Feasibility of enriched amplicon circulating tumor DNA sequencing to detect minimal residual disease (MRD) after prostatectomy in localized prostate cancer.

Abstract

402 Background: Nearly one third of men with prostate cancer experience relapse after radical prostatectomy, often despite achieving undetectable PSA nadir. An assay to detect minimal residual disease would be valuable to identify patients who could benefit from adjuvant therapy. Methods: Eligible patients had biopsy proven prostate cancer and planned to undergo prostatectomy for definitive therapy. Blood was drawn at pre-specified timepoints (TP) including prior to prostatectomy (TP1), on the day after surgery or at the 1-week post-op catheter removal visit (TP2), and at 1-month post-op with no interval treatment (TP3). We performed tumor-guided plasma DNA analysis using a novel method based on single-stranded adapter ligation, incorporation of unique molecular identifiers (UMIs), targeted PCR, normalization of amplicons using hybrid-capture, and targeted sequencing. Using tumor and germline exome sequencing, we designed and validated multiplexed assays to target somatic founder mutations. We prepared targeted sequencing libraries using a median of 6.7 ng input plasma DNA. Results: 11 patients were enrolled after IRB approval. 1 (9.09%) had grade group 2, 1 (9.09%) grade group 3, 5 (45.45%) grade group 4, 4 (36.36%) grade group 5 disease. Median PSA pre-op was 9.3 ng/mL (range: 1.7 – 21.47). Tumor DNA sequencing was successful and targeted assays were generated for all patients (11/11). Median number of targets tested was 20 (range 4 to 88). We analyzed 31 plasma DNA samples obtained from 11 patients. Median on-target rate in plasma DNA was 90.5% (range 76.0% to 96.3%). Prior to surgery (TP1), 5/11 (45%) patients had detectable ctDNA at a median tumor fraction of 0.077% (range: 0.006% to 3.4%). At post-op TP (TP2), the ctDNA was detectable in 7/11 patients (64%) at a median tumor fraction of 0.024% (range: 0.004% to 3.1%). Detectable ctDNA was observed at 1 month (TP3) in 5/8 patients (62.5%) at a median tumor fraction of 0.022% (range 0.010% to 0.037%). For an exploratory analysis, we examined whether persistent ctDNA detection at the 1 month TP3 was associated with later relapse. Of the 5 patients with PSA relapse, 3 (60%) of patients had detectable residual ctDNA at TP3 with median follow up time of 61.75 months. Conclusions: Localized prostate cancer has been noted to have low tumor shed, limiting meaningful ctDNA detection rates with prior assays (Hennigan 2019). Our results show promising feasibility of a novel tumor-informed ctDNA assay in this setting. In addition, there was preliminary evidence of residual ctDNA detection predicting relapse.