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