Fig. 1

A Schematic of the bioinformatics pipeline. After whole genome sequencing of cell-free DNA from body fluids, adapter sequences are trimmed and aligned to the human genome. The cancer pipeline aligns human reads and counts reads over moving windows across the human genome [12, 17]. The microbial pipeline aligns non-human reads to a microbial database, taxonomically classifies the microbial aligned reads, and identifies pathogens [2, 18]. B Sample type composition of the 205 body fluid samples. C Contingency table comparing conventional cancer detection to sequencing in patients with malignancy. Negative controls did not have a history of cancer and were explained by infections with positive microbiological testing (top). Patients with cancer detected by positive cytology and/or flow cytometry testing of body fluid (bottom). Patients diagnosed with cancer but with negative or ambiguous detection based on conventional clinical testing in the same fluid by cytology or cytometry. D Detection accuracy and tumor fractions. Detection of malignancies through CNV detection in 2 cancer-positive case categories described in C. The “New” category refers to samples collected from patients with a new diagnosis who have no previous cancer history and have not been treated. Tumor fractions were estimated through the magnitude of copy changes detected (see online Methods, “Equation 1”)