1. Rate of breast cancer-specific survival Months Low gene expression (N=252) High gene expression (N=37) P < 0.0001(Log-rank) a Months Low gene expression (N=118) High gene expression (N=171) P = 0.0040 (Log-rank) b Months Low gene expression (N=212) High gene expression (N=79) P = 0.51(Log-rank) c Months Low gene expression (N=172) High gene expression (N=42) P = 0.28 (Log-rank) f Months Low gene expression (N=67) High gene expression (N=147) P = 0.80 (Log-rank) e Rate of breast cancer- specific survival Months Low gene expression (N=192) High gene expression (N=22) P = 0.045 (Log-rank) d C6ORF97 C6ORF211 C6ORF96 Entire cohortER + / Her2- cohort Rate of breast cancer- specific survival Supplementary Fig. 1

2. Supplementary Fig. 2 Rate of relapse free survival Years a Rate of relapse free survival Years b Rate of relapse free survival Years c Rate of relapse free survival Years f Rate of relapse free survival Years e Rate of relapse free survival Years d Luminal ALuminal B (N=297) (N=187) (N=81) (N=175) (N=30) (N=32) (N=43) (N=41) (N=69) (N=200) (N=230) (N=286) Untreated Hormonal therapy only With chemotherapy

3. Supplementary Fig. 3 Rate of relapse free survival Years Rate of relapse free survival Years Rate of relapse free survival Years Rate of relapse free survival Years Rate of relapse free survival Years Rate of relapse free survival Years Luminal ALuminal B (N=51) (N=33) (N=43) (N=19) (N=138) (N=118) (N=307) (N=177) (N=228) (N=288) (N=97) (N=172) Untreated Hormonal therapy only With chemotherapy a b c f e d

4. Years Luminal A Luminal B (N=123) (N=60) (N=143) (N=341) Rate of relapse free survival a b Supplementary Fig. 4 Years (N=212) (N=395) Rate of relapse free survival c (N=106) (N=318) ER positive