A Novel Tissue-Free Method to Estimate Tumor-Derived Cell-Free DNA Quantity Using Tumor Methylation Patterns.

Area of Science:

• Oncology
• Genomics
• Biochemistry

Background:

• Estimating circulating tumor DNA (ctDNA) abundance is crucial for approximating tumor burden and has significant clinical applications.
• Current methods for ctDNA quantification often require matched tumor tissue, limiting their broad applicability.
• Cell-free DNA (cfDNA) methylation patterns hold potential for non-invasive cancer detection and monitoring.

Purpose of the Study:

• To develop and validate a novel statistical method for quantifying ctDNA abundance using cfDNA methylation patterns.
• To establish a methylation-based metric, tumor methylated fraction (TMeF), for estimating ctDNA levels without matched tumor biopsies.
• To assess the correlation of TMeF with established ctDNA quantification methods and clinical parameters.

Main Methods:

• Developed a statistical algorithm to identify cancer-indicative differentially methylated regions (DMRs) by comparing cancer tissue and non-cancer cfDNA methylation data.
• Quantified TMeF by counting cfDNA fragments matching hyper/hypo-methylated patterns within DMRs in plasma samples.
• Validated TMeF by correlating it with small variant allele fraction (SVAF) and assessing performance in synthetic cfDNA dilutions.

Main Results:

• The novel method successfully estimated ctDNA abundance via TMeF, even at low concentrations (10^-3 to 10^-4).
• TMeF showed a strong correlation (Spearman's coefficient: 0.73) with SVAF estimates of ctDNA.
• Synthetic dilution experiments demonstrated TMeF accuracy, with 95% and 77% of samples within two-fold at 10^-3 and 10^-4 dilutions, respectively.
• TMeF levels positively correlated with cancer stage and tumor size, and inversely correlated with patient survival probability.

Conclusions:

• A novel, broadly applicable statistical method allows for the estimation of ctDNA abundance using cfDNA methylation patterns.
• The developed tumor methylated fraction (TMeF) provides a non-invasive approximation of tumor burden without the need for tumor biopsies.
• This methylation-based approach has the potential to significantly impact clinical decision-making in oncology by enabling non-invasive tumor burden monitoring.