Markers and Methods for Assessing and Treating Ulcerative Colitis and Related Disorders Using 66 Gene Panel
First Claim
Patent Images
1. 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;
1-66 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.
1 Assignment
0 Petitions
Accused Products
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.
11 Citations
49 Claims
-
1. 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;
1-66 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. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 48)
-
-
18. 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 represented by nucleic acids consisting of at least one member from the group consisting of SEQ ID NOS;
1-26,29, 30, and 38 to defect 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.
-
-
19. 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 consisting of SEQ ID NOS;
1-66 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, - View Dependent Claims (20, 21, 22, 23, 24, 25, 26, 27, 28)
-
-
29. 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:
- 1-66, a polypeptide encoded by at least a portion of one of SEQ ID NOS;
1-66, and a ligand for the polypeptide encoded by at least a portion of one of SEQ ID NOS;
1-66. - View Dependent Claims (30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46)
- 1-66, a polypeptide encoded by at least a portion of one of SEQ ID NOS;
-
40. 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 master gene, wherein the marker gene is selected from the group consisting of SEQ ID NOS:
- 1-66.
-
41. 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 ceils expressing the marker gene, wherein the marker gene is selected from the group consisting of SEQ ID NOS:
- 1-66.
-
47. A method for prognostic or diagnostic assessment of a gastrointestinal-related disorder in a subject, comprising:
-
d) preparing a sample of nucleic acids from a specimen obtained from the subject; e) 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;
1-66 to detect the levels of the panel segments;f) 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 g) correlating the magnitude of change with the presence or resolution of the gastrointestinal-related disorder.
-
-
49. Any invention described herein.
Specification