Markers and Methods for Assessing and Treating Ulcerative Colitis and Related Disorders Using a 20 Gene Panel
First Claim
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1. 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 2 members from the group consisting of the nucleotide sequences corresponding to SEQ ID NOS;
1-20 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 2 members 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.
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Abstract
A method for assessment of the suitability of a target therapy for a gastrointestinal-related disorder, such as ulcerative colitis, in a subject evaluates the presence, absence, and/or magnitude of expression of one or more genes in a 20- or 5-member gene panel in a sample. The method enables identification of the effectiveness of target therapies prior to starting a patient on such therapies.
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Citations
64 Claims
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1. A method for predicting the suitability of treatment with a target therapy for a gastrointestinal-related disorder in a subject, comprising:
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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 2 members from the group consisting of the nucleotide sequences corresponding to SEQ ID NOS;
1-20 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 2 members 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. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
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18. A method for predicting the suitability of treatment with a target therapy for a gastrointestinal-related disorder in a subject, comprising:
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e) preparing a sample of nucleic acids from a specimen obtained from the subject; 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;
3, 5, 9, 10, and 14 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 suitability of treatment of the target therapy for the gastrointestinal-related disorder. - View Dependent Claims (19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36)
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37. An array-based testing method for predicting the suitability of treatment with a target therapy for a gastrointestinal-related disorder in a patient, comprising:
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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;
1-20 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. - View Dependent Claims (38, 39, 40, 41, 42, 43, 44, 45, 46)
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47. 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:
- 1-20, a polypeptide encoded by at least a portion of one of the nucleotide sequences corresponding to SEQ ID NOS;
1-20, and a ligand for the polypeptide encoded by at least a portion of one of the nucleotide sequences corresponding to SEQ ID NOS;
1-20. - View Dependent Claims (48, 49, 50, 51, 52, 53, 54, 55, 59, 60, 61, 62)
- 1-20, a polypeptide encoded by at least a portion of one of the nucleotide sequences corresponding to SEQ ID NOS;
- 56. 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:
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58. A kit for screening the suitability of a therapeutic agent for UC, 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:
- 1-20.
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63. A method for treating a subject having a gastrointestinal-related disorder with a target therapy, comprising:
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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 2 members from the group consisting of the nucleotide sequences corresponding to SEQ ID NOS;
1-20 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 2 members present in the sample; d) correlating the magnitude of change with the suitability of treatment with the target therapy for the gastrointestinal-related disorder; and e) treating the subject with the target therapy.
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64. Any invention described herein.
Specification