# US 2014/0154275 A1 · Gene expression markers for crohn's disease > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2014/0154275 A1 - Document ID: US20140154275A1 - Status: Published application - Kind: A1 - Application number: 14/020,628 - Filed: 2013-09-06 - Published: 2014-06-05 - Earliest claimed: 2009-07-20 - Assignees: Genentech, Inc. - Applicants: Genentech, Inc. - Inventors: Alexander R. Abbas; Hilary Clark; Lauri Diehl; Charles Lees; Colin L. Noble; Jack Satsangi - Web page: https://patentgrep.com/patent/US20140154275A1 ## CPC - C12Q 1/6883: for diseases caused by alterations of genetic material - A61P 1/04: for ulcers, gastritis or reflux esophagitis, e.g. antacids, inhibitors of acid secretion, mucosal protectants - A61P 29/00: Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID] - A61P 37/06: Immunosuppressants, e.g. drugs for graft rejection - C12Q 2600/158: Expression markers - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES - A61P: SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS ## Abstract The present invention relates to methods of gene expression profiling for inflammatory bowel disease pathogenesis, in which the differential expression in a test sample from a mammalian subject of one or more IBD markers relative to a control is determined, wherein the differential expression in the test sample is indicative of an IBD in the mammalian subject from which the test sample was obtained. ## Claims ### Claim 1 A method of diagnosing the presence of an inflammatory bowel disease (IBD) in a mammalian subject, comprising determining a differential expression level of a nucleic acid encoding a polypeptide shown as any one of SEQ ID NOS: 5, 6, 8, 11, 12, 2, 14, 16, 18, 20, and 22 in a test sample obtained from the subject relative to the expression level of a control, wherein said differential level of expression is indicative of the presence of an IBD in the subject from which the test sample was obtained. ### Claim 2 (depends on 1) The method of claim 1, wherein the differential level of expression is a lower level of expression for a nucleic acid encoding a polypeptide shown as any one of SEQ ID NOS: 5, 6, 8, 11, 12, 2, 14, and 16, wherein the lower level of expression is indicative of the presence of an IBD in the subject from which the test sample was obtained. ### Claim 3 (depends on 1) The method of claim 1, wherein the differential level of expression is a higher level of expression for a nucleic acid encoding a polypeptide shown as any one of SEQ ID NOS: 18, 20, and 22, wherein the higher level of expression is indicative of the presence of an IBD in the subject from which the test sample was obtained. ### Claim 4 (depends on 1) The method of claim 1 wherein said mammalian subject is a human patient. ### Claim 5 (depends on 4) The method of claim 4 wherein evidence of said expression level is obtained by a method of gene expression profiling. ### Claim 6 (depends on 4) The method of claim 4 wherein said method is a PCR-based method. ### Claim 7 (depends on 5) The method of claim 5 wherein said expression levels are normalized relative to the expression levels of one or more reference genes, or their expression products. ### Claim 8 (depends on 1) The method of claim 1 comprising determining evidence of the expression levels of at least two of said genes, or their expression products. ### Claim 9 (depends on 1) The method of claim 1 comprising determining evidence of the expression levels of at least three of said genes, or their expression products. ### Claim 10 (depends on 1) The method of claim 1 comprising determining evidence of the expression levels of at least four of said genes, or their expression products. ### Claim 11 (depends on 1) The method of claim 1 comprising determining evidence of the expression levels of at least five of said genes, or their expression products. ### Claim 12 (depends on 1) The method of claim 1 further comprising the step of creating a report summarizing said IBD detection. ### Claim 13 (depends on 1) The method of claim 1 wherein said IBD is Crohn's disease. ### Claim 14 (depends on 1) The method of claim 1 wherein said test sample is from a colonic tissue biopsy. ### Claim 15 (depends on 14) The method of claim 14, wherein said biopsy is from a tissue selected from the group consisting of the terminal ileum, the ascending colon, the descending colon, and the sigmoid colon. ### Claim 16 (depends on 14) The method of claim 14, wherein said biopsy is from an inflamed colonic area. ### Claim 17 (depends on 14) The method of claim 14, wherein said biopsy is from a non-inflamed colonic area. ### Claim 18 (depends on 1) The method of claim 1 wherein said determining step is indicative of a recurrence of an IBD in said mammalian subject, and wherein said mammalian subject was previously diagnosed with an IBD and treated for said previously diagnosed IBD. ### Claim 19 (depends on 18) The method of claim 18, wherein said treatment comprised surgery. ### Claim 20 (depends on 1) The method of claim 1 wherein said determining step is indicative of a flare-up of said IBD in said mammalian subject. ### Claim 21 A method of treating an inflammatory bowel disorder (IBD) in a mammalian subject in need thereof, the method comprising the steps of (a) determining a differential expression level of a nucleic acid encoding a polypeptide shown as any one of SEQ ID NOS: 5, 6, 8, 11, 12, 2, 14, 16, and 18, in a test sample obtained from said subject relative to the expression level of a control, wherein said differential level of expression is indicative of the presence of an IBD in the subject from which the test sample was obtained; and (b) administering to said subject an effective amount of an IBD therapeutic agent. ### Claim 22 (depends on 21) The method of claim 21, wherein the differential level of expression is a lower level of expression for a nucleic acid encoding a polypeptide shown as any one of SEQ ID NOS: 5, 6, 8, 11, 12, 2, 14, and 16, wherein the lower level of expression is indicative of the presence of an IBD in the subject from which the test sample was obtained. ### Claim 23 (depends on 21) The method of claim 21, wherein the differential level of expression is a higher level of expression for a nucleic acid encoding a polypeptide shown as any one of SEQ ID NOS: 18, 20, and 22, wherein the higher level of expression is indicative of the presence of an IBD in the subject from which the test sample was obtained. ### Claim 24 (depends on 21) The method of claim 21 wherein said mammalian subject is a human patient. ### Claim 25 (depends on 24) The method of claim 24 wherein evidence of said expression level is obtained by a method of gene expression profiling. ### Claim 26 (depends on 24) The method of claim 24 wherein said method is a PCR-based method. ### Claim 27 (depends on 26) The method of claim 26 wherein said expression levels are normalized relative to the expression levels of one or more reference genes, or their expression products. ### Claim 28 (depends on 21) The method of claim 21 comprising determining evidence of the expression levels of at least two of said genes, or their expression products. ### Claim 29 (depends on 21) The method of claim 21 comprising determining evidence of the expression levels of at least three of said genes, or their expression products. ### Claim 30 (depends on 21) The method of claim 21 comprising determining evidence of the expression levels of at least four of said genes, or their expression products. ### Claim 31 (depends on 21) The method of claim 21 comprising determining evidence of the expression levels of at least five of said genes, or their expression products. ### Claim 32 (depends on 21) The method of claim 21 further comprising the step of creating a report summarizing said IBD detection. ### Claim 33 (depends on 21) The method of claim 21 wherein said IBD is Crohn's disease. ### Claim 34 (depends on 21) The method of claim 21 wherein said test sample is from a colonic tissue biopsy. ### Claim 35 (depends on 34) The method of claim 34, wherein said biopsy is from a tissue selected from the group consisting of the terminal ileum, the ascending colon, the descending colon, and the sigmoid colon. ### Claim 36 (depends on 34) The method of claim 34, wherein said biopsy is from an inflamed colonic area. ### Claim 37 (depends on 34) The method of claim 34, wherein said biopsy is from a non-inflamed colonic area. ### Claim 38 (depends on 21) The method of claim 21 wherein said determining step is indicative of a recurrence of an IBD in said mammalian subject, and wherein said mammalian subject was previously diagnosed with an IBD and treated for said previously diagnosed IBD. ### Claim 39 (depends on 38) The method of claim 38, wherein said treatment comprised surgery. ### Claim 40 (depends on 21) The method of claim 21 wherein said determining step is indicative of a flare-up of said IBD in said mammalian subject. ### Claim 41 (depends on 21) The method of claim 21 wherein said IBD therapeutic agent is an aminosalicylate. ### Claim 42 (depends on 21) The method of claim 21 wherein said IBD therapeutic agent is a corticosteroid. ### Claim 43 (depends on 21) The method of claim 21 wherein said IBD therapeutic agent is an immunosuppressive agent.