Cell-Free DNA Detection of Tumor Mutations in Heterogeneous, Localized Prostate Cancer Via Targeted, Multiregion Sequencing

Abstract

PURPOSE Cell-free DNA (cfDNA) may allow for minimally invasive identification of biologically relevant genomic alterations and genetically distinct tumor subclones. Although existing biomarkers may detect localized prostate cancer, additional strategies interrogating genomic heterogeneity are necessary for identifying and monitoring aggressive disease. In this study, we aimed to evaluate whether circulating tumor DNA can detect genomic alterations present in multiple regions of localized prostate tumor tissue. METHODS Low-pass whole-genome and targeted sequencing with a machine-learning guided 2.5-Mb targeted panel were used to identify single nucleotide variants, small insertions and deletions (indels), and copy-number alterations in cfDNA. The majority of this study focuses on the subset of 21 patients with localized disease, although 45 total individuals were evaluated, including 15 healthy controls and nine men with metastatic castration-resistant prostate cancer. Plasma cfDNA was barcoded with duplex unique molecular identifiers. For localized cases, matched tumor tissue was collected from multiple regions (one to nine samples per patient) for comparison. RESULTS Somatic tumor variants present in heterogeneous tumor foci from patients with localized disease were detected in cfDNA, and cfDNA mutational burden was found to track with disease severity. Somatic tissue alterations were identified in cfDNA, including nonsynonymous variants in FOXA1, PTEN, MED12, and ATM. Detection of these overlapping variants was associated with seminal vesicle invasion ( P = .019) and with the number of variants initially found in the matched tumor tissue samples ( P = .0005). CONCLUSION Our findings demonstrate the potential of targeted cfDNA sequencing to detect somatic tissue alterations in heterogeneous, localized prostate cancer, especially in a setting where matched tumor tissue may be unavailable (ie, active surveillance or treatment monitoring).

Early Plasma Circulating Tumor DNA as a Potential Biomarker of Disease Recurrence in Non-metastatic Prostate Cancer

“…Although the target gene sequencing via liquid biopsy for nmPCa is hampered by the low overall abundance of ctDNA [22], we found that ctDNA was detectable 65.5% of the studied patients, which is consistent with a previous study that has reported the variant detection rate of 57% [23]. Additionally, the clinicopathological features including PSA, Gleason score and clinical stage were not strongly associated with the ctDNA status in the present study, but the patients with aggressive disease subtypes tended to have detectable ctDNA.…”

“…Specially, we observed that ctDNA samples shared no concurrent alteration with tumor samples. As ctDNA proves to have the potential ability to capture both likely clonal and subclonal alterations from multiple tumor cell populations [23], our results substantially support that ctDNA reflecting the comprehensive mutational status could be used in the evaluation of heterogeneous nmPCa.…”

Spatiotemporal genomic profiling of intestinal metaplasia reveals clonal dynamics of gastric cancer progression

“…Our study also chiefly used Mutect2 as the main variant caller due to its sensitivity in detecting low VAF (<1%) somatic mutations. 63 , 64 , 65 While low VAF mutations are more challenging to experimentally validate, our data suggests that a substantial number of these mutations are of functional significance, through integration of existing databases ( STAR methods ), exhibition of mutational signatures similar to higher VAF mutations ( Figures S1 E and S1F), and being rarely identified in control blood samples subjected to the same sequencing and analysis pipeline ( STAR methods ). A third limitation was that while we were able to validate the presence of several IM driver genes in an independent cohort, the current lack of other large-scale IM genomic datasets with mature follow-up information prevented us from independently validating the genome-clinical predictive models.…”

Liquid Biopsy in Diagnosis and Prognosis of Non-Metastatic Prostate Cancer

“…In its turn, ctDNA may be an object for identifying clinically relevant genomic alterations and tumor subclones. Thus, in the study by Chen et al [ 45 ], somatic tissue alterations were identified in ctDNA derived from the blood plasma of PCa patients with localized prostate cancer, in 57% of cases, including such alterations as nonsynonymous variants in FOXA1, PTEN, MED12, and ATM.…”