IP Library › Granted Patent US 12,412,642
Granted Patent B2
US 12,412,642 · App. 18/454,312 · Granted Sep 9, 2025

Method to use gene expression to determine likelihood of clinical outcome of renal cancer

Inventors: Wayne Cowens; Steven Shak (Hillsborough, CA); Audrey Goddard (San Francisco, CA); Dejan Knezevic (Palo Alto, CA); Joffre Baker (Montara, CA); Michael C. Kiefer (Walnut Creek, CA); Tara Maddala (Sunnyvale, CA); Frederick L. Baehner (San Francisco, CA)
Assignee: Genomic Health, Inc.
G16B99/00G01N33/57438G06N7/01G16B25/10C12Q2600/112C12Q2600/118C12Q2600/158
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Quick Facts
Patent No.
US 12,412,642
App. No.
18/454,312
Granted
Sep 9, 2025
Kind
B2
Abstract

The present disclosure provides gene and gene sets, the expression of which is important in the classification and/or prognosis of cancer, in particular of renal cell carcinoma.

Claims (34)

1. A method of analyzing the expression of RNA transcripts of genes in a human renal cancer patient, the method comprising:

measuring levels of RNA transcripts, in a renal tumor sample from the patient, of a panel of genes consisting of:

a set of genes consisting of one or more angiogenesis genes selected from: ADD1, ANGPTL3, APOLD1, CEACAM1, EDNRB, EMCN, ENG, EPAS1, FLT1, JAG1, KDR, KL, LDB2, NOS3, NUDT6, PPAP2B, PRKCH, PTPRB, RGS5, SHANK3, SNRK, TEK, ICAM2, and VCAM1; and

a set of genes consisting of one or more immune response genes selected from: CCL5, CCR7, CD8A, CX3CL1, CXCL10, CXCL9, HLA-DPB1, IL6, IL8, and SPP1; and

a set of genes consisting of one or more cell cycle genes selected from: BUB1, C13orf15, CCNB1, PTTG1, TPX2, LMNB1, and TUBB2A; and optionally

EIF4EBP1.

2. The method of claim 1 , wherein the renal cancer is renal cell carcinoma (RCC).

3. The method of claim 2 , wherein the RCC is clear cell renal cell carcinoma (ccRCC).

4. The method of claim 1 , wherein the level of the RNA transcripts is measured by quantitative RT-PCR.

5. The method of claim 1 , wherein the renal tumor sample is paraffin-embedded and fixed.

6. The method of claim 1 , wherein the panel consists of: at least two angiogenesis genes, at least two immune response genes, and at least two cell cycle genes, and optionally EIF4EBP1.

7. The method of claim 1 , wherein the method further comprises performing global normalization of the levels of the RNA transcripts of the panel of genes.

8. A method of analyzing the expression of RNA transcripts of genes in a human renal cancer patient, the method comprising:

measuring levels of RNA transcripts, in a renal tumor sample from the patient, of a panel of genes consisting of:

a set of genes consisting of one or more angiogenesis genes selected from: ADD1, ANGPTL3, APOLD1, CEACAM1, EDNRB, EMCN, ENG, EPAS1, FLT1, JAG1, KDR, KL, LDB2, NOS3, NUDT6, PPAP2B, PRKCH, PTPRB, RGS5, SHANK3, SNRK, TEK, ICAM2, and VCAM1; and

a set of genes consisting of one or more immune response genes selected from: CCL5, CCR7, CD8A, CX3CL1, CXCL10, CXCL9, HLA-DPB1, IL6, IL8, and SPP1; and

a set of genes consisting of one or more cell cycle genes selected from: BUB1, C13orf15, CCNB1, PTTG1, TPX2, LMNB1, and TUBB2A; and

a set of genes consisting of one or more transport genes selected from: AQP1, SGK1, and both AQP1 and SGK1; and

a set of genes consisting of one or more cell adhesion/extracellular matrix genes selected from: ITGB1, A2M, ITGB5, LAMB1, LOX, MMP14, TGFBR2, TIMP3, and TSPAN7; and optionally

EIF4EBP1.

9. The method of claim 8 , wherein the renal cancer is renal cell carcinoma (RCC).

10. The method of claim 9 , wherein the RCC is clear cell renal cell carcinoma (ccRCC).

11. The method of claim 8 , wherein the level of the RNA transcripts is measured by quantitative RT-PCR.

12. The method of claim 8 , wherein the renal tumor sample is obtained from a biopsy.

13. The method of claim 8 , wherein the renal tumor sample is paraffin-embedded and fixed.

14. The method of claim 8 , wherein the method further comprises performing global normalization of the levels of the RNA transcripts of the panel of genes.

15. A method of analyzing the expression of RNA transcripts of genes in a human renal cancer patient, the method comprising:

measuring levels of RNA transcripts, in a renal tumor sample from the patient, of a panel of genes consisting of:

at least five genes selected from the group consisting of: EMCN, PPAP2B, CCL5, CXCL9, NOS3, NUDT6, AQP1, APOLD1, ITGB5, CCR7, CX3CL1, CEACAM1, PRKCH, CASP10, SNRK, and PTPRB.

16. The method of claim 15 , wherein the renal cancer is renal cell carcinoma (RCC).

17. The method of claim 16 , wherein the RCC is clear cell renal cell carcinoma (ccRCC).

18. The method of claim 15 , wherein the level of the RNA transcripts is measured by quantitative RT-PCR.

19. The method of claim 15 , wherein the renal tumor sample is paraffin-embedded and fixed.

20. The method of claim 15 , wherein the method further comprises performing global normalization of the levels of the RNA transcripts of the panel of genes.

Assignments (2)
TERMINATION AND RELEASE OF SECURITY INTEREST IN PATENT RIGHTS (REEL/FRAME 69898/0380) Recorded Mar 27, 2026
From: JPMORGAN CHASE BANK, N.A.
To: GENOMIC HEALTH, INC.
Reel/Frame 075294/0821 →
PATENT SECURITY AGREEMENT Recorded Jan 14, 2025
From: GENOMIC HEALTH, INC.
To: JPMORGAN CHASE BANK, N.A.
Reel/Frame 069898/0380 →
Continuity (6)
Continuation 16952566 · Nov 19, 2020
Continuation 15368979 · Dec 5, 2016
Continuation 12987023 · Jan 7, 2011
Provisional Application 61346230 · May 19, 2010
Provisional Application 61294038 · Jan 11, 2010
Related Publication 20240096451A1 · Mar 21, 2024
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