Methods to predict clinical outcome of cancer

A method of analyzing expression levels of RNA transcripts of genes in a breast cancer patient, comprising:

• obtaining a breast tumor tissue sample from the breast cancer patient;
• extracting RNA from the tissue sample;
• reverse transcribing RNA transcripts from the extracted RNA to produce cDNA amplicons;
• and
• determining levels of cDNA amplicons of each of GRB7, ERBB2, ESR1, PGR, BCL2, SCUBE2 (CEGP1), BIRC5 (SURV), Ki67 (MKI67), CCNB1, STK15 (AURKA), GSTM1, and BAG1, wherein the cDNA levels are determined by digital gene expression DNA sequencing, and wherein at least one of the following primer and probe sequence sets is used to determine the levels of the cDNA amplicons:
• GRB7, SEQ ID Nos:
• 210, 594, and 978;
• ERBB2, SEQ ID Nos:
• 224, 608, and 992;
• ESR1, SEQ ID Nos:
• 163, 547, and 931;
• PGR, SEQ ID Nos:
• 329, 713, and 1097;
• BCL2, SEQ ID Nos:
• 43, 427, and 811;
• SCUBE2 (CEGP1), SEQ ID Nos:
• 92, 476, and 860;
• BIRC5 (SURV), SEQ ID Nos:
• 362, 746, and 1130;
• Ki67 (MK167), SEQ ID Nos:
• 275, 659, and 1043;
• CCNB1, SEQ ID Nos:
• 66, 450, and 834;
• STK15 (AURKA), SEQ ID Nos:
• 359, 743, and 1127;
• GSTM1, SEQ ID Nos:
• 215, 599, and 983;
• or
• BAG1:
• SEQ ID Nos:
• 35, 419, and 803.

A method of analyzing expression levels of RNA transcripts of genes in a breast cancer patient, comprising:

• obtaining a breast tumor tissue sample from the breast cancer patient;
• extracting RNA from the tissue sample;
• reverse transcribing RNA transcripts from the extracted RNA to produce cDNA amplicons;
• and
• determining levels of cDNA amplicons of each of GRB7, ERBB2, ESR1, PGR, BCL2, SCUBE2 (CEGP1), BIRC5 (SURV), Ki67 (MKI67), CCNB1, STK15 (AURKA), GSTM1, and BAG1, wherein the cDNA levels are determined by digital gene expression DNA sequencing, wherein the cDNA amplicons comprise at least one of the following polynucleotides:
• SEQ ID NO:
• 1362 (for GRB7);
• SEQ ID NO:
• 1376 (for ERBB2);
• SEQ ID NO:
• 1323 (for ESR1);
• SEQ ID NO:
• 1481 (for PGR);
• SEQ ID NO:
• 1196 (for BCL2);
• SEQ ID NO:
• 1514 (for BIRC5 (SURV));
• SEQ ID NO:
• 1427 (for Ki67 (MK167));
• SEQ ID NO:
• 1218 (for CCNB1);
• SEQ ID NO:
• 1511 (for STK15 (AURKA));
• SEQ ID NO:
• 1367 (for GSTM1);
• or
• SEQ ID NO:
• 1187 (for BAG1).