Cancer diagnosis and treatment increasingly rely on molecular analysis to understand the specific genetic makeup of a tumor. Modern testing requires precise quantification of the cancer material present in a biological sample. This necessity established tumor fraction as an important metric derived from advanced genetic testing. Tumor fraction provides a quantitative estimate of the proportion of cancer-derived material within a total sample, guiding oncologists in interpreting test results and making informed decisions.
What Tumor Fraction Represents
Tumor fraction is a quantitative measure, typically expressed as a percentage, that defines the amount of malignant material within a collected sample. In a solid tumor biopsy, it represents the ratio of malignant cancer cells to the surrounding non-cancerous cells, such as immune cells and connective tissue (stroma). This measure is important because healthy cells dilute the tumor’s genetic signal, potentially obscuring important mutations.
The concept shifts slightly in a liquid biopsy, which analyzes blood for circulating tumor DNA (ctDNA). Here, the circulating tumor fraction is the ratio of ctDNA, released from dying tumor cells, to the total pool of cell-free DNA (cfDNA) in the bloodstream. Since cfDNA includes fragments shed from both healthy and tumor cells, the tumor signal is often highly diluted.
Tumor fraction is closely related to, but distinct from, the Variant Allele Frequency (VAF). VAF is the percentage of DNA sequences containing a specific genetic mutation at a single location. Tumor fraction, conversely, is the overall proportion of all DNA that originated from the tumor, regardless of the specific mutations it carries.
Methods Used to Determine Tumor Fraction
For solid tumors, the initial step involves histological assessment, where a pathologist microscopically estimates the percentage of tumor cells in a stained tissue slide. This visual estimation ensures the sample contains enough tumor material for molecular tests. Advanced sequencing techniques, such as Next-generation sequencing (NGS) and SNP microarrays, are then applied to formalin-fixed paraffin-embedded (FFPE) samples. Bioinformatic algorithms detect genomic features unique to cancer cells, like chromosomal copy number alterations, and use their frequency to calculate the proportion of cancer cell DNA.
In a liquid biopsy, the measurement process is complex due to the extreme dilution of ctDNA in the bloodstream. NGS is performed on the cfDNA extracted from the blood. The tumor fraction is estimated primarily by analyzing the Variant Allele Frequencies (VAFs) of known somatic mutations to mathematically infer the overall tumor DNA content. Alternative methods analyze patterns of DNA fragmentation or leverage aberrant DNA methylation patterns to specifically count tumor-derived fragments.
How Tumor Fraction Guides Patient Care
The resulting tumor fraction measurement has profound implications for a patient’s clinical trajectory. A higher circulating tumor fraction is consistently associated with a greater tumor burden and indicates a more advanced disease. This allows the measurement to serve as an independent prognostic biomarker, with elevated fractions, such as those at or above ten percent, being linked to worsened overall survival.
Serial monitoring of the tumor fraction over time is a powerful tool for assessing a patient’s response to therapy. A sustained drop in the circulating tumor fraction signals that the treatment is successfully reducing the number of viable cancer cells. Conversely, an increase in the fraction can be an early indicator of disease progression, therapeutic resistance, or recurrence, sometimes months before detection by traditional imaging methods.
Tumor fraction also plays a role in interpreting liquid biopsy results for treatment selection. A sufficiently high tumor fraction, often defined as one percent or more, provides confidence in the accuracy of the overall test. When the fraction is high, a negative finding for an actionable mutation is considered an informative negative, suggesting the alteration is truly absent from the tumor.
If a liquid biopsy returns a negative result but the corresponding tumor fraction is very low (e.g., below one percent), the result is considered indeterminate. This low fraction suggests the assay may not have sampled enough tumor DNA to reliably rule out a mutation, increasing the risk of a false negative. In these scenarios, the low tumor fraction prompts the physician to prioritize follow-up tissue testing. The measurement is also foundational for detecting minimal residual disease (MRD) after surgery.
Biological Factors Affecting Tumor Fraction Measurement
Tumor fraction is influenced by several biological and pre-analytical variables, not solely tumor size. The rate at which cancer cells release DNA into the bloodstream, known as shedding, varies significantly between tumor types. Some cancers, like colorectal carcinoma, are “good shedders,” while others, such as renal cell carcinoma, are “poor shedders.”
Tumor aggressiveness also affects shedding, as faster-growing tumors tend to release more DNA fragments into the circulation. Tumor heterogeneity is another factor, where different regions of a single tumor possess distinct genetic profiles. This variation can lead to a discrepancy between the tumor fraction calculated from a single tissue biopsy site and the fraction measured in the systemic circulation.
Sample collection and processing methods introduce additional variability, particularly for liquid biopsies. Pre-analytical factors, such as the type of blood collection tube or the time elapsed before plasma processing, can affect the stability of the cell-free DNA. Careful standardization of these steps is necessary to ensure the tumor fraction measurement is accurate and reliable.