In a study published in cancer discoveryCanadian researchers tested the use of a cell-free DNA (cfDNA)-based multimodal liquid biopsy assay for early cancer detection in patients with Li-Fraumeni syndrome.
The researchers found that the assay showed improved detection sensitivity compared to unimodal assays and could also detect cancer-related signals before traditional cancer diagnosis.
Li-Fraumeni syndrome (LFS) is a genetic disease caused by germline mutations in tumor suppressor genes. TP53 (abbreviation for tumor protein 53). This increases a carrier’s risk of developing at least one type of cancer by up to 100%.
Elevated cancer risk requires frequent surveillance in the form of diagnostic tests, tests, and imaging, as early detection is associated with improved outcomes for cancer patients. However, there are several physical, economic, psychological, and logistical barriers to intensive monitoring of LFS patients.
Liquid biopsy has emerged as a promising and relatively less invasive solution that can accurately detect cancer-related genetic signatures such as circulating tumor DNA (ctDNA) in blood samples, thereby reducing the logistical burden of testing. barriers are eliminated.
To address the lack of data on the use of cfDNA in high cancer risk groups such as LFS patients, researchers in this study developed a cfDNA-based multimodal approach to detect a wide range of cancer-related signals in patients. Developed.
In this study, 193 venous blood samples (154 cancer-negative and 39 cancer-positive) were retrospectively collected from 89 people with the following diseases: TP53 mutation(TP53m) Age range from 1 to 67 years.
Carriers were classified as follows: those who had never had cancer (LFS-H, n=42), those with a history of cancer and who had recovered from cancer (LFS-PC, n= 21), active cancer patients (LFS-AC, n=21) n=26). about 18 TP53m-Carriers were “phenoconverters” who could switch between cancer-negative and cancer-positive states or have multiple cancers.
Median clinical follow-up for this study was 48.1 months.Consistent with previous literature, the current cohort TP53m– Carriers had a higher prevalence of breast cancer compared to other types.
DNA and peripheral blood mononuclear cells (PBMCs) were extracted from blood samples. Genomic DNA was extracted from PBMCs and DNA libraries were prepared for targeted panel sequencing (TS), shallow whole genome sequencing (sWGS), and cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq).
Bioinformatics tools such as ConsensusCruncher, Genome Analysis Toolkit, MuTect2, and MedRemix were used for targeted sequence variation analysis and cell-free methylome analysis.
Various ctDNA metrics were determined, including somatic. TP53mcopy number, tumor fraction, genome-wide fragmentation score, TP53 Fragmentation score, global cancer methylation score, LFS-specific, and LFS breast cancer methylation score. Sensitivity and specificity of the individual assays and the combined assay were estimated.
Results and discussion
A higher proportion of short DNA fragments (<150 bp) was observed compared to healthy controls. TP53m-Further increase in carriers and cancer positive people TP53m– Comparison of carriers and cancer-negative carriers.
Integrating genomic, fragment, and epigenomic analysis of 38 cancer-positive samples allows detection of cancer-related signals in 81.6% of samples, with a sensitivity improvement of 31.6% to 55.8% compared to unimodal analysis. was obtained.
The improvement in detection sensitivity was more pronounced in late-stage cancer samples than in early-stage cancer samples. The false positive rate within the samples was found to be 18.3%, while only 2 out of 57 samples were found to be false negatives.
When the cancer is gone TP53m When analyzing carriers, the negative predictive value was found to be 95.4%, an improvement of 16.6 to 34.6% over unimodal analysis. Cancer-related signals could be detected in his 35.6% of patients at a clinically cancer-free stage. However, intensive follow-up is required to determine which of these are actually false positives.
When analyzing individual LFS cases, multimodal analysis was found to be as sensitive or superior to traditional clinical screening approaches. Therefore, according to this study, incorporating cfDA-based diagnosis can complement existing diagnostic and management methods for cancer, especially in high-risk populations.
These integrated tests are relatively less invasive and may allow for increased testing frequency in high-risk patients. However, this study is limited by its retrospective design and low adoption rate of cfMeDIP-seq in clinical practice compared to TS and sWGS methods.
Further studies are needed to clinically validate this cfDNA-based method and improve outcomes in LFS patients.
In conclusion, the integrated cfDNA approach used in this study shows improved sensitivity and earlier detection of cancer in LFS patients compared to conventional imaging.
The use of available multimodal assays in combination with traditional screening methods has the potential to improve the sensitivity, specificity, and robustness of cancer detection and optimize the care of patients at high cancer risk.