Abstract: The present invention provides methods for incorporating transcript chromosomal locus information for identification of biomarkers of disease recurrence risk.
Type:
Application
Filed:
September 27, 2019
Publication date:
April 2, 2020
Applicant:
Genomic Health, Inc.
Inventors:
Michael C. Kiefer, Francois Collin, Samuel Levy, Joffre B. Baker, Michael R. Crager, Mark R. Segal
Abstract: The present disclosure relates to uses of a multiple gene-expression based Genomic Prostate Score™ (GPS™) algorithm for assessment of various clinical endpoints in prostate cancer patients, such as risks of clinical recurrence (CR), biochemical recurrence (BCR), distant metastasis (Mets), and prostate cancer death (PCD). In some embodiments, GPS result is determined for low and intermediate risk prostate cancer patients in order to assist in determining treatment strategies for those patients.
Type:
Application
Filed:
February 12, 2018
Publication date:
February 6, 2020
Applicant:
Genomic Health, Inc.
Inventors:
Ruixiao LU, Michael CRAGER, Nan ZHANG, Tara MADDALA, Phillip FEBBO, Hugh Jeffrey LAWRENCE
Abstract: The present invention relates to biomarkers associated with breast cancer prognosis. These biomarkers include coding transcripts and their expression products, as well as non-coding transcripts, and are useful for predicting the likelihood of breast cancer recurrence in a breast cancer patient. The present invention also relates to a novel method of identifying intergenic sequences that correlate with a clinical outcome.
Type:
Application
Filed:
January 17, 2019
Publication date:
August 22, 2019
Applicant:
GENOMIC HEALTH, INC.
Inventors:
Joffre B. BAKER, Dominick SINICROPI, Robert J. PELHAM, Michael R. CRAGER, Francois COLLIN, James C. STEPHANS, Mei-Lan LIU, John D. MORLAN, Kunbin QU
Abstract: Molecular assays that involve measurement of expression levels of prognostic biomarkers, or co-expressed biomarkers, from a biological sample obtained from a prostate cancer patient, and analysis of the measured expression levels to provide information concerning the likely prognosis for said patient, and likelihood that said patient will have a recurrence of prostate cancer, or to classify the tumor by likelihood of clinical outcome or TMPRSS2 fusion status, are provided herein.
Type:
Application
Filed:
February 22, 2019
Publication date:
August 15, 2019
Applicant:
GENOMIC HEALTH, INC.
Inventors:
Steven SHAK, Frederick L. BAEHNER, Tara MADDALA, Mark LEE, Robert J. PELHAM, Wayne COWENS, Diana CHERBAVAZ, Michael C. KIEFER, Michael CRAGER, Audrey GODDARD, Joffre B. BAKER
Abstract: The present invention provides methods to determine the prognosis and appropriate treatment for patients diagnosed with cancer, based on the expression levels of one or more biomarkers. More particularly, the invention relates to the identification of genes, or sets of genes, able to distinguish breast cancer patients with a good clinical prognosis from those with a bad clinical prognosis. The invention further provides methods for providing a personalized genomics report for a cancer patient. The inventions also relates to computer systems and software for data analysis using the prognostic and statistical methods disclosed herein.
Type:
Application
Filed:
January 9, 2019
Publication date:
August 8, 2019
Applicant:
GENOMIC HEALTH, INC.
Inventors:
Joffre B. BAKER, Maureen T. CRONIN, Francois COLLIN, Mei-Lan LIU
Abstract: The present disclosure includes assays that involve measurement of expression levels of prognostic biomarkers, or co-expressed biomarkers, from a biological sample obtained from a prostate cancer patient, and analysis of the measured expression levels to provide information concerning the likely prognosis for the patient, and likelihood that the patient will have a recurrence of prostate cancer, or to classify the tumor by likelihood of clinical outcome or TMPRSS2 fusion status.
Type:
Grant
Filed:
October 20, 2015
Date of Patent:
April 16, 2019
Assignee:
Genomic Health, Inc.
Inventors:
Steven Shak, Frederick L. Baehner, Tara Maddala, Mark Lee, Robert J. Pelham, Wayne Cowens, Diana Cherbavaz, Michael C. Kiefer, Michael Crager, Audrey Goddard, Joffre B. Baker
Abstract: The present invention provides algorithm-based molecular assays that involve measurement of expression levels of genes from a biological sample obtained from a kidney cancer patient. The present invention also provides methods of obtaining a quantitative score for a patient with kidney cancer based on measurement of expression levels of genes from a biological sample obtained from a kidney cancer patient. The genes may be grouped into functional gene subsets for calculating the quantitative score and the gene subsets may be weighted according to their contribution to cancer recurrence.
Type:
Application
Filed:
November 26, 2018
Publication date:
March 28, 2019
Applicant:
Genomic Health, Inc.
Inventors:
Steven SHAK, George Andrew WATSON, Michael R. CRAGER, Tara MADDALA, Margarita LOPATIN, Audrey GODDARD, Dejan KNEZEVIC, Christer SVEDMAN
Abstract: The invention concerns sensitive methods to measure mRNA levels in biopsied tumor tissues, including archived paraffin-embedded biopsy material. The 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.
Type:
Grant
Filed:
June 9, 2006
Date of Patent:
March 26, 2019
Assignee:
Genomic Health, Inc.
Inventors:
Joffre B. Baker, Maureen T. Cronin, Michael C. Kiefer, Steve Shak, Michael Graham Walker
Abstract: Algorithm-based molecular assays that involve measurement of expression levels of prognostic and/or predictive genes, or co-expressed genes thereof, from a biological sample obtained from a cancer patient, and analysis of the measured expression levels to provide information concerning the likelihood of recurrence of colorectal cancer and/or the likelihood of a beneficial response to chemotherapy for the patient are provided herein. Methods of analysis of gene expression values of prognostic and/or predictive genes, as well as methods of identifying gene expression-tumor region ratios, tumor-associated stromal surface area, and gene cliques, i.e. genes that co-express with a validated biomarker and thus may be substituted for that biomarker in an assay, are also provided.
Type:
Grant
Filed:
April 30, 2010
Date of Patent:
January 15, 2019
Assignee:
Genomic Health, Inc.
Inventors:
Steven Shak, Drew Watson, Xitong Li, Lawrence Lee, Kim Clark-Langone
Abstract: The present invention provides algorithm-based molecular assays that involve measurement of expression levels of genes from a biological sample obtained from a kidney cancer patient. The present invention also provides methods of obtaining a quantitative score for a patient with kidney cancer based on measurement of expression levels of genes from a biological sample obtained from a kidney cancer patient. The genes may be grouped into functional gene subsets for calculating the quantitative score and the gene subsets may be weighted according to their contribution to cancer recurrence.
Type:
Grant
Filed:
May 29, 2014
Date of Patent:
January 15, 2019
Assignee:
Genomic Health, Inc.
Inventors:
Steven Shak, George Andrew Watson, Michael R. Crager, Tara Maddala, Margarita Lopatin, Audrey Goddard, Dejan Knezevic, Christer Svedman
Abstract: The present invention relates to gene fusions and alternative spliced junctions associated with breast cancer. The present invention also relates to novel methods of identifying gene fusions and alternative spliced junctions in RNA sequencing data. The present invention further relates to predicting prognosis of a breast cancer patient based on the number of gene fusion events.
Type:
Grant
Filed:
November 4, 2013
Date of Patent:
January 1, 2019
Assignee:
Genomic Health, Inc.
Inventors:
Yan Ma, Kunbin Qu, Mei-Lan Liu, Ranjana Ambannavar, James Stephans
Abstract: The invention relates to methods of depleting RNA from a nucleic acid sample. The RNA may be any RNA, including, but not limited to, rRNA, tRNA, and mRNA. The method is useful for depleting RNA from a nucleic acid sample obtained from a fixed paraffin-embedded tissue (FPET) sample. The method may also be used to prepare cDNA, in particular, a cDNA library for further analysis or manipulation.
Abstract: The invention relates to methods of depleting RNA from a nucleic acid sample. The RNA may be any RNA, including, but not limited to, rRNA, tRNA, and mRNA. The method is useful for depleting RNA from a nucleic acid sample obtained from a fixed paraffin-embedded tissue (FPET) sample. The method may also be used to prepare cDNA, in particular, a cDNA library for further analysis or manipulation.
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.
Type:
Application
Filed:
August 11, 2017
Publication date:
February 22, 2018
Applicants:
Genomic Health, Inc., NSABP Foundation, Inc.
Inventors:
Joffre B. BAKER, John L. BRYANT, Soonmyung PAIK, Steven SHAK
Abstract: The present invention provides methods to determine the prognosis and appropriate treatment for patients diagnosed with cancer, based on the expression levels of one or more biomarkers. More particularly, the invention relates to the identification of genes, or sets of genes, able to distinguish breast cancer patients with a good clinical prognosis from those with a bad clinical prognosis. The invention further provides methods for providing a personalized genomics report for a cancer patient. The inventions also relates to computer systems and software for data analysis using the prognostic and statistical methods disclosed herein.
Type:
Application
Filed:
February 3, 2017
Publication date:
July 27, 2017
Applicant:
GENOMIC HEALTH, INC.
Inventors:
Joffre B. BAKER, Maureen T. CRONIN, Francois COLLIN, Mei-Lan LIU
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.
Type:
Application
Filed:
December 5, 2016
Publication date:
May 4, 2017
Applicant:
GENOMIC HEALTH, INC.
Inventors:
Wayne COWENS, Steven SHAK, Audrey GODDARD, Dejan KNEZEVIC, Joffre BAKER, Michael C. KIEFER, Tara MADDALA, Frederick L. BAEHNER
Abstract: The present invention provides sets of genes the expression of which is important in the prognosis of cancer. In particular, the invention provides gene expression information useful for predicting whether cancer patients are likely to have a beneficial treatment response to chemotherapy FHIT; MTA1; ErbB4; FUS; BBC3; IGF1R; CD9; TP53BP1; MUC1; IGFBP5; rhoC; RALBP1; STAT3; ERK1; SGCB; DHPS; MGMT; CRIP2; ErbB3; RAP1GDS1; CCND1; PRKCD; Hepsin; AK055699; ZNF38; SEMA3F; COL1A1; BAG1; AKT1; COL1A2; Wnt.5a; PTPD1; RAB6C; GSTM1, BCL2, ESR1; or the corresponding expression product, is determined, said report includes a prediction that said subject has a decreased likelihood of response to chemotherapy.
Type:
Grant
Filed:
November 8, 2010
Date of Patent:
March 28, 2017
Assignee:
Genomic Health, Inc.
Inventors:
Joffre B. Baker, Steven Shak, Luca Gianni
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.
Type:
Grant
Filed:
January 7, 2011
Date of Patent:
January 24, 2017
Assignee:
Genomic Health, Inc.
Inventors:
Wayne Cowens, Steven Shak, Audrey Goddard, Dejan Knezevic, Joffre Baker, Michael C. Kiefer, Tara Maddala, Frederick L. Baehner