Supplementary Figure S1 from Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer
Year: 2024
Type: supplementary-materials
Abstract: Supplementary Fig.S1 Overview of branched logic architecture used for the classification of variant cellular origin in plasma. Cell-free DNA (cfDNA) variants in plasma were assigned an origin classification of tumor-, germline- or clonal haematopoiesis (CH)-derived, using all available sequencing data. Patients with matched tumor tissue next-generation sequence (NGS) data available (n=24) from either whole exome sequencing or clinical tumor mutation profiling, were evaluated using our tumor-informed approach (Methods) for the identification of circulating tumor DNA (ctDNA) variants. As single tissue biopsies can be limited by sampling heterogeneity, patients with matched tumor NGS but no detectable tissue-specific variants in plasma (n=3) were further evaluated using our WBC-informed approach for identification of ctDNA variants missing by tissue sequencing. Patients with no detectable tumor-derived variants in plasma according to both approaches were subsequently classified as undetectable. Six patients without matched tumor tissue NGS available were evaluated using our WBC-informed approach for assignment of variant cellular origin (Methods). VUO, variant of unknown origin.
Authors: Joseph C. Murray, Lavanya Sivapalan, Karlijn Hummelink, Archana Balan, James R. White, Noushin Niknafs, Lamia Rhymee, Gavin Pereira, Nisha Rao, Benny Weksler, Nathan Bahary, Jillian Phallen, Alessandro Leal, David L. Bartlett, Kristen A. Marrone, Jarushka Naidoo, Akul Goel, Benjamin Levy, Samuel Rosner, Christine L. Hann, Susan C. Scott, Josephine Feliciano, Vincent K. Lam, David S. Ettinger, Qing Kay Li, Peter B. Illei, Kim Monkhorst, Robert B. Scharpf, Julie R. Brahmer, Victor E. Velculescu, Ali H. Zaidi, Patrick M. Forde, Valsamo Anagnostou
Language: English
Subfield: Cancer Research
Domain: Life Sciences
Open Access status: gold
OpenAlex ID: W4390950652