In this study we analyzed 458 plasma cell-free DNA samples collected at baseline and progression timepoints from 202 metastatic castration resistant prostate cancer patients treated with the AR signaling inhibitors abiraterone and enzalutamide in the context of a randomized phase II trial. We identified numerous treatment-driven somatic changes converging upon the AR gene.
In this multi-centre randomized phase II trial, we compared the efficacy of cabazitaxel and androgen receptor pathway inhibitors in 95 patients with metastatic castration resistant prostate cancer, and analyzed serial plasma cfDNA samples from all participating patients.
In this multi-centre randomized phase II crossover trial, we investigated the relative efficacy of abiraterone and enzalutamide in 202 patients with metastatic castration resistant prostate cancer.
In this study, we analyzed plasma cell-free DNA biopsies collected from 202 patients participating in a randomized phase II crossover trial comparing abiraterone and enzalutamide in metastatic castration resistant prostate cancer. We showed that circulating tumor DNA abundance in blood, along with TP53 alterations and homologous recombination repair pathway defects detected in circulating tumor DNA associate with poor treatment response. We also demonstrated that somatic genomic rearrangements producing ligand-independent AR isoforms can be detected in circulating tumor DNA.
In this study, we analyzed plasma cell-free DNA samples collected from 53 patients with newly diagnosed metastatic castration-sensitive prostate cancer, and found a detectable circulating tumor DNA fraction in 74% of patients. We also showed that circulating tumor DNA is eliminated from the bloodstream within a week after initiation of androgen deprivation therapy. Finally, we demonstrated high concordance for somatic mutations detected in diagnostic tissue biopsies and plasma cell-free DNA biopsies.
In this study, we analyzed 45 pairs of time-matched metastatic tissue biopsies and plasma cell-free DNA biopsies collected from 42 patients with metastatic prostate cancer. We showed that 76% of cell-free DNA samples had a detectable level of ctDNA, and that 94% of somatic mutations detected in metastatic tissue were concordantly detected in matched cell-free DNA samples. This was the first published study systematically comparing a large cohort of metastatic tissue biopsies and cell-free DNA biopsies in the context of metastatic prostate cancer.
In this study, we analyzed plasma cell-free DNA samples from 433 metastatic prostate cancer patients with detectable circulating tumor DNA, and identified 16 patients with a hypermutator phenotype driven by a defective DNA mismatch repair pathway. These patients exhibited a tendency towards tumor suppressor inactivation by mutation rather than copy number loss, and a high frequency of hotspot mutations in AKT1, PIK3CA, CTNNB1, and the AR ligand binding domain. They also had a poor clinical prognosis and exhibited high clonal diversity.
In this study, we analyzed targeted germline sequencing data from 319 patients with metastatic castration resistant prostate cancer, and confirmed previous reports that 8 - 12% of these patients harbor germline defects disrupting the homologous recombination repair (HRR) pathway. We showed preliminary evidence that these patients have a poor prognosis on initial androgen deprivation therapy. We also collected plasma cell-free DNA biopsies from multiple patients, and demonstrated that germline defects in the HRR pathway were accompanied with somatic loss-of-heterozygosity in almost all cases, and that these loss-of-heterozygosity events could be detected in circulating tumor DNA.
In this study, we analyzed plasma cell-free DNA biopsies collected from 51 patients with aggressive bladder cancer, including 37 patients with metastatic disease. We showed that the majority of patients with metastatic bladder cancer carry detectable levels of circulating tumor DNA in their blood, enabling genomic characterization. This was the first published study testing the efficacy of plasma cell-free DNA biopsies in aggressive bladder cancer.
In this study, we sequenced the untranslated regions of 72 established driver genes in 712 plasma cell-free DNA samples collected from patients with metastatic prostate cancer and identified FOXA1 3'-UTR mutations in 12% of patients. The indel-dominant pattern of somatic mutation extended into the FOXA1 coding region, where it was shaped by clonal selection to yield a cluster of non-frameshift indels inside the forkhead domain.
In this case study, we used a plasma cell-free DNA biopsy and metastatic tissue biopsy to identify a somatic biallelic BRCA2 loss in a patient with metastatic neuroendocrine prostate cancer. The patient exhibited a dramatic response to platinum therapy and subsequent treatment with PARP inhibitors, and now several years later remains in complete remission. Resistance against PARP inhibitor treatment in BRCA2-defective patients typically arises through reversion mutations that recover the function of at least one BRCA2 copy. In a patient with BRCA2 biallelic deletion, this type of resistance cannot arise.