Detection of nucleic acids and proteins

1. A method for diagnosing bladder or colorectal cancer, the method comprising the steps of:

a) obtaining a sample comprising at least one target protein selected from the group consisting of MMP-2 and MMP-9 and at least one target nucleic acid selected from the group consisting of: FGFR3, K-ras, K-ras2, APC, DCC, TP53, PRC1, NUSAPI, CAPZ, PFKP, EVER1, FLT1, ESPL1, AKAP2, CDC45L, RAMP, SYNGR2, NDRG1, and ZNF533;

b) conducting a single assay, wherein the assay measures the level detects both the of each target nucleic acid and the level of each target protein; and

c) determining a cutoff level for each measured target protein and target nucleic acid by comparing the measured levels of said target protein and said target nucleic acid to reference standard values indicative of the presence of bladder or colorectal cancer and reference standard values indicative of the absence of bladder or colorectal cancer, wherein measured values of said target nucleic acid and said target protein above the determined cutoff values are indicative of the presence of bladder or colorectal cancer and measured values below the determined cutoff values are indicative of the absence of bladder or colorectal cancer, thereby diagnosing the presence or the absence of bladder or colorectal cancer based on the results of the assay.

2. The method of claim 1 , wherein the sample comprises: blood, serum, sputum, stool, saliva, urine, cerebral spinal fluid, breast nipple aspirate, and pus.

3. The method according to claim 1 , wherein prior to the conducting step, the method further comprises introducing an aptamer that binds to the target protein in the sample.

4. The method according to claim 1 , wherein the assay comprises the steps of: performing PCR on the target nucleic acid; performing PCR on the aptamer; introducing a first detectably labeled probe that binds to the amplified target nucleic acid; introducing a second detectably labeled probe that binds to the amplified aptamer; detecting the first probe thereby detecting the nucleic acid in the sample; and detecting the second probe that is bound to the amplified aptamer, wherein detecting the second probe detects the target protein.

5. The method according to claim 1 , further comprising quantifying the target nucleic acid.

6. The method according to claim 1 , further comprising quantifying the target protein.

7. The method according to claim 1 , wherein prior to conducting the assay, the method further comprises introducing an aptamer that binds to the target protein in the sample.

8. The method according to claim 7 , wherein the assay comprises the steps of: performing PCR on the target nucleic acid; performing PCR on the aptamer; introducing a first detectably labeled probe that binds to the amplified target nucleic acid; introducing a second detectably labeled probe that binds to the amplified aptamer; detecting the first probe thereby detecting the nucleic acid in the sample; and detecting the second probe that is bound to the amplified aptamer, wherein detecting the second probe detects the target protein.

9. The method according to claim 1 , wherein the levels of said one or more target nucleic acids are quantitatively measured for expression levels, methylation patterns, or nucleic acid mutations.