Parsons, Heather ARhoades, JustinReed, Sarah CGydush, GregoryRam, PriyankaExman, PedroXiong, KanLo, Christopher CLi, TianyuFleharty, MarkKirkner, Gregory JRotem, DenisseCohen, OfirYu, FangyanFitarelli-Kiehl, MarianaLeong, Ka WaiHughes, Melissa ERosenberg, Shoshana MCollins, Laura CMiller, Kathy DBlumenstiel, BrendanTrippa, LorenzoCibulskis, CarrieNeuberg, Donna SDeFelice, MatthewFreeman, Samuel SLennon, Niall JWagle, NikhilHa, GavinStover, Daniel GChoudhury, Atish DGetz, GadWiner, Eric PMeyerson, MatthewLin, Nancy UKrop, IanLove, J ChristopherMakrigiorgos, G MikePartridge, Ann HMayer, Erica LGolub, Todd RAdalsteinsson, Viktor AengP50 CA168504/CA/NCI NIH HHS/R01 CA221874/CA/NCI NIH HHS/Clin Cancer Res. 2020 Jun 1;26(11):2556-2564. doi: 10.1158/1078-0432.CCR-19-3005. Epub 2020 Mar 13.
PURPOSE: Existing cell-free DNA (cfDNA) methods lack the sensitivity needed for detecting minimal residual disease (MRD) following therapy. We developed a test for tracking hundreds of patient-specific mutations to detect MRD with a 1,000-fold lower error rate than conventional sequencing. EXPERIMENTAL DESIGN: We compared the sensitivity of our approach to digital droplet PCR (ddPCR) in a dilution series, then retrospectively identified two cohorts of patients who had undergone prospective plasma sampling and clinical data collection: 16 patients with ER+/HER2- metastatic breast cancer (MBC) sampled within 6 months following metastatic diagnosis and 142 patients with stage 0 to III breast cancer who received curative-intent treatment with most sampled at surgery and 1 year postoperative. We performed whole-exome sequencing of tumors and designed individualized MRD tests, which we applied to serial cfDNA samples. RESULTS: Our approach was 100-fold more sensitive than ddPCR when tracking 488 mutations, but most patients had fewer identifiable tumor mutations to track in cfDNA (median = 57; range = 2-346). Clinical sensitivity was 81% (n = 13/16) in newly diagnosed MBC, 23% (n = 7/30) at postoperative and 19% (n = 6/32) at 1 year in early-stage disease, and highest in patients with the most tumor mutations available to track. MRD detection at 1 year was strongly associated with distant recurrence [HR = 20.8; 95% confidence interval, 7.3-58.9]. Median lead time from first positive sample to recurrence was 18.9 months (range = 3.4-39.2 months). CONCLUSIONS: Tracking large numbers of individualized tumor mutations in cfDNA can improve MRD detection, but its sensitivity is driven by the number of tumor mutations available to track.