Prediction of likelihood of cancer recurrence

• US 7,056,674 B2
• Filed: 06/17/2004
• Issued: 06/06/2006
• Est. Priority Date: 06/24/2003
• Status: Active Grant

• Current Assignee: Genomic Health Incorporated (Exact Sciences Corporation)
• Original Assignee: Genomic Health Incorporated (Exact Sciences Corporation), NSABP Foundation, Inc.
• Inventors: Paik, Soonmyung, Shak, Steven, Baker, Joffre B., Bryant, John L.
• Primary Examiner(s): GOLDBERG, JEANINE ANNE
• Application Number:
  US10/872,063
• Publication Number:
  US 20050079518A1
• Time in Patent Office: 719 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 435/287.2, 536/23.1, 536/24.3
• US Class Current: 435/6.14
• 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

Abstract

The present invention provides gene sets the expression of which is important in the diagnosis and/or prognosis of cancer, in particular of breast cancer.

Claims

1. A method of predicting the likelihood of long-term survival of an ER positive breast cancer patient without the recurrence of breast cancer, comprising determining the expression level of the RNA transcripts of GRB7 and STMY3 or their expression products in an ER positive breast cancer cell obtained from said patient, normalized against the expression level of all RNA transcripts or their products in said ER positive breast cancer cell, or of a reference set of RNA transcripts or their expression products;

wherein expression of GRB7 and STMY3 indicates a decreased likelihood of long-term survival without breast cancer recurrence.

2. The method of claim 1 wherein said cancer is node negative, ER positive breast cancer.

3. The method of claim 1 wherein said RNA comprises intronic RNA.

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

5. The method of claim 1 wherein said RNA is isolated from core biopsy tissue or fine needle aspirate cells.

6. A method of predicting the likelihood of long-term survival of a patient diagnosed with invasive ER positive breast cancer, without the recurrence of breast cancer, comprising the steps of

(a) determining the expression levels of the RNA transcripts GRB7 and STMY3 or their expression products in a breast cancer cell obtained from said patient, normalized against the expression levels of all RNA transcripts or their expression products in said breast cancer cell, or of a reference set of RNA transcripts or their products;

(b) subjecting the data obtained in step (a) to statistical analysis; and

;

(c) determining whether the likelihood of said long-term survival has increased or decreased.

7. A method of preparing a personalized genomics profile for a patient diagnosed with an ER positive breast cancer, comprising the steps of

(a) subjecting RNA extracted from breast cancer cells obtained from the patient to gene expression analysis;

(b) determining the expression level in the tissue of the RNA transcripts of GRB7 and STMY3, wherein the expression level is normalized against a control gene or genes and optionally is compared to the amount found in a breast cancer reference tissue set; and

(c) creating a report summarizing the data obtained by said gene expression analysis wherein the report includes a prediction of the likelihood of long term survival of the patient wherein expression of GRB7 and STMY3 indicates a decreased likelihood of long-term survival without breast cancer recurrence.

8. The method of claim 7 wherein said breast tissue is obtained from a fixed, paraffin-embedded biopsy sample.

9. The method of claim 8 wherein said RNA is fragmented.

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