Genomic Health, Inc.

United States of America

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Date
2024 March 1
2024 (YTD) 1
2023 1
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IPC Class
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids 37
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer 9
C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical 6
C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides 6
G01N 33/574 - Immunoassay; Biospecific binding assay; Materials therefor for cancer 5
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Status
Pending 3
Registered / In Force 46
Found results for  patents

1.

Method to Use Gene Expression to Determine Likelihood of Clinical Outcome of Renal Cancer

      
Application Number 18454312
Status Pending
Filing Date 2023-08-23
First Publication Date 2024-03-21
Owner Genomic Health, Inc. (USA)
Inventor
  • Cowens, Wayne
  • Shak, Steven
  • Goddard, Audrey
  • Knezevic, Dejan
  • Baker, Joffre
  • Kiefer, Michael C.
  • Maddala, Tara
  • Baehner, Frederick L.

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.

IPC Classes  ?

  • G16B 99/00 - Subject matter not provided for in other groups of this subclass
  • G01N 33/574 - Immunoassay; Biospecific binding assay; Materials therefor for cancer
  • G06N 7/01 - Probabilistic graphical models, e.g. probabilistic networks
  • G16B 25/10 - Gene or protein expression profiling; Expression-ratio estimation or normalisation

2.

DNA Methylation and Mutational Analysis Methods for Bladder Cancer Surveillance

      
Application Number 18130547
Status Pending
Filing Date 2023-04-04
First Publication Date 2023-11-23
Owner Genomic Health, Inc. (USA)
Inventor
  • Lopatin, Margarita
  • Tsiatis, Athanasios
  • Silk, Christopher N.
  • Miller, David P.
  • Crager, Michael R.
  • Febbo, Phillip
  • Knezevic, Dejan

Abstract

The present disclosure relates to methods of monitoring bladder cancer patients and analyzing patient samples for presence of methylated DNA and optionally particular gene mutations. In some embodiments, analysis results are correlated with clinical outcome measures such as risk of bladder cancer recurrence.

IPC Classes  ?

  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • A61P 35/00 - Antineoplastic agents

3.

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

      
Application Number 16952566
Grant Number 11776664
Status In Force
Filing Date 2020-11-19
First Publication Date 2022-02-17
Grant Date 2023-10-03
Owner Genomic Health, Inc. (USA)
Inventor
  • Cowens, Wayne
  • Shak, Steven
  • Goddard, Audrey
  • Knezevic, Dejan
  • Baker, Joffre
  • Kiefer, Michael C.
  • Maddala, Tara
  • Baehner, Frederick L.

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.

IPC Classes  ?

  • G01N 33/574 - Immunoassay; Biospecific binding assay; Materials therefor for cancer
  • G16B 99/00 - Subject matter not provided for in other groups of this subclass
  • G16B 25/10 - Gene or protein expression profiling; Expression-ratio estimation or normalisation
  • G06N 7/01 - Probabilistic graphical models, e.g. probabilistic networks

4.

Gene expression profile algorithm for calculating a recurrence score for a patient with kidney cancer

      
Application Number 17086850
Grant Number 11551782
Status In Force
Filing Date 2020-11-02
First Publication Date 2022-02-10
Grant Date 2023-01-10
Owner Genomic Health, Inc. (USA)
Inventor
  • Shak, Steven
  • Watson, George Andrew
  • Crager, Michael R.
  • Maddala, Tara
  • Lopatin, Margarita
  • Goddard, Audrey
  • Knezevic, Dejan
  • Svedman, Christer

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.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
  • G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
  • G16C 99/00 - Subject matter not provided for in other groups of this subclass
  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
  • G16Z 99/00 - Subject matter not provided for in other main groups of this subclass

5.

METHODS TO PREDICT CLINICAL OUTCOME OF CANCER

      
Application Number 17018143
Status Pending
Filing Date 2020-09-11
First Publication Date 2021-03-04
Owner GENOMIC HEALTH, INC. (USA)
Inventor
  • Baker, Joffre B.
  • Cronin, Maureen T.
  • Collin, Francois
  • Liu, Mei-Lan

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.

IPC Classes  ?

  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • G16B 25/00 - ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

6.

DNA methylation and mutational analysis methods for bladder cancer surveillance

      
Application Number 16612926
Grant Number 11649506
Status In Force
Filing Date 2018-05-17
First Publication Date 2020-05-28
Grant Date 2023-05-16
Owner Genomic Health, Inc. (USA)
Inventor
  • Lopatin, Margarita
  • Tsiatis, Athanasios
  • Silk, Christopher N.
  • Miller, David P.
  • Crager, Michael
  • Febbo, Phillip
  • Knezevic, Dejan

Abstract

The present disclosure relates to methods of monitoring bladder cancer patients and analyzing patient samples for presence of methylated DNA and optionally particular gene mutations. In some embodiments, analysis results are correlated with clinical outcome measures such as risk of bladder cancer recurrence.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • A61P 35/00 - Antineoplastic agents

7.

Systems and methods for pre-analytical substrate processing

      
Application Number 16449075
Grant Number 11807900
Status In Force
Filing Date 2019-06-21
First Publication Date 2019-12-26
Grant Date 2023-11-07
Owner Genomic Health, Inc. (USA)
Inventor
  • Yeung, Hubert
  • Yuan, Amy Lee Hsieh
  • Lee, Chun Wai
  • Moraleda, Gabriel Jesus Samuel Perlas
  • Cassel, Jonathan M.

Abstract

Some embodiments presented in this disclosure concern an Automated Tissue Dissection (ATD) System. An ATD system is a one stop, and potentially low-cost, system to perform dissections on a substrate from pathologist digital mark or pen mark on the substrate using non-contact and/or mechanical method to extract a Formalin-Fixed Paraffin-Embedded (FFPE) tissue sample with: (a) only the ROI or ROIs as area to be saved; and (b) remove or decompose nucleic acid content in the region of no interest (RONI) and collect all tissue sample from a standard microscope substrate into a specific container.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q 1/686 - Polymerase chain reaction [PCR]
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
  • C12Q 1/6865 - Promoter-based amplification, e.g. nucleic acid sequence-based amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]
  • C12Q 1/6813 - Hybridisation assays

8.

Gene expression markers for breast cancer prognosis

      
Application Number 15897617
Grant Number 11220715
Status In Force
Filing Date 2018-02-15
First Publication Date 2018-08-16
Grant Date 2022-01-11
Owner Genomic Health, Inc. (USA)
Inventor
  • Cobleigh, Melody A.
  • Shak, Steven
  • Baker, Joffre B.
  • Cronin, Maureen T.

Abstract

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

IPC Classes  ?

  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer

9.

Methods for depleting RNA from nucleic acid samples

      
Application Number 15866840
Grant Number 11149297
Status In Force
Filing Date 2018-01-10
First Publication Date 2018-07-26
Grant Date 2021-10-19
Owner Genomic Health, Inc. (USA)
Inventor
  • Sinicropi, Dominick
  • Morlan, John

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.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
  • C12Q 1/6848 - Nucleic acid amplification reactions characterised by the means for preventing contamination or increasing the specificity or sensitivity of an amplification reaction
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

10.

Prediction of likelihood of cancer recurrence

      
Application Number 15674817
Grant Number 10619215
Status In Force
Filing Date 2017-08-11
First Publication Date 2018-02-22
Grant Date 2020-04-14
Owner Genomic Health, Inc. (USA)
Inventor
  • Baker, Joffre B.
  • Bryant, John L.
  • Paik, Soonmyung
  • Shak, Steven

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.

IPC Classes  ?

  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer

11.

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

      
Application Number 15368979
Grant Number 10892038
Status In Force
Filing Date 2016-12-05
First Publication Date 2017-05-04
Grant Date 2021-01-12
Owner Genomic Health, Inc. (USA)
Inventor
  • Cowens, Wayne
  • Shak, Steven
  • Goddard, Audrey
  • Knezevic, Dejan
  • Baker, Joffre
  • Kiefer, Michael C.
  • Maddala, Tara
  • Baehner, Frederick L.

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.

IPC Classes  ?

  • G01N 33/574 - Immunoassay; Biospecific binding assay; Materials therefor for cancer
  • G16B 99/00 - Subject matter not provided for in other groups of this subclass
  • G06N 7/00 - Computing arrangements based on specific mathematical models

12.

Gene expression profile algorithm for calculating a recurrence score for a patient with kidney cancer

      
Application Number 14779428
Grant Number 10181008
Status In Force
Filing Date 2014-05-29
First Publication Date 2016-02-18
Grant Date 2019-01-15
Owner Genomic Health, Inc. (USA)
Inventor
  • Shak, Steven
  • Watson, George Andrew
  • Crager, Michael R.
  • Maddala, Tara
  • Lopatin, Margarita
  • Goddard, Audrey
  • Knezevic, Dejan
  • Svedman, Christer

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.

IPC Classes  ?

  • G06F 19/00 - Digital computing or data processing equipment or methods, specially adapted for specific applications (specially adapted for specific functions G06F 17/00;data processing systems or methods specially adapted for administrative, commercial, financial, managerial, supervisory or forecasting purposes G06Q;healthcare informatics G16H)
  • G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment

13.

Methods for depleting RNA from nucleic acid samples

      
Application Number 14644455
Grant Number 09902991
Status In Force
Filing Date 2015-03-11
First Publication Date 2015-10-22
Grant Date 2018-02-27
Owner GENOMIC HEALTH, INC. (USA)
Inventor
  • Sinicropi, Dominick
  • Morlan, John

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.

IPC Classes  ?

  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

14.

Gene fusions and alternatively spliced junctions associated with breast cancer

      
Application Number 14440582
Grant Number 10169530
Status In Force
Filing Date 2013-11-04
First Publication Date 2015-10-22
Grant Date 2019-01-01
Owner Genomic Health, Inc. (USA)
Inventor
  • Ma, Yan
  • Qu, Kunbin
  • Liu, Mei-Lan
  • Ambannavar, Ranjana
  • Stephans, James

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.

IPC Classes  ?

  • G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • G06F 19/22 - for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism [SNP] discovery or sequence alignment
  • G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems

15.

Gene expression markers for breast cancer prognosis

      
Application Number 14257723
Grant Number 09944990
Status In Force
Filing Date 2014-04-21
First Publication Date 2014-09-25
Grant Date 2018-04-17
Owner GENOMIC HEALTH, INC. (USA)
Inventor
  • Cobleigh, Melody A.
  • Shak, Steven
  • Baker, Joffre B.
  • Cronin, Maureen T.

Abstract

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

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

16.

Gene expression markers for colorectal cancer prognosis

      
Application Number 13413338
Grant Number 08367345
Status In Force
Filing Date 2012-03-06
First Publication Date 2012-07-05
Grant Date 2013-02-05
Owner
  • Genomic Health Inc. (USA)
  • NSABP Foundation, Inc. (USA)
Inventor
  • Cowens, Wayne
  • Baker, Joffre B.
  • Clark-Langane, Kim
  • Hackett, James
  • Watson, Drew
  • Paik, Soonmyung

Abstract

A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

17.

Gene expression markers for prediction of patient response to chemotherapy

      
Application Number 13278934
Grant Number 08632980
Status In Force
Filing Date 2011-10-21
First Publication Date 2012-02-16
Grant Date 2014-01-21
Owner
  • Genomic Health, Inc. (USA)
  • NSABP Foundation, Inc (USA)
Inventor
  • Baker, Joffre B.
  • Cowens, Wayne
  • Langone, Kim
  • Hackett, James
  • Watson, Drew
  • Paik, Soonmyung

Abstract

The present invention relates to gene sets useful in assessing prognosis and/or predicting the response of cancer, e.g. colorectal cancer to chemotherapy. In addition, the invention relates to a clinically validated cancer test, e.g. colorectal test, for assessment of prognosis and/or prediction of patient response to chemotherapy, using expression analysis. The present invention accommodates the use of archived paraffin embedded biopsy material for assay of all markers in the relevant gene sets and therefore is compatible with the most widely available type of biopsy material.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

18.

Genes involved in estrogen metabolism

      
Application Number 12971874
Grant Number 08906625
Status In Force
Filing Date 2010-12-17
First Publication Date 2011-11-10
Grant Date 2014-12-09
Owner Genomic Health, Inc. (USA)
Inventor
  • Kiefer, Michael C.
  • Baker, Joffre B.
  • Hackett, James

Abstract

The invention concerns genes that have been identified as being involved in estrogen metabolism, and are useful as diagnostic, prognostic and/or predictive markers in cancer. In particular, the invention concerns genes the tumor expression levels of which are useful in the diagnosis of cancers associated with estrogen metabolism, and/or in the prognosis of clinical outcome and/or prediction of drug response of such cancers.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

19.

Genes involved in estrogen metabolism

      
Application Number 12972148
Grant Number 08808994
Status In Force
Filing Date 2010-12-17
First Publication Date 2011-11-10
Grant Date 2014-08-19
Owner Genomic Health, Inc. (USA)
Inventor
  • Kiefer, Michael C.
  • Baker, Joffre B.
  • Hackett, James

Abstract

The invention concerns genes that have been identified as being involved in estrogen metabolism, and are useful as diagnostic, prognostic and/or predictive markers in cancer. In particular, the invention concerns genes the tumor expression levels of which are useful in the diagnosis of cancers associated with estrogen metabolism, and/or in the prognosis of clinical outcome and/or prediction of drug response of such cancers.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12P 19/32 - Nucleotides having a condensed ring system containing a six-membered ring having two nitrogen atoms in the same-ring, e.g. purine nucleotides, nicotineamide-adenine dinucleotide

20.

Predicting response to chemotherapy using gene expression markers

      
Application Number 13049568
Grant Number 08868352
Status In Force
Filing Date 2011-03-16
First Publication Date 2011-07-21
Grant Date 2014-10-21
Owner GENOMIC HEALTH, INC. (USA)
Inventor
  • Baker, Joffre B.
  • Bryant, John L.
  • Paik, Soonmyung
  • Shak, Steven

Abstract

The present invention provides gene expression information useful for predicting whether a cancer patient is likely to have a beneficial response to treatment with chemotherapy, comprising measuring, in a biological sample comprising a breast tumor sample obtained from the patient, the expression levels of gene subsets to obtain a risk score associated with a likelihood of a beneficial response to chemotherapy, wherein the score comprises at least one of the following variables: (i) Recurrence Score, (ii) ESRI Group Score; (iii) Invasion Group Score; (iv) Proliferation Group Score; and (v) the expression level of the RNA transcript of at least one of MYBL2 and SCUBE2, or the corresponding expression product. The invention further comprises a molecular assay-based algorithm to calculate the likelihood that the patient will have a beneficial response to chemotherapy based on the risk score.

IPC Classes  ?

  • G06F 19/24 - for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
  • G06F 19/20 - for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation

21.

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

      
Application Number 12987023
Grant Number 09551034
Status In Force
Filing Date 2011-01-07
First Publication Date 2011-07-14
Grant Date 2017-01-24
Owner Genomic Health, Inc. (USA)
Inventor
  • Cowens, Wayne
  • Shak, Steven
  • Goddard, Audrey
  • Knezevic, Dejan
  • Baker, Joffre
  • Kiefer, Michael C.
  • Maddala, Tara
  • Baehner, Frederick L.

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.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • G01N 33/574 - Immunoassay; Biospecific binding assay; Materials therefor for cancer

22.

Gene expression markers for predicting response to chemotherapy

      
Application Number 12941877
Grant Number 09605318
Status In Force
Filing Date 2010-11-08
First Publication Date 2011-06-02
Grant Date 2017-03-28
Owner Genomic Health, Inc. (USA)
Inventor
  • Baker, Joffre B.
  • Shak, Steven
  • Gianni, Luca

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.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

23.

Methods for depleting RNA from nucleic acid samples

      
Application Number 12940981
Grant Number 09005891
Status In Force
Filing Date 2010-11-05
First Publication Date 2011-05-12
Grant Date 2015-04-14
Owner Genomic Health, Inc. (USA)
Inventor
  • Sinicropi, Dominick
  • Morlan, John

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.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA

24.

Gene expression markers for colorectal cancer prognosis

      
Application Number 13009733
Grant Number 08198024
Status In Force
Filing Date 2011-01-19
First Publication Date 2011-05-12
Grant Date 2012-06-12
Owner
  • Genomic Health, Inc. (USA)
  • NSABP Foundation, Inc. (USA)
Inventor
  • Watson, Drew
  • Paik, Soonmyung
  • Cowens, Wayne
  • Baker, Joffre B.
  • Clark, Kim
  • Hackett, James

Abstract

A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

25.

Gene expression markers for colorectal cancer prognosis

      
Application Number 12911519
Grant Number 08273537
Status In Force
Filing Date 2010-10-25
First Publication Date 2011-04-28
Grant Date 2012-09-25
Owner
  • Genomic Health, Inc. (USA)
  • NSABP Foundation, Inc. (USA)
Inventor
  • Watson, Drew
  • Paik, Soonmyung
  • Cowens, Wayne
  • Baker, Joffre B.
  • Clark, Kim
  • Hackett, James

Abstract

A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

26.

Gene expression markers for colorectal cancer prognosis

      
Application Number 12911532
Grant Number 08029995
Status In Force
Filing Date 2010-10-25
First Publication Date 2011-02-17
Grant Date 2011-10-04
Owner
  • Genomic Health, Inc. (USA)
  • NSABP Foundation, Inc. (USA)
Inventor
  • Watson, Drew
  • Paik, Soonmyung
  • Cowens, Wayne
  • Baker, Joffre B.
  • Clark, Kim
  • Hackett, James

Abstract

A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

27.

Gene expression markers for colorectal cancer prognosis

      
Application Number 12911544
Grant Number 08153380
Status In Force
Filing Date 2010-10-25
First Publication Date 2011-02-17
Grant Date 2012-04-10
Owner
  • Genomic Health, Inc. (USA)
  • NSABP Foundation, Inc. (USA)
Inventor
  • Watson, Drew
  • Paik, Soonmyung
  • Cowens, Wayne
  • Baker, Joffre B.
  • Clark, Kim
  • Hackett, James

Abstract

A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

28.

Gene expression markers for colorectal cancer prognosis

      
Application Number 12911551
Grant Number 08026060
Status In Force
Filing Date 2010-10-25
First Publication Date 2011-02-17
Grant Date 2011-09-27
Owner
  • Genomic Health, Inc. (USA)
  • NSABP Foundation, Inc. (USA)
Inventor
  • Watson, Drew
  • Paik, Soonmyung
  • Cowens, Wayne
  • Baker, Joffre B.
  • Clark, Kim
  • Hackett, James

Abstract

A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

29.

Gene expression markers for colorectal cancer prognosis

      
Application Number 12911526
Grant Number 08153379
Status In Force
Filing Date 2010-10-25
First Publication Date 2011-02-17
Grant Date 2012-04-10
Owner
  • Genomic Health, Inc. (USA)
  • NSABP Foundation, Inc. (USA)
Inventor
  • Watson, Drew
  • Paik, Soonmyung
  • Cowens, Wayne
  • Baker, Joffre B.
  • Clark, Kim
  • Hackett, James

Abstract

A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

30.

Methods of predicting cancer risk using gene expression in premalignant tissue

      
Application Number 12755368
Grant Number 08765383
Status In Force
Filing Date 2010-04-06
First Publication Date 2010-11-18
Grant Date 2014-07-01
Owner Genomic Health, Inc. (USA)
Inventor
  • Cowens, Wayne
  • Cronin, Maureen T.
  • Millward, Carl L.
  • Collin, Francois
  • Crager, Michael

Abstract

The present disclosure provides methods for assessing a patient's cancer risk and/or recurrence risk, which methods comprise assaying, in a biological sample obtained from the gastrointestinal (GI) tract of the patient, an expression level of a risk gene. The present disclosure also provides methods involving a cancer risk/recurrence risk sequence, i.e. the V600E mutation of the BRAF gene, which is useful for assessing cancer risk and/or recurrence risk in a patient.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

31.

Gene expression profile algorithm and test for likelihood of recurrence of colorectal cancer and response to chemotherapy

      
Application Number 12772136
Grant Number 10179936
Status In Force
Filing Date 2010-04-30
First Publication Date 2010-11-11
Grant Date 2019-01-15
Owner Genomic Health, Inc. (USA)
Inventor
  • Shak, Steven
  • Watson, Drew
  • Li, Xitong
  • Lee, Lawrence
  • Clark-Langone, Kim

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.

IPC Classes  ?

  • C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
  • G06F 19/20 - for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation
  • G01N 33/574 - Immunoassay; Biospecific binding assay; Materials therefor for cancer
  • G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
  • G06F 19/00 - Digital computing or data processing equipment or methods, specially adapted for specific applications (specially adapted for specific functions G06F 17/00;data processing systems or methods specially adapted for administrative, commercial, financial, managerial, supervisory or forecasting purposes G06Q;healthcare informatics G16H)

32.

Gene expression markers for breast cancer prognosis

      
Application Number 12478632
Grant Number 08034565
Status In Force
Filing Date 2009-06-04
First Publication Date 2010-09-02
Grant Date 2011-10-11
Owner Genomic Health, Inc. (USA)
Inventor
  • Cobleigh, Melody A.
  • Shak, Steven
  • Baker, Joffre B.
  • Cronin, Maureen T.

Abstract

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

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

33.

Gene expression markers for colorectal cancer prognosis

      
Application Number 12696934
Grant Number 08153378
Status In Force
Filing Date 2010-01-29
First Publication Date 2010-07-29
Grant Date 2012-04-10
Owner
  • Genomic Health, Inc. (USA)
  • NSABP Foundations, Inc. (USA)
Inventor
  • Cowens, Wayne
  • Baker, Joffre B.
  • Clark, Kim
  • Hackett, James
  • Watson, Drew
  • Paik, Soonmyung

Abstract

A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

34.

Gene expression markers for prediction of patient response to chemotherapy

      
Application Number 12404268
Grant Number 08067178
Status In Force
Filing Date 2009-03-13
First Publication Date 2009-12-10
Grant Date 2011-11-29
Owner
  • Genomic Health, Inc. (USA)
  • NSABP Foundation, Inc. (USA)
Inventor
  • Baker, Joffre B.
  • Cowens, Wayne
  • Langone, Kim
  • Hackett, James
  • Watson, Drew
  • Paik, Soonmyung

Abstract

The present invention relates to gene sets useful in assessing prognosis and/or predicting the response of cancer, e.g. colorectal cancer to chemotherapy. In addition, the invention relates to a clinically validated cancer test, e.g. colorectal test, for assessment of prognosis and/or prediction of patient response to chemotherapy, using expression analysis. The present invention accommodates the use of archived paraffin embedded biopsy material for assay of all markers in the relevant gene sets and therefore is compatible with the most widely available type of biopsy material.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • G01N 33/53 - Immunoassay; Biospecific binding assay; Materials therefor

35.

Predictors of patient response to treatment with EGF receptor inhibitors

      
Application Number 12465503
Grant Number 08273534
Status In Force
Filing Date 2009-05-13
First Publication Date 2009-12-03
Grant Date 2012-09-25
Owner
  • Genomic Health, Inc. (USA)
  • Bristol-Myers Squibb Company (USA)
Inventor
  • Baker, Joffre B.
  • Watson, Drew
  • Maddala, Tara
  • Shak, Steven
  • Mauro, David J.
  • Ford, Shirin K.

Abstract

The present invention provides methods and compositions to facilitate determining whether an EGFR-expressing cancer in an individual is an EGFR inhibitor-responsive cancer, as well as methods for determining the likelihood that a patient having an EGFR-expressing cancer will exhibit a beneficial response to an EGFR inhibitor therapy. The methods generally involve determining a normalized expression level of a gene product that correlates with EGFR inhibitor responsiveness.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

36.

Gene expression markers for colorectal cancer prognosis

      
Application Number 11653102
Grant Number 07695913
Status In Force
Filing Date 2007-01-11
First Publication Date 2009-11-26
Grant Date 2010-04-13
Owner
  • Genomic Health, Inc. (USA)
  • NSABP Foundation, Inc. (USA)
Inventor
  • Cowens, Wayne
  • Baker, Joffre B.
  • Clark, Kim
  • Hackett, James
  • Watson, Drew
  • Paik, Soonmyung

Abstract

A method of predicting clinical outcome in a subject diagnosed with colorectal cancer comprising determining evidence of the expression of one or more predictive RNA transcripts or their expression products in a biological sample of cancer cells obtained from the subject.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

37.

Method and system to characterize transcriptionally active regions and quantify sequence abundance for large scale sequencing data

      
Application Number 12121412
Grant Number 08566039
Status In Force
Filing Date 2008-05-15
First Publication Date 2009-11-19
Grant Date 2013-10-22
Owner Genomic Health, Inc. (USA)
Inventor
  • Li, Xitong
  • Stineman, Kenneth

Abstract

This invention provides a quantitative method to determine transcriptionally active regions and quantify sequence abundance from large scale sequencing data. The invention also provides a system based on reference sequences to design and implement the method. The system processes large scale sequence data from high throughput sequencing, generates transcriptionally active region sequences as necessary, and quantifies the sequence abundance of the gene or transcriptionally active region. The method and system are useful for many analyses based on RNA expression profiling.

IPC Classes  ?

  • G01N 33/48 - Biological material, e.g. blood, urine; Haemocytometers
  • G06F 19/00 - Digital computing or data processing equipment or methods, specially adapted for specific applications (specially adapted for specific functions G06F 17/00;data processing systems or methods specially adapted for administrative, commercial, financial, managerial, supervisory or forecasting purposes G06Q;healthcare informatics G16H)

38.

Expression profile algorithm and test for cancer prognosis

      
Application Number 12406831
Grant Number 07939261
Status In Force
Filing Date 2009-03-18
First Publication Date 2009-11-12
Grant Date 2011-05-10
Owner
  • GENOMIC HEALTH, INC. (USA)
  • GENOMIC HEALTH, INC. (USA)
Inventor
  • Baker, Joffre B.
  • Bryant, John L.
  • Paik, Soonmyung
  • Shak, Steven

Abstract

The present invention provides a noninvasive, quantitative test for prognosis determination in cancer patients. The test relies on measurements of the tumor levels of certain messenger RNAs (mRNAs). These mRNA levels are inserted into a polynomial formula (algorithm) that yields a numerical recurrence score, which indicates recurrence risk.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • G06F 19/00 - Digital computing or data processing equipment or methods, specially adapted for specific applications (specially adapted for specific functions G06F 17/00;data processing systems or methods specially adapted for administrative, commercial, financial, managerial, supervisory or forecasting purposes G06Q;healthcare informatics G16H)

39.

Universal amplification of fragmented RNA

      
Application Number 11959251
Grant Number 08329398
Status In Force
Filing Date 2007-12-18
First Publication Date 2009-02-12
Grant Date 2012-12-11
Owner Genomic Health, Inc. (USA)
Inventor
  • Kiefer, Michael C.
  • Hoyt, Kenneth W.

Abstract

The invention relates to methods of using fragmented RNA, such as RNA obtained from archived fixed paraffin-embedded tissue material (FPET RNA) or other clinically biopsied tissue specimens for universal gene expression profiling.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C07H 21/02 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with ribosyl as saccharide radical

40.

Genes involved estrogen metabolism

      
Application Number 11731196
Grant Number 07888019
Status In Force
Filing Date 2007-03-30
First Publication Date 2007-11-29
Grant Date 2011-02-15
Owner Genomic Health, Inc. (USA)
Inventor
  • Kiefer, Michael C.
  • Baker, Joffre B.
  • Hackett, James

Abstract

The invention concerns genes that have been identified as being involved in estrogen metabolism, and are useful as diagnostic, prognostic and/or predictive markers in cancer. In particular, the invention concerns genes the tumor expression levels of which are useful in the diagnosis of cancers associated with estrogen metabolism, and/or in the prognosis of clinical outcome and/or prediction of drug response of such cancers.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

41.

Prediction of likelihood of cancer recurrence

      
Application Number 11345611
Grant Number 07723033
Status In Force
Filing Date 2006-01-31
First Publication Date 2006-12-21
Grant Date 2010-05-25
Owner GENOMIC HEALTH, INC. (USA)
Inventor
  • Baker, Joffre B.
  • Bryant, John L.
  • Paik, Soonmyung
  • Shak, Steven

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.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical

42.

Predicting response to chemotherapy using gene expression markers

      
Application Number 11267769
Grant Number 07930104
Status In Force
Filing Date 2005-11-04
First Publication Date 2006-07-27
Grant Date 2011-04-19
Owner GENOMIC HEALTH, INC. (USA)
Inventor
  • Baker, Joffre B.
  • Bryant, John L.
  • Paik, Soonmyung
  • Shak, Steven

Abstract

The present invention provides gene expression information useful for predicting whether a cancer patient is likely to have a beneficial response to treatment with chemotherapy, comprising measuring, in a biological sample comprising a breast tumor sample obtained from the patient, the expression levels of gene subsets to obtain a risk score associated with a likelihood of a beneficial response to chemotherapy, wherein the score comprises at least one of the following variables: (i) Recurrence Score, (ii) ESRI Group Score; (iii) Invasion Group Score; (iv) Proliferation Group Score; and (v) the expression level of the RNA transcript of at least one of MYBL2 and SCUBE2, or the corresponding expression product. The invention further comprises a molecular assay-based algorithm to calculate the likelihood that the patient will have a beneficial response to chemotherapy based on the risk score.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • G01N 33/48 - Biological material, e.g. blood, urine; Haemocytometers
  • G06G 7/58 - Analogue computers for specific processes, systems, or devices, e.g. simulators for chemical processes

43.

Molecular indicators of breast cancer prognosis and prediction of treatment response

      
Application Number 11267807
Grant Number 07622251
Status In Force
Filing Date 2005-11-04
First Publication Date 2006-07-27
Grant Date 2009-11-24
Owner
  • Genomic Health, Inc. (USA)
  • NSABP Foundation, Inc. (USA)
Inventor
  • Baker, Joffre B.
  • Bryant, John L.
  • Paik, Soonmyung
  • Shak, Steven

Abstract

The present invention relates to quantitative molecular indicators that can guide clinical decisions in breast cancer, such as estrogen receptor (ESR1)-positive, lymph node-negative breast cancer. In particular, the invention concerns certain genes, the varied expression of which indicates the likelihood of recurrence of surgically resected breast cancer in patients who are not treated with a therapeutic agent in the adjuvant setting. In addition, the invention concerns the use of quantitative measurement of the expression of certain genes, including the ESR1 gene, that measure as a continuous variable, to determine (a) the likelihood of a beneficial response to the anti-estrogen therapeutic agent, such as tamoxifen; and (b) the potential magnitude of beneficial response to chemotherapy.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

44.

Method for quantitative PCR data analysis system (QDAS)

      
Application Number 10886501
Grant Number 07587279
Status In Force
Filing Date 2004-07-06
First Publication Date 2006-01-12
Grant Date 2009-09-08
Owner Genomic Health (USA)
Inventor
  • Li, Xitong
  • Stineman, Kenneth

Abstract

T) value and classifying the status of the QPCR results.

IPC Classes  ?

  • G01N 33/48 - Biological material, e.g. blood, urine; Haemocytometers
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

45.

Gene expression markers for predicting response to chemotherapy

      
Application Number 11102228
Grant Number 07871769
Status In Force
Filing Date 2005-04-07
First Publication Date 2005-11-24
Grant Date 2011-01-18
Owner GENOMIC HEALTH, INC. (USA)
Inventor
  • Baker, Joffre B.
  • Shak, Steven
  • Gianni, Luca

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.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • G01N 33/53 - Immunoassay; Biospecific binding assay; Materials therefor
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical

46.

Prediction of likelihood of cancer recurrence

      
Application Number 10872063
Grant Number 07056674
Status In Force
Filing Date 2004-06-17
First Publication Date 2005-04-14
Grant Date 2006-06-06
Owner GENOMIC HEALTH, INC. (USA)
Inventor
  • Baker, Joffre B.
  • Bryant, John L.
  • Paik, Soonmyung
  • Shak, Steven

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.

IPC Classes  ?

  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

47.

Expression profile algorithm and test for cancer prognosis

      
Application Number 10883303
Grant Number 07526387
Status In Force
Filing Date 2004-06-30
First Publication Date 2005-03-03
Grant Date 2009-04-28
Owner
  • GENOMIC HEALTH, INC. (USA)
  • GENOMIC HEALTH, INC. (USA)
Inventor
  • Baker, Joffre B.
  • Bryant, John L.
  • Paik, Soonmyung
  • Shak, Steven

Abstract

The present invention provides a noninvasive, quantitative test for prognosis determination in cancer patients. The test relies on measurements of the tumor levels of certain messenger RNAs (mRNAs). These mRNA levels are inserted into a polynomial formula (algorithm) that yields a numerical recurrence score, which indicates recurrence risk.

IPC Classes  ?

  • G06F 19/00 - Digital computing or data processing equipment or methods, specially adapted for specific applications (specially adapted for specific functions G06F 17/00;data processing systems or methods specially adapted for administrative, commercial, financial, managerial, supervisory or forecasting purposes G06Q;healthcare informatics G16H)
  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

48.

Gene expression markers for breast cancer prognosis

      
Application Number 10758307
Grant Number 07569345
Status In Force
Filing Date 2004-01-14
First Publication Date 2004-10-21
Grant Date 2009-08-04
Owner GENOMIC HEALTH INC., (USA)
Inventor
  • Cobleigh, Melody A.
  • Shak, Steve
  • Baker, Joffre B.
  • Cronin, Maureen T.

Abstract

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

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids

49.

Use of intronic RNA to measure gene expression

      
Application Number 10783884
Grant Number 07767391
Status In Force
Filing Date 2004-02-19
First Publication Date 2004-09-30
Grant Date 2010-08-03
Owner Genomic Health, Inc. (USA)
Inventor
  • Scott, Randy
  • Baker, Joffre B.
  • Kiefer, Michael C.

Abstract

The invention is based on the use of intronic RNA in monitoring gene expression. Accordingly, the present invention concerns methods of gene expression profiling using intronic RNA, the expression of which correlates with the expression of corresponding exonic RNA, and diagnostic and prognostic methods based on the results of such gene expression studies.

IPC Classes  ?

  • C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
  • C07H 21/04 - Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids with deoxyribosyl as saccharide radical