Compositions and methods for detection of colorectal cancer
View Patent ↗We have identified a new variant of ileal bile acid binding protein (IBABP), designated IBABP-L, which is a biomarker for colorectal cancer. The transcript for IBABP-L arises from an alternative start site and includes three exons that are absent in IBABP. IBABP-L also shares part of a fourth exon with IBABP. The protein encoded by IBABP-L contains a deduced 49 residue N-terminal sequence that is not found in the IBABP protein. The present invention provides methods for diagnosing colorectal cancer and other compositions and methods based on this discovery.
1. A method of determining a ratio of IBABP-L polynucleotide to IBABP polynucleotide in a sample that comprises IBABP-L polynucleotide and IBABP polynucleotide, the method comprising (a) contacting the sample with a first probe that hybridizes selectively to IBABP-L polynucleotide; (b) measuring hybridization of the first probe to the IBABP-L polynucleotide in the sample, (c) contacting the sample with a second probe that hybridizes selectively to IBABP polynucleotide and IBABP-L polynucleotide; (d) measuring the hybridization of the second probe to the IBABP polynucleotide and the IBABP-L polynucleotide in the sample; and (e) calculating the ratio of IBABP-L polynucleotide to IBABP polynucleotide in the sample.
2. The method of claim 1 wherein the IBABP-L polynucleotide is an mRNA.
3. The method of claim 1 comprising (a) contacting the sample with at least one primer that hybridizes selectively to the IBABP-L polynucleotide and performing a first amplification reaction to produce a first amplification product that indicates the presence of the IBABP-L polynucleotide in the sample; (b) contacting the sample with at least one primer that hybridizes selectively to IBABP polynucleotide and the IBABP-L polynucleotide and performing a second amplification reaction to produce a second amplification product that indicates the presence of IBABP polynucleotide and the IBABP-L polynucleotide in the sample; (c) measuring the first amplification product and the second amplification product; (d) calculating the ratio of IBABP-L polynucleotide to IBABP polynucleotide in the sample.
4. The method of claim 1 wherein the sample is selected from the group consisting of a cell, a tissue sample, a gastrointestinal tissue sample, a fecal sample, and a blood sample.