Gene expression profiling in biopsied tumor tissues

• US 7,081,340 B2
• Filed: 03/12/2003
• Issued: 07/25/2006
• Est. Priority Date: 03/13/2002
• Status: Active Grant

• Current Assignee: Genomic Health Incorporated (Exact Sciences Corporation)
• Original Assignee: Genomic Health Incorporated (Exact Sciences Corporation)
• Inventors: Kiefer, Michael C., Baker, Joffre B., Cronin, Maureen T., Shak, Steve, Walker, Michael Graham
• Primary Examiner(s): GOLDBERG, JEANINE ANNE
• Application Number:
  US10/388,360
• Publication Number:
  US 20030225528A1
• Time in Patent Office: 1,231 Days
• Field of Search: None
• US Class Current: 435/6.16
• CPC Class Codes: C12N 15/1003 Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: G01N 33/57415 of breast
• CPC Class Codes: G01N 33/57484 involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites

Abstract

The invention concerns sensitive methods to measure mRNA levels in biopsied tumor tissues, including archived paraffin-embedded biopsy material. Th invention also concerns breast cancer gene sets important in the diagnosis and treatment of breast cancer, and methods for assigning the most optimal treatment options to breast cancer patient based upon knowledge derived from gene expression studies.

Claims

1. A method of predicting the likelihood of long-term survival of a breast cancer patient without the recurrence of breast cancer, following surgical removal of the primary tumor, comprising determining the expression level of Bcl2, STK15, CEGP1, Ki-67, GSTM1, PR, SURV, TFRC, EstR1, CCNB1, BAGI1, and Her2, wherein overexpression of STK15, Ki-67, SURV, TFRC, CCNB1, and Her2, indicates a decreased likelihood of long-term survival without breast cancer recurrence, and the overexpression of Bcl2, CEGP1, GSTM1, PR, EstR1, BAGl1, indicates an increased likelihood of long-term survival without breast cancer recurrence.

2. The method of claim 1 wherein said RNA is isolated from a fixed, wax-embedded breast cancer tissue specimen of said patient.

3. The method of claim 1, wherein said RNA is fragmented RNA.

4. The method of claim 1, wherein said RNA is isolated from a fine needle biopsy sample.

5. The method of claim 1, further comprising creating a report summarizing the data obtained by the determination of said gene expression levels.

6. The method of claim 5, wherein said report includes prediction of the likelihood of long term survival of said patient without the recurrence of breast cancer following surgical removal of the primary tumor.

7. The method of claim 6, wherein said report includes recommendation for a treatment modality of said patient.