Markers and methods for assessing and treating crohn's disease and related disorders
AssigneeJanssen Biotech, Inc.
InventorsMarion Blank, Gary Toedter
Life of this patent
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Abstract
A method for assessment of the suitability of and/or effectiveness of a target therapy for a gastrointestinal-related disorder, such as Crohn's disease, in a subject evaluates the presence, absence, and/or magnitude of expression of one or more genes in a 10-member gene panel in a sample. The method enables identification of the effectiveness of target therapies prior to or after starting a patient on such therapies.
Claims71
A method for predicting the suitability of treatment with a target therapy for a gastrointestinal-related disorder in a subject, comprising:
- a) preparing a sample of nucleic acids from a specimen obtained from the subject;
- b) contacting the sample with a panel of nucleic acid segments consisting of at least a portion of at least one member from the group consisting of the nucleotide sequences corresponding to SEQ ID NOS:1-10 to detect levels of the panel segments;
- c) evaluating the sample against a reference standard to determine the magnitude of change in the amounts of at least one member present in the sample;
- and
- d) correlating the magnitude of change with the suitability of treatment with the target therapy for the gastrointestinal-related disorder.
A method for evaluating the effectiveness of treatment with a target therapy for a gastrointestinal-related disorder in a subject, comprising:
- e) preparing a sample of nucleic acids from a specimen obtained from the subject, the subject having received the target therapy before the specimen is obtained;
- f) contacting the sample with a panel of nucleic acid segments consisting of at least one member from the group consisting of the nucleotide sequences corresponding to SEQ ID NOS:1-10 to detect the levels of the panel segments;
- g) evaluating the sample against a reference standard to determine the magnitude of change in the amount of the at least one member present in the sample;
- and
- h) correlating the magnitude of change with the effectiveness of the target therapy for the gastrointestinal-related disorder.
An array-based testing method for predicting the suitability of treatment with a target therapy for a gastrointestinal-related disorder in a patient, comprising:
- a) preparing a mixture of nucleic acids from a specimen obtained from the patient;
- b) labeling said specimen nucleic acids with a detectable marker to form a sample;
- c) contacting the sample with an array comprising a plurality of nucleic acid segments, wherein each nucleic acid segment is immobilized to a discrete and known address on a substrate surface of the array, wherein at least two members of a gastrointestinal-related gene panel consisting of the nucleotide sequences corresponding to SEQ ID NOS:1-10 are identified as features of the array by address, and wherein said array further comprises at least one calibration nucleic acid at a known address on the substrate;
- d) determining the degree of binding of the specimen nucleic acids to the nucleic acid segments;
- and
- e) comparing the degree of binding to a reference standard to enable an assessment of the suitability of treatment.
A reagent for testing the suitability of a target therapy for a gastrointestinal-related disorder in a cell or subject, comprising at least one member selected from the group consisting of an oligonucleotide comprising at least 15 nucleotides comprising or complementary to a nucleotide sequence of one of the nucleotide sequences corresponding to SEQ ID NOS:1-10, a polypeptide encoded by at least a portion of one of the nucleotide sequences corresponding to SEQ ID NOS:1-10, and a ligand for the polypeptide encoded by at least a portion of one of the nucleotide sequences corresponding to SEQ ID NOS:1-10.
A kit for prognostic or diagnostic use, comprising an oligonucleotide comprising at least 15 nucleotides comprising or complementary to a polynucleotide comprising the nucleotide sequence of a marker gene or the complementary strand thereof and cells expressing the marker gene, wherein the marker gene is selected from the group consisting of the nucleotide sequences corresponding to SEQ ID NOS:1-10.
A kit for screening the suitability of a therapeutic agent for Crohn's disease, the kit comprising an antibody which recognizes a peptide comprising an amino acid sequence encoded by a marker gene and cells expressing the marker gene, wherein the marker gene is selected from the group consisting of the nucleotide sequences corresponding to SEQ ID NOS:1-10.
Any invention described herein.
Dependencies are inferred from the claim text.