Fig S4 from Dynamics of Sequence and Structural Cell-Free DNA Landscapes in Small-Cell Lung Cancer
Year: 2023
Type: other
Abstract: (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.
Language: English
Subfield: Cancer Research
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W4366253532