10. TMC5. 683 238478_at. 12. BNC2. 644 1553434_at. 10. CYP4Z2P. 684 213290_at. 12. COL6A2. 645 237395_at. 10. CYP4Z1. 685 212489_at. 12. COL5A1.
Additional File 1 Supplemental Tables for Correlation of Microarray-based Breast Cancer Molecular Subtypes and Clinical Outcomes: Implications for Treatment Optimization Kuo-Jang Kao, Kai-Ming Chang, Hui-Chi Hsu and Andrew T. Huang
Tables S1-S6 Table S1 Twenty three pivotal genes used to identify probe-sets showing linear or quadratical correlation. Table S2 List of 783 probe-sets used for molecular subtyping of breast cancer and their gene cluster designation as shown in Figure S3. Table S3 Thirty probe-sets representing cell-cycle and proliferation genes Table S4 Probe-set IDs and genes from the OncotypeDX and MammaPrint predictors. Table S5 Survival differences between patients treated with CMF and CAF adjuvant chemotherapy in each molecular subtype of breast cancer. Table S6 Statistical comparison of pertinent clinical parameters between subtype I patients treated with CAF and CMF adjuvant chemotherapy.
1
Table S1. Twenty three pivotal genes used to identify probe‐sets showing linear or quadratical correlation. The 23 pivotal genes were selected from the literature for their known involvement in the tumorigenesis and biology of breast cancer.
Gene Symbol
Probe-set
References Clin Cancer Res 6:127-34, 2000; Anticancer Res 22:1839-43, 2002; Clin Cancer Res 14:2681-9, 2008.
BIRC5
202094_at
BRCA1
204531_s_at
CD24
208650_s_at
Am J Hum Genet 52:702-10, 1993; Lancet 341:1101-2, 1993; N Engl J Med 334:137-42, 1996. Cancer Lett 143:87-94, 1999; Clin Cancer Res 11:1154-9, 2005; Breast Cancer Res 8:R59, 2006.
CEACAM6
203757_s_at
Clin Cancer Res 12:4773-83, 2006;Clin Cancer Res 14:40511, 2008.
CENPF
207828_s_at
CLDN1
218182_s_at
EGFR
201984_s_at
ERBB2
216836_s_at
ESR1
205225_at
FGFR2
203638_s_at
FOXA1
204667_at
Carcinogenesis 30:269-74, 2009; Nature 447:1087-93, 2007. Int J Cancer 120:1013-22, 2007; Clin Cancer Res 13:441521, 2007; Biochem Biophys Res Commun 365:711-7, 2008.
FOXC1
1553613_s_at
Proc Natl Acad Sci, U S A. 105:14076-81, 2008; J. R. Soc. Interface 3:367-381, 2006.
FOXO1
202723_s_at
Cell 117:421–426, 2004; Oncogene 24:7410–7425, 2005.
GRB7
210761_s_at
EMBO J 13:1331-40, 1994.
HMGA1
206074_s_at
Clinl Cancer Res 10:7637-7644, 2004; Oncogene 23:777-85, 2004; Mol Cell Biol 23:2225-38, 2003
MAP3K1
225927_at
Carcinogenesis 30:269-74, 2009; J Biol Chem 279:33085-92, 2004.
MKI67
212022_s_at
Eur J Cancer 29A:1501-2, 1993; Br J Cancer 96:1504-13, 2007; Nature 447:1087-93, 2007.
PGR PRC1
208305_at 218009_s_at
Breast Cancer Res Treat 3:103-10, 1983; Ann N Y Acad Sci 286:90-100, 1977. Cancer Sci 98:174-81, 2007;Exp Mol Med 40:345-53, 2008.
PRKAA1
225984_at
PTEN
225363_at
Crit Rev Oncol Hematol 67:1-7, 2008. Science 275:1943-7, 1997; Oncogene 17:123-7,1998; Mod Pathol 14:672-6, 2001.
TOP2A
201292_at
Br J Cancer 95:1334-41, 2006; Mod Pathol 13:542-7, 2000.
TOX3
214774_x_at
Breast Cancer Res 11:R10, 2009; Nature 447:1087-93,2007.
Int J Cancer. 120:1434-43, 2007. Breast Cancer Res 7:R296-305, 2005; Int J Mol Med. 20:13943, 2007. J Clin Oncol . 19:3376-84, 2001; BMC Genomics 31;8:258, 2007; Cancer Res 65:11018-25, 2005. Science 135:277-282, 1982; J Clin Oncol 19:3376-84, 2001; Human Mol Genetics, 12:3245–3258, 2003 Ann Surg 182:342-351, 1975; Cancer Research (suppl.) 46:4256s-4264s, 1986; Breast Cancer Res Treat 3:10310,1983.
2
Table S2 a-to-j. List of 783 probe-sets used for molecular subtyping of breast cancer and their gene cluster designation as shown in Figure S3.
Table
S2a
228278_at 229341_at 205375_at 226029_at 213432_at 220196_at 204724_s_at 221029_s_at 217728_at 222784_at 226611_s_at 238759_at 239233_at 223075_s_at 1552532_a_at 1553989_a_at 200824_at 201984_s_at 203637_s_at 242671_at
Gene cluster 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Gene Symbol NFIX TFCP2L1 MDFI VANGL2 MUC5B MUC16 COL9A3 WNT5B S100A6 SMOC1 PRR6 CCDC88A CCDC88A C9orf58 ATP6V1C2 ATP6V1C2 GSTP1 EGFR MID1
223062_s_at 201030_x_at 213564_x_at 214581_x_at 231034_s_at 232105_at 218796_at 226907_at 205350_at 221016_s_at 204304_s_at 215729_s_at 206373_at 233320_at 213122_at 220624_s_at 228214_at 226425_at 1553613_s_at 225421_at
1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
PSAT1 LDHB LDHB TNFRSF21 NHSL1
No.
Probeset ID
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40
FERMT1 PPP1R14C CRABP1 TCF7L1 PROM1 VGLL1 ZIC1 TCAM1 TSPYL5 ELF5 CLIP4 FOXC1 PM20D2
No.
Probeset ID
41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60
225431_x_at 230291_s_at 230791_at 202965_s_at 209815_at 224400_s_at 208399_s_at 209270_at 219932_at 202036_s_at 202037_s_at 209842_at 212730_at 1553977_a_at 213456_at 211002_s_at 212236_x_at 213680_at 219545_at 204745_x_at
61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80
206461_x_at 211456_x_at 212859_x_at 216336_x_at 219936_s_at 203021_at 203510_at 227238_at 213711_at 221609_s_at 214614_at 233446_at 239911_at 205766_at 224447_s_at 210761_s_at 216836_s_at 228066_at 1565595_at 1569940_at
Gene cluster 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2
Gene Symbol PM20D2 NFIB CAPN6 PTCH1 CHST9 EDN3 LAMB3 SLC27A6 SFRP1 SFRP1 SOX10 DMN CYP39A1 SOSTDC1 TRIM29 KRT17 KRT6B KCTD14 MT1G MT1H / MT1P2 MT1P2 MT1E MT1M GPR87 SLPI MET MUC15 KRT81 WNT6 MNX1 ONECUT2 ONECUT2 TCAP C17orf37 GRB7 ERBB2
SLC6A16
3
Table
S2b
List
of
783
probe‐sets
used
for
classification
of
breast
cancer
Gene cluster 2 2 2 2 2 2 2 2 2 2
Gene Symbol GALNT14 PHLDA2 S100A7 S100A8 S100A9 PPP1R1B SUSD2 HSD17B2 NANOS1 TRPV6
1554712_a_at 243585_at 242350_s_at 242414_at 220414_at 216641_s_at 219010_at 225316_at 207076_s_at 213094_at 202411_at 219211_at 204475_at 205568_at 207469_s_at 240788_at 204058_at 204059_s_at 218883_s_at 229305_at
2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 3 3
GLYATL2 ATP13A5
228033_at 204886_at 204887_s_at 205034_at 204026_s_at 203214_x_at 210559_s_at 225655_at 229551_x_at 211713_x_at
3 3 3 3 3 3 3 3 3 3
No.
Probeset ID
81 82 83 84 85 86 87 88 89 90
219271_at 209803_s_at 205916_at 202917_s_at 203535_at 225165_at 234310_s_at 204818_at 228523_at 206827_s_at
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120
No.
Probeset ID
121 122 123 124 125 126 127 128 129 130
222848_at 214710_s_at 228729_at 228559_at 219105_x_at 219493_at 201710_at 223570_at 228273_at 204162_at
Gene cluster 3 3 3 3 3 3 3 3 3 3
ME1 ME1 MLF1IP MLF1IP
131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150
225834_at 228069_at 204033_at 205339_at 204822_at 202870_s_at 209408_at 202095_s_at 202094_at 204318_s_at 218662_s_at 203554_x_at 218755_at 207746_at 206102_at 204092_s_at 208079_s_at 219306_at 202954_at 210052_s_at
3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
E2F7 PLK4 PLK4 CCNE2 ZWINT CDC2 CDC2 UHRF1 ZNF367 KIAA0101
151 152 153 154 155 156 157 158 159 160
218355_at 222077_s_at 38158_at 214804_at 223381_at 229538_s_at 219148_at 204170_s_at 204709_s_at 203362_s_at
3 3 3 3 3 3 3 3 3 3
QPRT CALML5 LAD1 C1orf106 MFSD2 ASS1 GPR126 IFI27 USP18 MMP1 AQP9 PIR
Gene Symbol CENPK CCNB1 CCNB1 CENPN ORC6L SHCBP1 MYBL2 MCM10 NDC80 FAM72A / 72B FAM54A TRIP13 STIL TTK CDC20 KIF2C BIRC5 BIRC5 GTSE1 NCAPG PTTG1 KIF20A POLQ GINS1 AURKA AURKA KIF15 UBE2C TPX2 KIF4A / KIF4B RACGAP1 ESPL1 NUF2 IQGAP3 PBK CKS2 KIF23 MAD2L1
4
Table
S2c
List
of
783
probe‐sets
used
for
classification
of
breast
cancer
No.
Probeset ID
161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200
213226_at 222958_s_at 235545_at 204444_at 218542_at 218009_s_at 203755_at 218039_at 228323_at 204825_at 206364_at 219918_s_at 202705_at 203764_at 225687_at 1552619_a_at 222608_s_at 212022_s_at 1555758_a_at 209714_s_at 207165_at 209709_s_at 202240_at 202107_s_at 204146_at 223307_at 235609_at 203145_at 223229_at 218585_s_at 222680_s_at 201292_at 207828_s_at 209172_s_at 204558_at 219787_s_at 225777_at 202779_s_at 203276_at 209680_s_at
Gene cluster 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
Gene Symbol CCNA2 DEPDC1 DEPDC1 KIF11 CEP55 PRC1 BUB1B NUSAP1 CASC5 MELK KIF14 ASPM CCNB2 DLG7 FAM83D ANLN ANLN MKI67 CDKN3 CDKN3 HMMR HMMR PLK1 MCM2 RAD51AP1 CDCA3 SPAG5 UBE2T DTL DTL TOP2A CENPF CENPF RAD54L ECT2 C9orf140 LOC731049 LMNB1 KIFC1
No.
Probeset ID
201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240
215623_x_at 233436_at 240247_at 244427_at 203744_at 228401_at 218782_s_at 222740_at 219215_s_at 228262_at 200935_at 222222_s_at 208502_s_at 209587_at 223530_at 201897_s_at 232065_x_at 219032_x_at 217388_s_at 205306_x_at 211138_s_at 203059_s_at 1558034_s_at 204846_at 228143_at 226021_at 222326_at 203708_at 211302_s_at 202728_s_at 207332_s_at 222939_s_at 206558_at 203304_at 208650_s_at 206023_at 214595_at 218051_s_at 226346_at 227512_at
Gene cluster 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
Gene Symbol SMC4 MTBP KIF23 HMGB3 ATAD2 ATAD2 SLC39A4 MAP7D2 CALR HOMER3 PITX1 PITX1 TDRKH CKS1B CENPL OPN3 KYNU KMO KMO PAPSS2 CP CP CP RDH10 PDE4B PDE4B LTBP1 TFRC SLC16A10 SIM2 BAMBI CD24 NMU KCNG1 NT5DC2 MEX3A MEX3A
5
Table
S2d
List
of
783
probe‐sets
used
for
classification
of
breast
cancer
No.
Probeset ID
241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280
206074_s_at 201195_s_at 205282_at 204695_at 217755_at 231195_at 233691_at 208767_s_at 208029_s_at 214039_s_at 203560_at 212142_at 222037_at 235003_at 222158_s_at 239392_s_at 210057_at 235167_at 241755_at 1558080_s_at 242352_at 226184_at 1565868_at 242903_at 1557810_at 225827_at 205967_at 235425_at 211883_x_at 221926_s_at 218182_s_at 213446_s_at 214336_s_at 220240_s_at 217777_s_at 224221_s_at 208084_at 227314_at 213839_at 235501_at
Gene cluster 4 4 4 4 4 4 4 4 4 4 4 4 4 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 6 6 6 6 6 7 7
Gene Symbol HMGA1 SLC7A5 LRP8 CDC25A HN1 KLRG2 LAPTM4B LAPTM4B LAPTM4B GGH MCM4 MCM4 UHMK1 C1orf121 SMG1 DKFZp547E087 UQCRC2 LOC144871 NIPBL FMNL2 CD44 IFNGR1 EIF2C2 HIST1H4C SGOL2 CEACAM1 IL17RC CLDN1 IQGAP1 COPA TMCO3 PTPLAD1 VAV3 ITGB6 ITGA2 KIAA0500
No.
Probeset ID
281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320
204364_s_at 204365_s_at 219686_at 243806_at 227764_at 202769_at 202770_s_at 211559_s_at 211538_s_at 219682_s_at 229576_s_at 204573_at 209522_s_at 203343_at 224989_at 210319_x_at 239066_at 206457_s_at 202862_at 215726_s_at 207843_x_at 209366_x_at 1558686_at 212218_s_at 1555800_at 243929_at 240024_at 225927_at 1564786_at 204607_at 206509_at 230238_at 239435_x_at 227702_at 223044_at 233123_at 239723_at 214622_at 235856_at 208451_s_at
Gene cluster 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7
Gene Symbol REEP1 REEP1 STK32B LYPD6 CCNG2 CCNG2 CCNG2 HSPA2 TBX3 TBX3 CROT CRAT UGDH MSX2 DIO1 FAH CYB5A CYB5A CYB5A FASN ZNF385B SEC14L2 MAP3K1 LOC338667 HMGCS2 PIP ANKRD43 SHROOM1 CYP4X1 SLC40A1 SLC40A1 CYP21A2 C4A / C4B
6
Table
S2e
List
of
783
probe‐sets
used
for
classification
of
breast
cancer
No.
Probeset ID
321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360
214428_x_at 202357_s_at 204070_at 206396_at 213664_at 211596_s_at 205776_at 215300_s_at 223125_s_at 218692_at 208788_at 225327_at 212195_at 212196_at 206869_at 226846_at 223864_at 237339_at 228256_s_at 202962_at 204015_s_at 204014_at 226034_at 228390_at 229072_at 201311_s_at 201312_s_at 239907_at 205933_at 213832_at 205453_at 216603_at 202752_x_at 216092_s_at 1560550_at 217013_at 203675_at 229838_at 1557867_s_at 236085_at
Gene cluster 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7
Gene Symbol C4A / C4B CFB RARRES3 SLC1A1 SLC1A1 LRIG1 FMO5 FMO5 C1orf21 GOLSYN ELOVL5 KIAA1370 IL6ST IL6ST CHAD PHYHD1 ANKRD30A hCG_25653 EPB41L4A KIF13B DUSP4 DUSP4
SH3BGRL SH3BGRL SETBP1 HOXB2 SLC7A8 SLC7A8 SLC7A8 LOC646282 NUCB2 NUCB2 C9orf117 CAPSL
No.
Probeset ID
361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400
202731_at 212593_s_at 212594_at 1553072_at 231084_at 232381_s_at 238657_at 222068_s_at 220173_at 241310_at 225305_at 232280_at 232290_at 226067_at 204378_at 207056_s_at 228175_at 227177_at 211695_x_at 207300_s_at 50965_at 234016_at 240733_at 222804_x_at 230679_at 219001_s_at 226511_at 208473_s_at 214324_at 203355_s_at 204284_at 1558612_a_at 227832_at 203998_s_at 213745_at 1563658_a_at 225911_at 214858_at 218640_s_at 222699_s_at
Gene cluster 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7
Gene Symbol PDCD4 PDCD4 PDCD4 BNIPL C10orf79 DNAH5 UBXD3 LRRC50 C14orf45 SLC25A29 SLC25A29 C20orf114 BCAS1 SLC4A8 CORO2A MUC1 F7 RAB26 ANKRD20B WDR32 WDR32 WDR32 WDR32 GP2 GP2 PSD3 PPP1R3C ATP1A4 MBD6 SYT1 ATRNL1 SYT9 NPNT PLEKHF2 PLEKHF2
7
Table
S2f
List
of
783
probe‐sets
used
for
classification
of
breast
cancer
No.
Probeset ID
401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440
203988_s_at 206346_at 206463_s_at 214079_at 201349_at 243579_at 201939_at 225915_at 205896_at 227929_at 1556221_a_at 239638_at 240838_s_at 225496_s_at 232914_s_at 1560850_at 1567101_at 205471_s_at 228915_at 219702_at 204531_s_at 206546_at 226446_at 220898_at 1559949_at 244579_at 224218_s_at 234351_x_at 221088_s_at 230290_at 233273_at 242022_at 219741_x_at 231820_x_at 223961_s_at 238077_at 235786_at 225064_at 225092_at 227550_at
Gene cluster 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 8 8 8 8 8 9 9 9 9 9 9 9 9 9 9
Gene Symbol FUT8 PRLR DHRS2 DHRS2 SLC9A3R1 MSI2 PLK2 CAB39L SLC22A4
LOC145837 SYTL2 SYTL2
DACH1 DACH1 PLAC1 BRCA1 SYCP2 HES6
TRPS1 TRPS1 PPP1R9A SCUBE3
ZNF552 ZNF587 CISH KCTD6 RABEP1 RABEP1 LOC143381
No.
Probeset ID
441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480
205696_s_at 230163_at 214440_at 227232_at 217838_s_at 244375_at 225418_at 1553622_a_at 212956_at 212960_at 204798_at 204667_at 210085_s_at 211712_s_at 228241_at 233388_at 210735_s_at 215867_x_at 218195_at 211235_s_at 205225_at 215551_at 232083_at 241466_at 214109_at 229381_at 223103_at 232322_x_at 204623_at 205009_at 223608_at 224443_at 201825_s_at 201826_s_at 231018_at 213201_s_at 204540_at 221585_at 210523_at 229975_at
Gene cluster 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9
Gene Symbol GFRA1 LOC143381 NAT1 EVL EVL PVRL2 FSIP1 TBC1D9 TBC1D9 MYB FOXA1 ANXA9 ANXA9 AGR3 CA12 CA12 C6orf211 ESR1 ESR1 ESR1 C20orf23 LRBA C1orf64 STARD10 STARD10 TFF3 TFF1 EFCAB2 C1orf97 SCCPDH SCCPDH LOC342979 TNNT1 EEF1A2 CACNG4 BMPR1B
8
Table
S2g.
List
of
783
probe‐sets
used
for
classification
of
breast
cancer
Gene cluster 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9
No.
Probeset ID
481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501
204966_at 243837_x_at 209911_x_at 230491_at 205509_at 207142_at 233059_at 210341_at 217191_x_at 230570_at 216356_x_at 227641_at 219051_x_at 232269_x_at 212686_at 205645_at 227425_at 236445_at 217133_x_at 206754_s_at 210272_at
502 503 504 505 506 507 508 509 510 511 512 513
1562821_a_at 237112_at 1561938_at 232034_at 211483_x_at 215771_x_at 223631_s_at 218657_at 223658_at 242657_at 207494_s_at 1552388_at
9 9 9 9 9 9 9 9 9 9 9 9
514 515 516 517 518 519 520
212551_at 235004_at 231291_at 209884_s_at 206325_at 233002_at 226809_at
9 9 9 9 9 9 9
Gene Symbol BAI2 HIST1H2BD CPB1 KCNJ3 MYT1
BAIAP3 FBXL16 METRN METRN PPM1H REPS2 REPS2 LOC731986 CYP2B6 CYP2B7P1 CYP2B7P1
LOC203274 CAMK2B RET C19orf33 RAPGEFL1 KCNK6 ZNF76 FLJ30901 CAP2 RBM24 SLC4A7 SERPINA6 KIAA1622 FLJ30428
No.
Probeset ID
521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541
242912_at 1557843_at 243241_at 1563369_at 219359_at 227379_at 203639_s_at 208228_s_at 203638_s_at 207147_at 235771_at 1559739_at 221675_s_at 230364_at 205769_at 218398_at 200648_s_at 223551_at 1553910_at 239337_at 241368_at
Gene cluster 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9
542 543 544 545 546 547 548 549 550 551 552 553
227966_s_at 244745_at 209459_s_at 209460_at 227182_at 208305_at 228554_at 209339_at 243907_at 205440_s_at 1563512_at 215153_at
9 9 9 9 9 9 9 9 9 9 9 9
554 555 556 557 558 559 560
218094_s_at 1567997_x_at 1556551_s_at 231713_s_at 240633_at 203685_at 232210_at
9 9 9 9 9 9 9
Gene Symbol
FLJ42957 ATHL1 MBOAT1 FGFR2 FGFR2 FGFR2 DLX2 CHPT1 CHPT1 CHPT1 SLC27A2 MRPS30 GLUL PKIB NBPF4 LOC400768 LSDP5 CCDC74A / 74B RERG ABAT ABAT SUSD3 PGR SIAH2 NPY1R NOS1AP NOS1AP SYS1DBNDD2 SLC39A6 ELP2 DOK7 BCL2
9
Table
S2h
List
of
783
probe‐sets
used
for
classification
of
breast
cancer
No.
Probeset ID
561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600
232614_at 201860_s_at 205948_at 219197_s_at 229764_at 209681_at 242662_at 204045_at 243967_at 241577_at 244696_at 216381_x_at 205355_at 226030_at 237350_at 1555893_at 212637_s_at 202554_s_at 209443_at 229158_at 1560260_at 219438_at 220540_at 212492_s_at 212495_at 212496_s_at 1563367_at 203928_x_at 206401_s_at 203929_s_at 225379_at 224909_s_at 224925_at 235049_at 205380_at 243168_at 223600_s_at 236114_at 210374_x_at 213933_at
Gene cluster 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9
Gene Symbol PLAT PTPRT SCUBE2 FAM79B SLC19A2 PCSK6 TCEAL1 AFF3
AKR7A3 ACADSB ACADSB LOC143941 WWP1 GSTM3 SERPINA5 WNK4 LOC285593 NKAIN1 KCNK15 JMJD2B JMJD2B JMJD2B MAPT MAPT MAPT MAPT PREX1 PREX1 ADCY1 PDZK1 KIAA1683 PTGER3 PTGER3
No.
Probeset ID
601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640
206091_at 231518_at 222379_at 223235_s_at 201667_at 217764_s_at 226736_at 231859_at 225363_at 205239_at 206115_at 208606_s_at 231944_at 218541_s_at 202458_at 204663_at 206143_at 212741_at 227722_at 236222_at 228528_at 232603_at 233413_at 227742_at 242913_at 207144_s_at 205710_at 230863_at 232850_at 1554007_at 228905_at 201963_at 225984_at 217276_x_at 217284_x_at 1553410_a_at 224146_s_at 204942_s_at 211237_s_at 1553394_a_at
Gene cluster 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 10 10 10 10 10 10 10 10 10
Gene Symbol MATN3 LOC283867 KCNE4 SMOC2 GJA1 RAB31 CHURC1 C14orf132 PTEN AREG EGR3 WNT4 ERO1LB C8orf4 PRSS23 ME3 SLC26A3 MAOA RPS23 C3orf15 DCDC5 CLIC6 CLIC6 CITED1 LRP2 LRP2
PCM1 ACSL1 PRKAA1 SERHL2 SERHL ABCC12 ABCC11 ALDH3B2 FGFR4 TFAP2B
10
Table
S2i.
List
of
783
probe‐sets
used
for
classification
of
breast
cancer
214451_at 219580_s_at 222904_s_at 1553434_at 237395_at 227971_at 231098_at
Gene cluster 10 10 10 10 10 10 10
Gene Symbol TFAP2B TMC5 TMC5 CYP4Z2P CYP4Z1 NRK
204351_at 201884_at 203757_s_at 211657_at 1553436_at 226960_at 241031_at 224576_at 230906_at 234785_at 210130_s_at 219300_s_at 219301_s_at 206378_at 206799_at 220622_at 214774_x_at 226455_at 236256_at 215559_at 214307_at 205221_at 214308_s_at 209959_at 242836_at 243296_at 213931_at 227952_at 215440_s_at 204412_s_at 227194_at 206994_at 237411_at
11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 12 12 12 12 12 12 12 12 12
S100P CEACAM5 CEACAM6 CEACAM6 MUC19 CXCL17 FAM148A ERGIC1 GALNT10
No.
Probeset ID
641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680
TM7SF2 CNTNAP2 CNTNAP2 SCGB2A2 SCGB1D2 LRRC31 TOX3 CREB3L4 ABCC6 HGD HGD HGD NR4A3 PBEF1 ID2 /// ID2B ZNF718 BEX4 NEFH FAM3B CST4 ADAMTS6
No.
Probeset ID
681 682 683 684 685 686 687
219087_at 224396_s_at 238478_at 213290_at 212489_at 213125_at 229084_at
Gene cluster 12 12 12 12 12 12 12
688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720
202410_x_at 204345_at 206101_at 209550_at 205381_at 214761_at 204519_s_at 227762_at 244697_at 210051_at 225987_at 230661_at 213900_at 204731_at 226625_at 222862_s_at 228653_at 240724_at 204636_at 216918_s_at 238827_at 225728_at 236656_s_at 225123_at 223168_at 208798_x_at 236307_at 226147_s_at 229659_s_at 201525_at 215271_at 232570_s_at 207761_s_at
12 12 12 12 12 12 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13
Gene Symbol ASPN ASPN BNC2 COL6A2 COL5A1 OLFML2B CNTN4 IGF2 / INSIGF2 COL16A1 ECM2 NDN LRRC17 ZNF423 PLLP
RAPGEF3 STEAP4 LOC286191 C9orf61 TGFBR3 TGFBR3 AK5 SAMD5 COL17A1 DST SORBS2
RHOU GOLGA8A PIGR APOD TNN ADAM33 METTL7A
11
Table
S2j.
List
of
783
probe‐sets
used
for
classification
of
breast
cancer
No.
Probeset ID
721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 721
244655_at 242868_at 1555564_a_at 212558_at 230130_at 228750_at 209540_at 209541_at 214920_at 243481_at 227874_at 231947_at 200795_at 232935_at 202920_at 209763_at 202242_at 207542_s_at 209047_at 227725_at 208891_at 208892_s_at 1553602_at 206164_at 206165_s_at 217528_at 218899_s_at 202948_at 203305_at 213139_at 205582_s_at 212358_at 205542_at 221841_s_at 201041_s_at 227404_s_at 204803_s_at 207317_s_at 213006_at 244655_at
Gene cluster 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13
Gene Symbol
No.
Probeset ID
LOC644192
760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783
1560049_at 203088_at 222043_at 209686_at 229839_at 235849_at 203435_s_at 238018_at 209576_at 203324_s_at 206953_s_at 208370_s_at 212724_at 215933_s_at 226931_at 211026_s_at 228766_at 241929_at 205913_at 207175_at 201785_at 202723_s_at 221268_s_at 222773_s_at
CFI SPRY1
IGF1 IGF1 THSD7A RHOJ EMCN MYCT1 SPARCL1 ANK2 CHRDL1 TSPAN7 AQP1 AQP1 ST6GALNAC1 DUSP6 DUSP6 MUCL1 CLCA2 CLCA2 CLCA2 BAALC IL1R1 F13A1 SNAI2 GGTLA1 CLIP3 STEAP1 KLF4 DUSP1 EGR1 RRAD CASQ2 CEBPD LOC644192
Gene cluster 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13
Gene Symbol FBLN5 CLU S100B SCARA5 SCARA5 MME FAM150B GNAI1 CAV2 LPHN2 RCAN1 RND3 HHEX TMTC1 MGLL CD36 PLIN ADIPOQ RNASE1 FOXO1 SGPP1 GALNT12
12
Table S3 Thirty probe-sets representing cell-cycle and proliferation genes were used to show distinctive differential expression of cell-cycle and proliferation genes among different molecular subtypes of breast cancer. These genes were identified as part of a common neoplastic signature from our previous study of paired hepatocelluar and adjacent non-tumorous liver tissues. Affymetrix Probe-set ID 201292_at
Gene Symbol TOP2A
202580_x_at
FOXM1
202705_at
CCNB2
202715_at
CAD
202870_s_at
CDC20
203109_at
UBE2M
203213_at
CDC2
203554_x_at
PTTG1
204641_at
NEK2
204720_s_at
DNAJC6
204768_s_at
FEN1
204822_at
TTK
204825_at
MELK
205047_s_at
ASNS
205393_s_at
CHEK1
207165_at
HMMR
207828_s_at
CENPF
209035_at
MDK
209408_at
KIF2C
209464_at
AURKB
209714_s_at
CDKN3
215090_x_at
NPEPPS
217714_x_at
STMN1
218009_s_at
PRC1
218355_at
KIF4A
218663_at
HCAP-G
219494_at
RAD54B
219918_s_at
ASPM
219978_s_at
NUSAP1
219990_at
E2F8
13
Table S4 Probe-set IDs and genes from the OncotypeDX and MammaPrint predictors that were used to score risk of distant recurrence. Sixteen genes in the OncotypeDX predictor can be matched to Affymetrix probe-set IDs and NKI-ID. Forty eight out of seventy MammaPrint predictor genes can be matched to Affymetrix probe-set IDs in the U133A GeneChip and used for the study.
14
Table S5. Survival comparison between patients treated with CMF and CAF adjuvant chemotherapy in each molecular subtype of breast cancer.
Patient No.
p value of Log-rank test ( CAF vs. CMF )
Breast cancer subtype
CAF
CMF
Metastasis.-free survival
Overall survival
I
10
13
0.82
0.82
II
5
6
0.62
0.76
III
16
4
0.58
0.51
IV
22
17
7.00E-05
0.002
V
12
8
0.41
0.96
VI
22
11
0.23
0.06
15
Table S6 Statistical comparison of pertinent clinical parameters between subtype I patients treated with CAF and CMF adjuvant chemotherapy.
Fisher exact CAF CMF test n= 10 n= 13 p value Age at diagnosis < 50 yr 7 >= 50 yr 3 TNM Path T 1 2 2 8 TNM Path N 0 5 1 5 TNM Path M 0 10 Positive Lymph Nodes 0 5 1-3 5 TNM Stage I 1 II 9 Nuclear Grade 1 0 2 1 3 9 Hormonal Therapy No 7 Yes 3 Post-op Radiation No 6 Yes 4
1 70.0% 30.0%
9 4
69.2% 30.8% 0.38
20.0% 80.0%
6 7
46.2% 53.8% 0.17
50.0% 50.0%
11 2
84.6% 15.4%
100.0%
13
100.0% 0.17
50.0% 50.0%
11 2
84.6% 15.4% 0.09
10.0% 90.0%
6 7
46.2% 53.8%
0.0% 10.0% 90.0%
1 2 9
7.7% 15.4% 69.2%
0.49
0.62 70.0% 30.0%
11 2
84.6% 15.4% 0.65
60.0% 40.0%
10 3
76.9% 23.1%
16
