Fig. 1

Summary of the methods used to generate 3D organoids and analyze cfDNA samples. A Overview of the organoid culture method. Triplicate normal lung, normal gastric, and gastric cancer organoids were seeded onto transwell inserts with a pore size of 0.4 μm, which prevented the transmission of cells. The medium was replaced with Y-27632-free medium after 48 h (day 2). After 96 h of culture in the proliferative state (day 6), the medium was harvested from the outer well and replaced with medium containing 2 µM staurosporine to induce apoptosis. After incubation with staurosporine for 24 h (day 7), the medium was collected from the outer wells. B Processing of cfDNA from culture medium and blood. Blood collected from a healthy donor and media from proliferative and apoptotic organoids were subjected to double centrifugation followed by cfDNA extraction. A portion of the cfDNA was used for the measurement of fragment size via capillary electrophoresis, and a portion was used for the preparation of single-stranded libraries. The prepared libraries were subjected to whole-genome sequencing (WGS). C WGS data were used to analyze various fragmentomic features, including fragment size, footprints, end motifs, repeat types at the end, and topology (circular DNA)