Methods for predicting drug responsiveness

A method of testing a tumor sample of a subject having a known cancer type and for which responsiveness to treatment with 5-fluorouracil (5-FU), irinotecan, or oxaliplatin is unknown, said method comprising:

• (a) contacting the tumor sample from the subject comprising one or more nucleic acid molecules with a device comprising:
• (i) single-stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of one or more biomarkers of resistance to 5-fluorouracil (5-FU), irinotecan, or oxaliplatin selected from the biomarkers of Table 2, Table 3, or Table 5, respectively;
• and/or
• (ii) single-stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of one or more biomarkers of sensitivity to 5-fluorouracil (5-FU), irinotecan, or oxaliplatin selected from the biomarkers of Table 1, Table 4, or Table 6, respectively;
• and
• (b) detecting a level of expression of the one or more biomarkers of resistance and/or the one or more biomarkers of sensitivity by performing microarray analysis or quantitative reverse transcriptase polymerase chain reaction (qRT-PCR).

A method of treating cancer in a subject in need thereof comprising administering 5-FU, irinotecan, or oxiplatin to said subject, wherein the subject has been determined to be responsive to 5-FU, irinotecan, or oxiplatin according to a method comprising:

• (a) contacting a tumor sample from the subject comprising one or more nucleic acid molecules with a device comprising:
• (i) single-stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of one or more biomarkers of resistance to 5-fluorouracil (5-FU), irinotecan, or oxaliplatin selected from the biomarkers of Table 2, Table 3, or Table 5, respectively;
• and/or
• (ii) single-stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of one or more biomarkers of sensitivity to 5-fluorouracil (5-FU), irinotecan, or oxaliplatin selected from the biomarkers of Table 1, Table 4, or Table 6, respectively;
• and
• (b) detecting a level of expression of the one or more biomarkers of resistance and/or the one or more biomarkers of sensitivity by performing microarray analysis or quantitative reverse transcriptase polymerase chain reaction (qRT-PCR).

A method of assessing the responsiveness of a subject to treatment with 5-FU, irinotecan, or oxaliplatin, comprising:

• (a) determining a level of expression of one or more biomarkers of sensitivity in one or more biological samples obtained from said subject;
• or
• (b) determining a level of expression of one or more biomarkers of resistance in one or more biological samples obtained from said subject;
• wherein said one or more biomarkers of sensitivity comprises a gene determined to have at least a 0.25 Pearson correlation between the mRNA expression level of said gene and growth inhibition of a cultured cell exposed to said 5-FU, irinotecan, or oxaliplatin, and/or said one or more biomarkers of resistance comprises a gene determined to have at least a −0.25 Pearson correlation between the mRNA expression level of said gene and growth inhibition of a cultured cell exposed to said 5-FU, irinotecan, or oxaliplatin;
• and
• wherein the levels of expression of said biomarker of sensitivity or said biomarker of resistance indicate whether said subject is responsive to said treatment.