(A) Genome-wide log2 copy ratios derived from targeted error-correction sequencing (TEC-Seq) data using CNVkit (Methods) are shown for each plasma sample, with copy number gains indicated in red and losses indicated in blue. Each row corresponds to a single plasma sample and rows are ordered with respect to consecutive sampling timepoints analyzed for each patient. (B-F) Genome-wide copy number profiles are shown for patients with matched tumor (WES) and plasma samples analyzed. We observed a high concordance between copy number profiles derived by whole exome sequencing, our approach (CNVkit) and ichorCNA for patients with detectable aneuploidy in plasma. (B) Patient 3 had undetectable ctDNA according to tumor-specific sequence alterations. However, this patient was classified as a molecular responder based on decrease of plasma aneuploidy to normal ploidy by the week 8 timepoint. (C) Patient 5 was classified as a molecular progressor based on the presence of tumor-specific sequence alterations and plasma aneuploidy across all timepoints analyzed. (D) Similarly, patient 9 was classified as a molecular progressor based on the persistence of mutations and plasma aneuploidy, which were detectable across all sampled timepoints from this patient. (E, F) Plasma copy number profiles for patients 11 and 14 indicated ploidy close to normal ploidy across all timepoints analyzed. These patients were classified as molecular responders based on tumor-derived sequence alterations.
ARTICLE ABSTRACT
Patients with small-cell lung cancer (SCLC) have an exceptionally poor prognosis, calling for improved real-time noninvasive biomarkers of therapeutic response.
We performed targeted error-correction sequencing on 171 serial plasmas and matched white blood cell (WBC) DNA from 33 patients with metastatic SCLC who received treatment with chemotherapy (n = 16) or immunotherapy-containing (n = 17) regimens. Tumor-derived sequence alterations and plasma aneuploidy were evaluated serially and combined to assess changes in total cell-free tumor load (cfTL). Longitudinal dynamic changes in cfTL were monitored to determine circulating cell-free tumor DNA (ctDNA) molecular response during therapy.
Combined tiered analyses of tumor-derived sequence alterations and plasma aneuploidy allowed for the assessment of ctDNA molecular response in all patients. Patients classified as molecular responders (n = 9) displayed sustained elimination of cfTL to undetectable levels. For 14 patients, we observed initial molecular responses, followed by ctDNA recrudescence. A subset of patients (n = 10) displayed a clear pattern of molecular progression, with persistence of cfTL across all time points. Molecular responses captured the therapeutic effect and long-term clinical outcomes in a more accurate and rapid manner compared with radiographic imaging. Patients with sustained molecular responses had longer overall (log-rank P = 0.0006) and progression-free (log-rank P < 0.0001) survival, with molecular responses detected on average 4 weeks earlier than imaging.
ctDNA analyses provide a precise approach for the assessment of early on-therapy molecular responses and have important implications for the management of patients with SCLC, including the development of improved strategies for real-time tumor burden monitoring.
