Markers and Methods for Assessing and Treating Ulcerative Colitis and Related Disorders Using a 43 Gene Panel
OwnerXilin Li, Xiao-Yu Songinventors
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Abstract
A method for prognostic or diagnostic assessment of a gastrointestinal-related disorder, such as ulcerative colitis, in a subject correlates the presence, absence, and/or magnitude of a gene in a sample with a reference standard to determine the presence and/or severity of the disorder, and/or the response to treatment for the disorder. The method enables identification of the effectiveness of candidate therapies.
Claims49
A method for prognostic or diagnostic assessment of 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 2 genes represented by nucleic acids from the group consisting of SEQ ID NOS:1-43 to detect the 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 presence or resolution of the gastrointestinal-related disorder.
A method for prognostic or diagnostic assessment of a gastrointestinal-related disorder in a subject, comprising:
- a) preparing a sample of nucleic acids from a sample obtained from a patient;
- b) contacting the sample with a panel of nucleic acid segments consisting of at least one member represented by nucleic acids from the group consisting of SEQ ID NOS:
- 1, 7, 10-13, 15-18, 21, 33, and 35 to detect the presence of the panel segments;
- c) evaluating the sample against a reference standard to determine the change and/or magnitude of change-in the expression level of the amounts of the at least one member present in the sample;
- and
- d) correlating the change and/or magnitude of expression level with the presence or resolution of the gastrointestinal-related disorder.
An array-based testing method for prognostic or diagnostic assessment of a gastrointestinal-related disorder in a patient, comprising:
- a) preparing a mixture of nucleic acids from a specimen obtained from a 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 represented by nucleic acids consisting of SEQ ID NOS:
- 1-43 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 a prognostic or diagnostic assessment.
A reagent for testing the responsiveness of a cell or subject to a therapy for a gastrointestinal-related disorder, comprising at least one member selected from the group consisting of an oligonucleotide comprising at least 15 nucleotides complementary to a nucleotide sequence of one of SEQ ID NOS:
- 1-43, a polypeptide encoded by at least a portion of one of SEQ ID NOS:
- 1-43, and a ligand for the polypeptide encoded by at least a portion of one of SEQ ID NOS:
- 1-43.
A kit for prognostic or diagnostic use, comprising an oligonucleotide comprising at least 15 nucleotides 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 represented by nucleic acids selected from the group consisting of SEQ ID NOS:
- 1-43.
A kit for screening for 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 represented by nucleic acids selected from the group consisting of SEQ ID NOS:
- 1-43.
A method for prognostic or diagnostic assessment of 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 2 members from the group of genes represented by nucleic acids selected from the group consisting of SEQ ID NOS:
- 1-43 to detect the levels of the panel segments;
- c) evaluating the sample against a reference standard to determine the magnitude of change in the amounts of the at least 2 members present in the sample;
- and
- d) correlating the magnitude of change with the presence or resolution of the gastrointestinal-related disorder.
Any invention described herein.
Dependencies are inferred from the claim text.