationOne Liquid CDx report. When a liquid biopsy sample reaches the 1% threshold, it is referred to as high ctDNA tumor fraction, and oncologists can be more confident in any negative results for short variants and rearrangements and initiate treatment. “If the sample has a low ctDNA tumor fraction and the oncologist does not see tumor markers, he or she must know that they could be missing something,” says Dr. Pasquina. “That low signal should be taken into consideration in deciding to get a tissue biopsy that wasn't originally on hand.”

Consider Tissue Biopsy at Metastatic Diagnosis and Liquid Biopsies at Disease Progression or When Tissue Unavailable

Dr. Pasquina explains that while quality tissue remains the gold standard for genomic testing, such tissue is not always readily available. In some cases, this is because the sample was obtained by small fine needle aspirate and was insufficient. In other cases, the sample may have a great deal of necrosis, making it challenging to analyze. Moreover, it may be difficult to obtain a new sample because such a sample may require particularly invasive surgery or a painful procedure. In addition, solid tissue biopsies require scheduling a procedure, processing the sample, sending it to a pathology laboratory, and then sending it to a central laboratory for testing. Because of these challenges with tissue biopsies, oncologists may choose to use liquid biopsies to provide an initial patient profile. Given the complexities of a given patient’s situation, they may choose to obtain a simple blood draw, bypass the many time-consuming and costly steps associated with tissue biopsy, and initiate treatment.

When there is disease progression, liquid biopsies are often used. These liquid biopsies can replace invasive biopsies in many instances and provide insights into different metastases across the patient’s tumor burden. This is because tissue biopsies only provide information about the part of the tumor the physician happens to capture by biopsy. In contrast, liquid biopsies include DNA shed from other portions of the same tumor, too (i.e., tumor heterogeneity), and as such, can provide a holistic view of the patient’s disease state including both primary tumor and metastases.

While liquid biopsy testing, in general, has advantages over tissue testing, FoundationOne Liquid CDx stands out among liquid biopsies. Not only does it have ctDNA tumor fraction, but it compares favorably to other tests in terms of number of genes analyzed and sensitivity for detecting rearrangements in those genes. This is because FoundationOne Liquid CDx was intentionally designed with fusion detection in mind. The fact that liquid biopsies can be such an important tool for oncologists reinforces the importance of ctDNA tumor fraction in helping physicians navigate negative liquid biopsy results and determine the next steps after. With ctDNA tumor fraction, oncologists can now have more confidence in the reported measurement of the amount of ctDNA within a liquid biopsy sample. The new advancement means that liquid biopsies are not only clear with a positive result, but they are now clearer with a negative result.

Foundation Medicine® and FoundationOne® are registered trademarks of Foundation Medicine, Inc.

FoundationOne®Liquid CDx is for prescription use only and is a qualitative next-generation sequencing based in vitro diagnostic test for advanced cancer patients with solid tumors. The test analyzes 324 genes utilizing circulating cell-free DNA and is FDA-approved to report short variants in 311 genes and as a companion diagnostic to identify patients who may benefit from treatment with specific therapies (listed in Table 1 of the Intended Use) in accordance with the approved therapeutic product labeling. Additional genomic findings may be reported and are not prescriptive or conclusive for labeled use of any specific therapeutic product. Use of the test does not guarantee a patient will be matched to a treatment. A negative result does not rule out the presence of an alteration. Patients being considered for eligibility for therapy based on detection of NTRK1/2/3 and ROS1 fusions should only be tested if tissue is unavailable. Patients who are negative for other companion diagnostic mutations should be reflexed to tumor tissue testing and mutation status confirmed using an FDA-approved tumor tissue test, if feasible. For the complete label, including companion diagnostic indications and complete risk information, please visit www.F1LCDxLabel.com.