Neoadjuvant chemotherapy alters the genomic landscape and immune microenvironment of breast cancers

To characterize the effects of neoadjuvant chemotherapy (NAC) on the genome,
transcriptome and tumor infiltrating leukocytes (TILs), we have conducted whole
exome and whole transcriptome sequencing of a comprehensive, longitudinal breast
cancer cohort consisting of 146 cases and 281 paired tumor samples. In total, 52 (38%)
patients achieved pathologic complete response (pCR) while 85 patients (62%) had
residual disease with standard chemotherapy regimen. Tumor biopsies were collected
for each patient at three time points – pre-treatment, three weeks after the first cycle of
anthracycline and cyclophosphamide (AC) and at the time of surgery after 3 more cycles
of AC followed by 4 cycles of taxane or taxane plus Herceptin in case of HER2+ subtype.EGA study EGAS00001003354