Biomarkers for inflammatory bowel disease and irritable bowel syndrome

1. A method for differentiating between inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) in a human subject, comprising:

(a) contacting a mRNA-derived nucleic acid sample obtained from a human subject suspected of having IBD or irritable bowel syndrome (IBS) under hybridizing conditions with at least 7 nucleotide probes, wherein a first nucleotide probe consists of 15 or more contiguous nucleotides of SEQ ID NO:5 (UBE2G1) or a full complement thereof, a second nucleotide probe consists of 15 or more contiguous nucleotides of SEQ ID NO:6 (CALM3) or a full complement thereof, a third nucleotide probe consists of 15 or more contiguous nucleotides of SEQ ID NO:9 (HIST1H2BK) or a full complement thereof, a fourth nucleotide probe consists of 15 or more contiguous nucleotides of SEQ ID NO:10 (PPP2R5A) or a full complement thereof, a fifth nucleotide probe consists of 15 or more contiguous nucleotides of SEQ ID NO:3BLCAP) or a full complement thereof, a sixth nucleotide probe and a seventh nucleotide probe consist of 15 or more contiguous nucleotides of a nucleic acid selected from the group consisting of:

(i) SEQ ID NO:1 (RAP1A) and SEQ ID NO:7 (GPX1) or full complements thereof;

(ii) SEQ ID NO:2 (RAP1A) and SEQ ID NO:7 (GPX1) or full complements thereof;

(iii) SEQ ID NO:1 (RAP1A) and SEQ ID NO:8 (GPX1) or full complements thereof; and

(iv) SEQ ID NO:2 (RAP1A) and SEQ ID NO:8 (GPX1) or full complements thereof;

(b) detecting formation of hybridization complexes between the nucleotide probes and the nucleic acid targets in the nucleic acid sample, wherein the hybridization complexes provide a measure of gene expression of the nucleic acid targets; and

(c) diagnosing whether the human subject is likely to have IBD or IBS based on the measure of gene expression of the nucleic acid targets, wherein gene expression levels of the nucleic acid targets differentiate between IBD and IBS.

2. The method of claim 1 , wherein the human subject suffers from one or more of abdominal pain, constipation, diarrhea, a change in bowel habits, vomiting, hematochezia, and weight change.

3. The method of claim 1 , wherein the mRNA-derived nucleic acid sample is obtained from peripheral blood mononuclear cells or red blood cell-depleted whole blood.

4. The method of claim 1 , further comprising analyzing gene expression of the nucleic acid targets by applying a weight to the number of hybridization complexes formed for each nucleic acid target.

5. A method for differentiating between inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) in a human subject, comprising:

(a) contacting a mRNA-derived nucleic acid sample obtained from a human subject suspected of having IBD or irritable bowel syndrome (IBS) under amplifying conditions with at least seven primer pairs, wherein a first primer pair selectively amplifies a detectable portion of SEQ ID NO:5 (UBE2G1) or a full complement thereof, a second primer pair selectively amplifies a detectable portion of SEQ ID NO:6 (CALM3) or a full complement thereof, a third primer selectively amplifies a detectable portion of SEQ ID NO:9 (HIST1H2BK) or a full complement thereof, a fourth primer pair selectively amplifies a detectable portion of SEQ ID NO:10 (PPP2R5A) or a full complement thereof, a fifth primer pair selectively amplifies a detectable portion of SEQ ID NO:3 (BLCAP) or a full complement thereof, and a sixth primer pair and seventh primer pair, respectively, selectively amplify a detectable portion of a nucleic acid selected from the group consisting of:

(i) SEQ ID NO:1 (RAP1A) and SEQ ID NO:7 (GPX1) or full complements thereof;

(ii) SEQ ID NO:2 (RAP1A) and SEQ ID NO:7 (GPX1) or full complements thereof;

(iii) SEQ ID NO:1 (RAP1A) and SEQ ID NO:8 (GPX1) or full complements thereof; and

(iv) SEQ ID NO:2 (RAP1A) and SEQ ID NO:8 (GPX1) or full complements thereof;

wherein each primer in each primer pair consists of at least 15 contiguous nucleotides of its respective nucleic acid target;

(b) detecting amplification products generated by amplification of nucleic acid targets in the nucleic acid sample by the at least seven primer pairs, wherein the amplification products provide a measure of gene expression of the nucleic acid targets; and

(c) diagnosing whether the human subject is likely to have IBD or IBS based on the measure of gene expression of the nucleic acid targets, wherein gene expression levels of the nucleic acid targets differentiate between IBD and IBS.

6. The method of claim 5 , wherein the human subject suffers from one or more of abdominal pain, constipation, diarrhea, a change in bowel habits, vomiting, hematochezia, and weight change.

7. The method of claim 5 , wherein the mRNA-derived nucleic acid sample is obtained from peripheral blood mononuclear cells or red blood cell-depleted whole blood.

8. The method of claim 5 , further comprising analyzing gene expression of the nucleic acid targets by applying a weight to the number of amplification products formed for each nucleic acid target.