Gene expression profiling of primary breast carcinomas using arrays of candidate genes

A method for the molecular characterization of a carcinoma comprising the steps of:

• (i) detecting in tumor cells corresponding to breast tumor cells at least one polynucleotide selected from a first group comprising:
• EST T89980 (SEQ ID No:
• 16),
• SOX 4 (SEQ ID No:
• 22, SEQ ID No:
• 23, SEQ ID No:
• 24),
• ENPP2 (SEQ ID No:
• 39, SEQ ID No:
• 40, SEQ ID No.41),
• MUC 1 (SEQ ID No:
• 57, SEQ ID No:
• 58),
• GATA3 (SEQ ID No:
• 76, SEQ ID No:
• 77, SEQ ID No:
• 78),
• TOP2B (SEQ ID No:
• 82, SEQ ID No:
• 83),
• IL2RB (SEQ ID No:
• 97, SEQ ID No:
• 98, ID No:
• 99),
• ERBB2 (SEQ ID No:
• 118, SEQ ID No:
• 119),
• EGFR (SEQ ID No:
• 135, SEQ ID No:
• 136, SEQ ID No:
• 137),
• THBS1 (SEQ ID No:
• 216, SEQ ID No:
• 217),
• PPP2R2C (SEQ ID No:
• 238, SEQ ID No:
• 239),
• ATF3 (SEQ ID No:
• 250, SEQ ID No:
• 251, SEQ ID No:
• 252),
• KIAA1075 (SEQ ID No:
• 322, SEQ ID No:
• 323),
• CDH1 (SEQ ID No:
• 326, SEQ ID No:
• 327, SEQ ID No:
• 328),
• ZNF144 (SEQ ID No:
• 329, SEQ ID No:
• 330),
• GSTP1 (SEQ ID No:
• 334, SEQ ID No:
• 335, SEQ ID No:
• 336),
• CD44 (SEQ ID No:
• 374, SEQ ID No:
• 375, SEQ ID No:
• 376),
• GZMA (SEQ ID No:
• 402, SEQ ID No:
• 403),
• EST T80406 (SEQ ID No:
• 430), and
• ESTs H30141 & H27466 (SEQ ID No:
• 438, SEQ ID No:
• 439)
• determining the expression level of the at least one polynucleotide from the first group to differentiate a tumor in which a lymph node has been invaded by a tumor cell from a tumor in which a lymph node has not been invaded by a tumor cell;
• (ii) detecting in tumor cells corresponding to breast tumor cells at least one polynucleotide selected from a second group comprising:
• SOX4 11 (SEQ ID No:
• 22, SEQ ID No:
• 23, SEQ ID No:
• 24),
• CSF1 (SEQ ID No:
• 48, SEQ ID No:
• 49, SEQ ID No:
• 50),
• VIL2 (SEQ ID No:
• 51, SEQ ID No:
• 52, SEQ ID No:
• 53),
• IGF2 (SEQ ID No:
• 59, SEQ ID No:
• 60, SEQ ID No:
• 61),
• KIAA0427 (SEQ ID No:
• 65, SEQ ID No:
• 66, SEQ ID No:
• 67),
• MYC (SEQ ID No:
• 73, SEQ ID No:
• 74, SEQ ID No:
• 75),
• GATA3 (SEQ ID No:
• 76, SEQ ID No:
• 77, SEQ ID No:
• 78),
• TOP2B (SEQ ID No:
• 82, SEQ ID No:
• 83),
• ERBB2 (SEQ ID No:
• 118, SEQ ID No:
• 119),
• EGFR (SEQ ID No:
• 135, SEQ ID No:
• 136, SEQ ID No:
• 137),
• CRABP2 (SEQ ID No 156, SEQ ID No:
• 157, SEQ ID No:
• 158),
• GZMB 73 (SEQ ID No:
• 178, SEQ ID No:
• 179),
• IGKC (SEQ ID No:
• 186),
• ANG (SEQ ID No:
• 194, SEQ ID No:
• 195),
• EFNA1 (SEQ ID No:
• 226, SEQ ID No:
• 227),
• MYBL2 (SEQ ID No:
• 308, SEQ ID No:
• 309, SEQ ID No:
• 310),
• CDH1 (SEQ ID No:
• 326, SEQ ID No:
• 327, SEQ ID No:
• 328),
• MST1 (SEQ ID No:
• 331, SEQ ID No:
• 332, SEQ ID No:
• 333),
• MYB (SEQ ID No:
• 354, SEQ ID No:
• 355),
• XBP1 (SEQ ID No:
• 385, SEQ ID No:
• 386, SEQ ID No:
• 387),
• SRF (SEQ ID No:
• 391, SEQ ID No:
• 392, SEQ ID No:
• 393),
• SOX9 (SEQ ID No:
• 394, SEQ ID No:
• 395), and
• ESTs H21879 & H21880 (SEQ ID No:
• 433, SEQ ID No:
• 434)
• determining the expression level of the at least one polynucleotide from the second group to distinguish tumors sensitive to anthracycline from tumors insensitive to anthracycline;
• (iii) detecting in tumor cells corresponding to breast tumor cells at least one polynucleotide selected from a third group comprising:
• CTSB (SEQ ID No:
• 30, SEQ ID No:
• 31),
• VIL2 (SEQ ID No:
• 51, SEQ ID No:
• 52, SEQ ID No:
• 53),
• MUC1 (SEQ ID No:
• 57, SEQ ID No:
• 58),
• EMR1 (SEQ ID No:
• 62, SEQ ID No:
• 63, SEQ ID No:
• 64),
• KIAA0427 (SEQ ID No:
• 65, SEQ ID No:
• 66, SEQ ID No:
• 67),
• GATA3 (SEQ ID No:
• 76, SEQ ID No:
• 77, SEQ ID No:
• 78),
• PRLR 39 (SEQ ID No:
• 94, SEQ ID No:
• 95, SEQ ID No:
• 96),
• GATA3 (SEQ ID No:
• 100, SEQ ID No:
• 101, SEQ ID No:
• 78),
• TC21 (SEQ ID No 106, SEQ ID No:
• 107, SEQ ID No:
• 108),
• BCL2 (SEQ ID No:
• 115, SEQ ID No:
• 116, SEQ ID No:
• 117),
• CRABP2 (SEQ ID No:
• 156, SEQ ID No:
• 157, SEQ ID No:
• 158),
• ANG (SEQ ID No:
• 194, No:
• 195),
• EGF (SEQ ID No:
• 199, SEQ ID No:
• 200),
• THBS1 (SEQ ID No:
• 216, SEQ ID No:
• 217),
• EDNRA (SEQ ID No:
• 228, SEQ ID No:
• 229),
• SMARCA2 (SEQ ID No:
• 235, SEQ ID No:
• 236, SEQ ID No:
• 237),
• ABCB1 (SEQ ID No:
• 257, SEQ ID No:
• 258),
• BIRC4 (SEQ ID No:
• 273, SEQ ID No:
• 274),
• DAP3 (SEQ ID No:
• 275, SEQ ID No:
• 276),
• GNRH1 (SEQ ID No:
• 277, SEQ ID No:
• 278),
• EST R97218 (SEQ ID No:
• 296, SEQ ID No:
• 297),
• BS69 (SEQ ID No:
• 342, SEQ ID No:
• 343, SEQ ID No:
• 344),
• MYB (SEQ ID No:
• 354, SEQ ID No:
• 355),
• CTSB (SEQ ID No:
• 361, SEQ ID No:
• 31),
• MLANA (SEQ ID No:
• 362, SEQ ID No:
• 363, SEQ ID No:
• 364),
• APR-1 (SEQ ID No:
• 365, SEQ ID No:
• 366, SEQ ID No:
• 367),
• CDKN3 (SEQ ID No:
• 377, SEQ ID No:
• 378, SEQ ID No:
• 379)
• XBP1 (SEQ ID No:
• 385, SEQ ID No:
• 386, SEQ ID No:
• 387),
• CDH15 (SEQ ID No:
• 396, SEQ ID No:
• 397, SEQ ID No:
• 398),
• EST W73386 168 ests (SEQ 1D No:
• 401),
• ILF1 (SEQ ID No:
• 406, SEQ ID No:
• 407, SEQ ID No:
• 408),
• ARHGDIA (SEQ ID No:
• 409, SEQ ID No:
• 410, SEQ ID No:
• 411),
• C4A (SEQ ID No:
• 412, SEQ ID No:
• 413),
• ESR1 (SEQ ID No:
• 420, SEQ ID No:
• 421, SEQ ID No:
• 422),
• PBX1 (SEQ ID No:
• 423, SEQ ID No:
• 424, SEQ ID No:
• 425),
• GLI3 (SEQ ID No:
• 426, SEQ ID No:
• 427, SEQ ID No:
• 428),
• ESTs H24628 & H24592 (SEQ ID No:
• 435, SEQ ID No:
• 436), and
• EST H28056 (SEQ ID No:
• 437)
• determining the expression levels of the at least one polynucleotide from the third group to classify good and poor prognosis primary breast tumors.