1. TATFACFAC Combined NEO pCRRDTotalpCRRDTotalpCRRDTotalpCRRDTotal ER+302482781719721413758960521581 ER-631241874992141226385134279413 Total933724656628935535139174194800994 GEOGSE25066 GSE23988 GSE20194 GSE20271 GSE22093 GSE20271 Table1: Clinical Summary Discovery Table 2: Clinical Summary Validation Table 3: Clinical Summary IHC Cohort AC+ T or I AC+/- T pCRRDTotalpCRRDTotal ER+10839355358 ER-5383136112738 Total63166229168096 GEOGSE41998GSE22226

2. FactorN (%) Age, (years) Mean Median 57.79 55.80 Nuclear Grade 123123 6 (8.2) 31 (41.8) 37 (50.0) ER Status Positive Negative 47 (63.5) 27 (36.5) PR status Positive Negative 38 (51.3) 36 (48.7) Her2 status Positive Negative 17 (24.0) 57 (77.0) Diagnosis IDC ILC IDLC 62 (83.8) 9 (12.2) 3 (4.0) Treatment ACT Platinum AC CT TFAC Other Unknown 35 (47.3) 12 (16.2) 5 (6.8) 6 (8.1) 3 (4.1) 10 (13.4) Table 3: Clinical Summary IHC Cohort

3. Discovery Data SetsValidation Data Sets GEOGSE25066GSE23988 GSE20271GSE22093GSE41998GSE22226 pCRRDpCRRDpCRRDpCRRDpCRRDpCRRDpCRRD ER+30248725713368310321083553 ER-63124131627521350183753831127 Mean age, y (range) 48.32 (24-75) 50.16 (24-75) 46.81 (34-53) 49.6 (26-67) 48.41 (31-64) 52.13 (26-79) 50.53 (39-59) 50.80 (26-74) 48.25 (31-75) 49.28 (30-78) 45.43 (29-69) 49.07 (25-79) 43.44 (33-56) 48.49 (29-65) Mean tumor size, mm (range)--- 5.96 (2.3-10) 6.95 (2-17.5)---- --- 5.68 (2.5-12) 7.24 (0-99) Clinical T- stage % T01.080.54--- ----1.08--- 1.45--- T16.455.38--- 11.767.57---1.50---2.90--- 2.5 T250.54 ---2.4444.1257.3057.896.7753.5752.17--- 56.2541.25 T332.2626.084029.2726.4716.7610.5339.8532.1424.64--- 43.7553.75 T49.6817.476068.2917.6516.7631.5821.8014.2918.84--- N/A----0.5430.08--- 2.5 Lymph node status % Negative29.0332.263534.1514.7131.3531.5832.337.1427.54--- Positive70.9767.746565.8585.2968.1168.4266.9210.7137.68--- Unknown----------0.54---0.7582.1434.78--- Grade % 11.087.26---2.442.946.49---10.53---4.35--- 10 211.8341.671539.028.8248.6510.5339.1017.8634.78--- 18.7548.75 378.4945.977553.6685.2940.5452.6336.0971.4339.13--- 7541.25 42.152.69--- 6.25--- N/A6.452.42104.882.944.3236.8414.2910.7121.74--- Neoadjuvant Therapy TATFAC TFAC/FACFACAC + T or IAC +/- T Table 4: Patient Characteristics Discovery and Validation Cohorts

4. Response KS P = 2.58E-09 GGI Signature - TA KS P = 1.04E-09 CIN70 Signature - TA Response S1 S2 Response KS P = 0.00108 RB Signature - TFAC GGI Signature - TFAC Response KS P = 0.00769 CIN70 Signature - TFAC Response KS P = 5.57E-05 Oncotype DX Proliferation Genes - TFAC Response KS P = 0.06619 Mammaprint Signature - TFAC Response KS P = 0.0015

5. RB Signature – ER+ Response KS P = 0.0011 RB Signature – ER- Response KS P = 0.00045 GGI Signature – ER+ Response KS P = 9.78E-05 GGI Signature – ER- Response KS P = 0.001787 CIN70 Signature – ER+ ResponseKS P = 0.00018 CIN70 Signature – ER- Response KS P = 0.00016 Oncotype DX Proliferation Genes – ER+ Response KS P = 0.00073 Response Oncotype DX Proliferation Genes – ER- KS P = 0.04734 S3 Mammaprint Signature – ER+ Mammaprint Signature – ER- Response KS P = 0.01288 KS P = 00131

6. DEK BCAM S4 S5 BCAM-IHC DEK-IHC

7. S6 Theraprint Signature Genes