In Sweden, the definition of TNBC is a tumor with ≤10% of cells with IHC-staining for ER and PR (thus including tumors with 1-10% stained cells) and an IHC HER2-staining score < 2, or for patients with IHC 2+ a non-amplified ISH-status. During September 1 2010 to March 31 2015, 408 patients were diagnosed with TNBC (localized or advanced disease with specified treatment status) in the Skåne healthcare region in southern Sweden, Scandinavia, based on data from the Swedish national breast cancer quality registry (NKBC) (Figure 1). 340 of these patients were enrolled in the SCAN-B study5 (link),33 (link),34 (link) (ClinicalTrials.gov ID NCT02306096), which is a prospective, observational, population-based cohort study, from which 254 with concurrent RNAseq were selected for extensive clinical review and WGS. Of reviewed cases, 153 (60%) patients were eligible for OS/IDFS survival analysis after standard of care adjuvant chemotherapy (FEC-based [combination of 5 fluorouracil, epirubicin, and cyclophosphamide] ± a taxane in 96% of cases) according to national guidelines. Of these (irrespective of clinical endpoint status), 41% had ≥5 years of follow-up, 25% 4-5 years, 31% 2-4 years, and 4% <2 years of follow-up. 148 of 153 patients (97%) were eligible for relapse analysis, of which 20% developed a relapse of some type (loco-regional or distant). Remaining cases received either neoadjuvant treatment, no adjuvant treatment (n=58), or were not treated in an adjuvant context (e.g. metastatic disease at diagnosis). As part of routine oncogenetic clinical screening, 49 of 254 recruited patients were previously screened for pathogenic germline variants in BRCA1 and BRCA2, with 12 positive findings (nine BRCA1- and three BRCA2-carriers). Patient cohort characteristics, enrolled SCAN-B patients, WGS analysed SCAN-B patients, and WGS analysed SCAN-B treatment subsets are described in Supplementary Table S2. Individual patient characteristics are provided in the Supplementary Data Table.