Liquid Biopsy Screening for Early Detection of Cancers in Patients

Highly Sensitive, Specific and Low Cost Method of Detecting Cancer in Bodily Fluids by Analyzing the Accessibility and Expression of Cancer Master Gene Regulators

This non-invasive method of liquid biopsy screening much more sensitively and specifically detects cancer in patients, including those with rare or novel mutations with cost in the order of less than $100 per test, compared to current liquid biopsy methods.

Available cancer screenings that utilize liquid biopsy rely on massive deep genomic sequencing to detect pre-determined cancer markers in bodily fluids. They are costly and are fraught with high false negative and false positive rates. Rare mutations are present in a sizable share of cancers; however, existing liquid biopsy tests designed for specific known mutation markers are prone to missing their presence in the sample. This new liquid biopsy screening assay detects cancer by analyzing the accessibility and expression profile of cancer master gene regulators, the key genes controlling the cancer initiation and progression of a specific cancer type. Detection of cancer master regulator expression provides a more sensitive and comprehensive assay than current methods. Many cancer master regulators are developmentally restricted and their expression is repressed in normal adult cells. Therefore, the inappropriate temporal accessibility or expression of cancer specific master regulators indicates a cancer state.

Researchers at the University of Florida have developed an improved liquid biopsy cancer screening assay. The assay detects abnormal chromosome accessibility of cancer master gene regulators or expression of transcription factors downstream of master gene regulators in liquid biopsy samples. Since the screening is not specific for individual gene mutations, the assay detects cancers caused by rare or novel mutations that might be missed by other liquid biopsy screens. The cost of the assay is less than $100 per test as it uses selective sequencing of amplified targets.

Application

Low cost, highly sensitive and specific biopsy screening method that detects cancer in patients, including those caused by rare or novel mutations

Advantages

• Uses chromosome accessibility or expression profiles of master gene regulators with high expression specifically during a cancer state to detect when cancer is present in patients in an early stage
• The assay also can be used to monitor treatment response in patients with existing cancer
• The assay is not specific to individual gene mutations, increasing its ability to detect cancers caused by rare or novel mutations
• High sensitivity and specificity
• Extremely low cost, allowing it to be included in routine annual health check-ups

Technology

This liquid biopsy assay identifies cancer cells by determining the status of chromosomal accessibility through analysis of epigenetic markers on genomic regions encoding cancer master gene regulators that are highly specific to the cancer state, and by measuring the expression level of one or more genes downstream of these master regulators.