This study is a correlative analysis project of a phase 2 trial of adjuvant chemotherapy in breast cancer (SBG2004-1 trial), in which 3 regimens of chemotherapy were compared. Archived tumor tissue from about 100 patients in the study will be used for targeted DNA sequencing (GMCK solid cancer panel) and a multiplex immunohistochemistry (IHC) assay using 9 markers (with focus on immune cell markers). One of the main objectives of the entire study is to test the association between mutational load, intratumoral heterogeneity (ITH) and host immune response. Conflicting data have been reported. One hypothesis maintains that a greater level of heterogeneity at the genomic and cellular level leads to a greater number of neoantigens, a stronger immune response (represented by a greater immune infiltrate) and better outcomes. In contrast, it has also been proposed that a low number of infiltrating immune cells causes diminished immune surveillance and immunoediting and thus leads to increased clonal heterogeneity.
Germline DNA will be extracted from a blood sample collected at inclusion in the trial to distinguish somatic (vs. germline) mutations. DNA libraries will be constructed using the Illumina TruSeq DNA PCR-free library prep kit. Panel DNA sequencing will be performed in all the available tumor samples using the Illumina NovaSeq 6000 System. The somatic mutational load will be calculated from insertions, deletions and substitutions in the coding region of genes, while structural rearrangements, aneuploidy, translocations or duplications as well as silent mutations will be excluded from the analysis. Genomic heterogeneity will be assessed using the MATH (mutant allele tumor heterogeneity) method, which uses the broadness of the distribution of mutant allele frequencies as a measure of ITH. Sequencing will be performed at the Clinical Genomics facility, at the Science for Life Laboratory (SciLifeLab), Stockholm.