TA TFAC FAC Combined NEO

pCR RD Total pCR RD Total pCR RD Total pCR RD TotalER+ 30 248 278 17 197 214 13 75 89 60 521 581ER- 63 124 187 49 92 141 22 63 85 134 279 413

Total 93 372 465 66 289 355 35 139 174 194 800 994

GEO GSE25066GSE23988GSE20194GSE20271

GSE22093GSE20271

Table1: Clinical Summary Discovery

Table 2: Clinical Summary Validation

Table 3: Clinical Summary IHC Cohort

AC+T or I

AC+/-T

pCR RD Total pCR RD TotalER+ 10 83 93 5 53 58ER- 53 83 136 11 27 38

Total 63 166 229 16 80 96

GEO GSE41998 GSE22226

Factor N (%)

Age, (years)

MeanMedian

57.7955.80

Nuclear Grade

123

6 (8.2)31 (41.8)37 (50.0)

ER Status

PositiveNegative

47 (63.5)27 (36.5)

PR status

PositiveNegative

38 (51.3)36 (48.7)

Her2 status

PositiveNegative

17 (24.0)57 (77.0)

Diagnosis

IDCILCIDLC

62 (83.8)9 (12.2)3 (4.0)

Treatment

ACTPlatinumACCTTFACOtherUnknown

35 (47.3)12 (16.2)5 (6.8)6 (8.1)3 (4.1)3 (4.1)10 (13.4)

Table 3: Clinical Summary IHC Cohort

Discovery Data Sets Validation Data SetsGEO GSE25066 GSE23988 GSE23988 GSE20271 GSE22093 GSE41998 GSE22226

pCR RD pCR RD pCR RD pCR RD pCR RD pCR RD pCR RDER+ 30 248 7 25 7 133 6 83 10 32 10 83 5 53ER- 63 124 13 16 27 52 13 50 18 37 53 83 11 27

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 %

T0 1.08 0.54 --- --- ---- 1.08 --- --- --- 1.45 --- ---T1 6.45 5.38 --- --- 11.76 7.57 --- 1.50 --- 2.90 --- --- --- 2.5T2 50.54 50.54 --- 2.44 44.12 57.30 57.89 6.77 53.57 52.17 --- --- 56.25 41.25T3 32.26 26.08 40 29.27 26.47 16.76 10.53 39.85 32.14 24.64 --- --- 43.75 53.75T4 9.68 17.47 60 68.29 17.65 16.76 31.58 21.80 14.29 18.84 --- --- --- ---N/A ---- 0.54 30.08 --- --- --- --- --- 2.5

Lymph node status %Negative 29.03 32.26 35 34.15 14.71 31.35 31.58 32.33 7.14 27.54 --- --- --- ---Positive 70.97 67.74 65 65.85 85.29 68.11 68.42 66.92 10.71 37.68 --- --- --- ---

Unknown --- ---- --- 0.54 --- 0.75 82.14 34.78 --- --- --- ---Grade %

1 1.08 7.26 --- 2.44 2.94 6.49 --- 10.53 --- 4.35 --- --- --- 102 11.83 41.67 15 39.02 8.82 48.65 10.53 39.10 17.86 34.78 --- --- 18.75 48.753 78.49 45.97 75 53.66 85.29 40.54 52.63 36.09 71.43 39.13 --- --- 75 41.254 2.15 2.69 --- --- --- --- --- --- --- --- --- --- 6.25 ---

N/A 6.45 2.42 10 4.88 2.94 4.32 36.84 14.29 10.71 21.74 --- --- --- ---Neoadjuvant

Therapy TA TFAC TFAC TFAC/FAC FAC AC + T or I AC +/- T

Table 4: Patient Characteristics Discovery and Validation Cohorts

Response KS P = 2.58E-09GGI Signature - TA

KS P = 1.04E-09CIN70 Signature - TA

Response

S1

S2

Response KS P = 0.00108RB Signature - TFAC

GGI Signature - TFACResponse KS P = 0.00769

CIN70 Signature - TFACResponse KS P = 5.57E-05

Oncotype DX Proliferation Genes - TFACResponse KS P = 0.06619

Mammaprint Signature - TFACResponse KS P = 0.0015

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+Response KS P = 0.00018

CIN70 Signature – ER-Response KS P = 0.00016

Oncotype DX Proliferation Genes – ER+Response KS P = 0.00073

ResponseOncotype DX Proliferation Genes – ER-

KS P = 0.04734

S3

Mammaprint Signature – ER+

Mammaprint Signature – ER-

Response

Response

KS P = 0.01288

KS P = 00131

DEK

BCAM

S4

S5BCAM-IHC DEK-IHC

S6 Theraprint Signature Genes

Theraprint Signature Genes

Theraprint Signature Genes