Blood samples, DNA extraction and ctDNA analysis
breast cancer
BLOOD, BREAST CANCER
Blood samples were collected prior to the 5th cycle of neoadjuvant treatment (midterm) and before and after breast cancer surgery. The preoperative blood samples were obtained 0–18 days before surgery (after completion of neoadjuvant treatment), and the postoperative blood samples were obtained 4–46 days after surgery. Plasma isolation and DNA extraction was performed as described previouslyThe assays are described in detail in the supplementary material. Bisulfite converted DNA extracted from blood and breast tissue from healthy women was used to test the specificity of the multiplex assay (Figure S3). The limit of blank (LOB) was determined with a 95% confidence limit by analyzing plasma samples from healthy women (Figure S4). A blood sample was defined as ctDNA-positive when the signal for one or more of the targets described above was above the LOB. The ctDNA analysis of plasma samples was performed blinded to clinical outcomes.