Fig. 1

Study design. Our study mainly consisted of three stages, including discovery, validation by developing classifiers and promoter changes analysis in cfDNA during EC-T treatment. In the discovery stage, the genes with differential coverage in cfDNA of between pCR and non-pCR patients were identified. In the validation stage, different classifiers were developed by using the differential features. In the last stage, differential promoter profile changes due to EC-T treatment in cfDNA of between pCR and non-pCR patients were analyzed. cfDNA, cell-free DNA; EC-T, 3 or 4 cycles of epirubicinneoa/cyclophosphamide (EC) treatment and subsequent 3 or 4 cycles of docetaxel treatment before surgery; pCR, pathological complete response; non-pCR, non-pathological complete response