# US 2017/0283884 A1 · Methods for predicting drug responsiveness

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- Number: US 2017/0283884 A1
- Document ID: US20170283884A1
- Status: Published application
- Kind: A1
- Application number: 15/509,798
- Filed: 2015-09-25
- Published: 2017-10-05
- Earliest claimed: 2014-09-26
- Assignees: Medical Prognosis Institute A/S
- Applicants: Medical Prognosis Institute A/S
- Inventors: Steen KNUDSEN
- Web page: https://patentgrep.com/patent/US20170283884A1

## CPC

- C12Q 1/6886: for cancer (immunoassay for cancer G01N33/575)
- A61K 9/0019: {Injectable compositions; Intramuscular, intravenous, arterial, subcutaneous administration; Compositions to be administered through the skin in an invasive manner (non-active ingredients are additionally classified in A61K47/00)}
- A61K 31/15: Oximes (>C=N—O—); Hydrazines (>N—N<); Hydrazones (>N—N=) {; Imines (C—N=C)}
- A61K 31/436: the heterocyclic ring system containing a six-membered ring having oxygen as a ring hetero atom, e.g. rapamycin
- A61K 31/4745: condensed with ring systems having nitrogen as a ring hetero atom, e.g. phenantrolines (yohimbine derivatives, vinblastine A61K31/475; ergoline derivatives A61K31/48)
- A61K 31/513: having oxo groups directly attached to the heterocyclic ring, e.g. cytosine
- A61K 31/519: ortho- or peri-condensed with heterocyclic rings
- A61K 31/555: containing heavy metals, e.g. hemin, hematin, melarsoprol
- A61K 38/14: Peptides containing saccharide radicals; Derivatives thereof {, e.g. bleomycin, phleomycin, muramylpeptides or vancomycin}
- C12Q 2600/106: Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
- C12Q 2600/118: Prognosis of disease development
- 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
- A61K: PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES (devices or methods specially adapted for bringing pharmaceutical products into particular physical or administering forms A61J3/00; chemical aspects of, or use of materials for deodorisation of air, for disinfection or sterilisation, or for bandages, dressings, absorbent pads or surgical articles A61L; soap compositions C11D)

## Abstract

The present invention provides drug response predictors and biomarkers useful for assessing the responsiveness of a subject to treatment with one or more target drugs of interest, such as 5-fluorouracil (5-FU), irinotecan, and/or oxaliplatin. In particular, the invention provides methods useful in determining whether a subject is sensitive or resistant to a target drug by, e.g., measuring the expression level of one or more biomarkers of sensitivity and/or resistance to the drug in a biological sample obtained from the subject. The invention further features devices and kits for assessing target drug responsiveness in a subject, for example, by determining the expression level of such biomarkers.

## Claims

### Claim at position 1

1-551. (canceled)

### Claim 552

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).

### Claim 553 (depends on 552)

The method of claim 552, further comprising, prior to step (a) or (b), providing said tumor sample from said subject.

### Claim 554 (depends on 552)

The method of claim 552, wherein said method further comprises (c) calculating a difference score for the subject by subtracting the mean expression levels of the one or more biomarkers of resistance from the mean expression levels of the one or more biomarkers of sensitivity.

### Claim 555 (depends on 552)

The method of claim 552, further comprising administering 5-FU, irinotecan, or oxaliplatin to said subject, wherein the subject has been determined to be responsive 5-FU, irinotecan, or oxaliplatin, respectively.

### Claim 556 (depends on 552)

The method of claim 552, wherein said device comprises:
(i) said single-stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of the one or more biomarkers of resistance to 5-fluorouracil (5-FU), irinotecan, or oxaliplatin; and
(ii) said single-stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of the one or more biomarkers of sensitivity to 5-fluorouracil (5-FU), irinotecan, or oxaliplatin.

### Claim 557 (depends on 552)

A method of treating cancer in a subject in need thereof comprising:
(a) performing the method of claim 552; and
(b) administering 5-FU, irinotecan, or oxiplatin to said subject.

### Claim 558

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).

### Claim 559 (depends on 558)

The method of claim 558, wherein said device comprises:
(i) said single-stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of the one or more biomarkers of resistance to 5-fluorouracil (5-FU), irinotecan, or oxaliplatin; and
(ii) said single-stranded nucleic acid molecules capable of specifically hybridizing with the nucleotides of the one or more biomarkers of sensitivity to 5-fluorouracil (5-FU), irinotecan, or oxaliplatin.

### Claim 560 (depends on 558)

The method of claim 558, further comprising administering one or more additional therapies to said subject, wherein said one or more additional therapies is administered:
(a) concurrently with said administration of 5-FU, irinotecan, or oxaliplatin; or
(b) separately from said administration of 5-FU, irinotecan, or oxaliplatin; or
(c) prior to with said administration of 5-FU, irinotecan, or oxaliplatin; or
(d) after with said administration of 5-FU, irinotecan, or oxaliplatin.

### Claim 561 (depends on 560)

The method of claim 560, wherein said one or more additional therapies is administered within 1 week of said administration of 5-FU, irinotecan, or oxaliplatin.

### Claim 562 (depends on 560)

The method of claim 560, wherein said one or more additional therapies comprises one or more additional therapeutic agents, surgery, or radiation therapy.

### Claim 563 (depends on 562)

The method of claim 562, wherein said one or more additional therapies comprises one or more additional therapeutic agents, wherein said 5-FU, irinotecan, or oxaliplatin is administered alone or in admixture with said one or more additional therapeutic agents.

### Claim 564 (depends on 563)

The method of claim 563 wherein said one or more additional therapeutic agents is selected from:
(a) the group consisting of: 5-FU, irinotecan, oxaliplatin, cetuximab, leucovorin, SN-38, everolimus, temsirolimus, bleomycin, lomustine, depsipeptide, carboplatin, bortezomib, erlotinib, gemcitabine, mitoxantrone, cisplatin, busulfan, epirubicin, arsenic trioxide, bendamustine, vincristine, fulvestrant, teniposide, adriamycin, decitabine, and estramustine; or
(b) everolimus, temsirolimus, bleomycin, or lomustine; or
(c) leucovorin and at least one of 5-FU, irinotecan, or oxaliplatin.

### Claim 565 (depends on 558)

The method of claim 558, wherein said 5-FU, irinotecan, or oxaliplatin is administered to said subject intravenously, orally, intraperitoneally, intramuscularly, topically, rectally, cutaneously, subcutaneously, nasally, intracerebroventricularly, intraparenchymally, intrathecally, intracranially, ocularly, via inhalation, or through the skin.

### Claim 566 (depends on 565)

The method of claim 565, wherein said 5-FU, irinotecan, or oxaliplatin is administered to said subject:
(a) once daily; and/or
(b) once daily, for up to four years; and/or
(c) once weekly, once every other week, or once every three weeks; and/or
(d) in six week cycles; and/or
(c) repeated 30 days after the completion of the previous administration; and/or
(d) repeated for at least 12 to 60 months.

### Claim 567 (depends on 558)

The method of claim 558, wherein said 5-FU, irinotecan, or oxaliplatin is administered in dosage form, wherein:
(a) said daily dose of 5-FU is up to 800 mg; or
(b) said daily dose of irinotecan is up to 125 mg/m2, 180 mg/m2, or 350 mg/m2; or
(c) said daily dose of oxaliplatin is up to 85 mg/m2.

### Claim 568 (depends on 558)

The method of claim 558, wherein said step (a) or (b) occurs:
(a) prior to said administration; or
(b) concurrent with said administration; or
(c) after said administration; and/or
(d) multiple times.

### Claim 569 (depends on 552)

The method of claim 552, wherein:
(a) said treatment is 5-FU and said biomarker of resistance is NT5E; or
(b) said treatment is irinotecan and said biomarker of sensitivity is PRF1; or
(c) said treatment is oxaliplatin and said biomarker of sensitivity is selected from MRPL16 and at least a second biomarker of sensitivity selected from the biomarkers of Table 5.

### Claim 570 (depends on 569)

The method of claim 569, wherein said second biomarker of sensitivity is selected from the group consisting of: ANP32A, SRSF2, PDSS1, PRIM1, HNRNPA1, NDUFAB1, GLTSCR2, RNPS1, and ICAM2.

### Claim 571 (depends on 569)

The method of claim 569, wherein said biomarker of sensitivity is selected from MRPL16 and said biomarker of resistance is selected from one or more of the biomarkers of Table 6.

### Claim 572 (depends on 571)

The method of claim 571, wherein said biomarker of resistance is selected from the group consisting of: LPP, RHOC, CAPN2, FLNA, WDR1, FLNA, ACTN1, CNN3, FLNA, and ACTN1.

### Claim 573 (depends on 552)

The method of claim 552, wherein the device is a microarray.

### Claim 574 (depends on 552)

The method of claim 552, wherein the device is for performing a qRT-PCR reaction.

### Claim 575 (depends on 552)

The method of claim 552, wherein:
(a) said treatment is 5-FU and said one or more biomarkers of resistance is selected from the group consisting of: NT5E, CNN3, ACTN1, FLNA, ATP2B4, CYR61, LGALS1, RHOC, RAB32, and TMEM158; and/or said one or more biomarkers of sensitivity is selected from the group consisting of: APRT, GSR, TUFM, MRPS2, MTHFD2, WDR59, ANP32B, PMM2, STOML2, and NDUFAB1; or
(b) said treatment is irinotecan and said one or more biomarkers of sensitivity is selected from the group consisting of: PRF1, GZMB, PTPRC, PTPRC, PTPRCAP, PDE4DIP, ACAP1, PTPRC, S1PR1, and DOCK2; and/or one or more biomarkers of resistance is selected from the group consisting of: CCND1, LGALS3, INPP4B, TMEM97, TCF7L2, SFN, LAPTM4B, LSR, SFN, and TMEM97; or
(c) said treatment is oxaliplatin and said one or more biomarkers of sensitivity is selected from the group consisting of: MRPL16, ANP32A, SRSF2, PDSS1, PRIM1, HNRNPA1, NDUFAB1, GLTSCR2, RNPS1, and ICAM2; and/or one or more biomarkers of resistance is selected from the group consisting of: LPP, RHOC, CAPN2, FLNA, WDR1, FLNA, ACTN1, CNN3, FLNA, and ACTN1.

### Claim 576 (depends on 575)

The method of claim 575, wherein:
(a) the level of expression of said one or more biomarkers of sensitivity in said subject is statistically the same as the level of expression of said one or more biomarkers of sensitivity in a control subject sensitive to said treatment and wherein the subject is sensitive to said treatment; or
(b) the level of expression of said one or more biomarkers of resistance in said subject is statistically different from the level of expression of said one or more biomarkers of resistance in a control subject resistant to said treatment and wherein the subject is sensitive to said treatment; or
(c) the level of expression of said one or more biomarkers of sensitivity in said subject is statistically different from the level of expression of said one or more biomarkers of sensitivity in a control subject sensitive to said treatment and wherein the subject is resistant to said treatment; or
(d) the level of expression of said one or more biomarkers of resistance in said subject is statistically the same as the level of expression of said one or more biomarkers of resistance in a control subject resistant to said treatment and wherein the subject is resistant to said treatment.

### Claim 577 (depends on 576)

The method of claim 576, wherein said level of expression in said subject is significantly higher or significantly lower than in said control.

### Claim 578 (depends on 552)

The method of claim 552, wherein responsiveness of the subject to combination treatment with oxaliplatin and 5-FU is unknown; and wherein the biomarker of sensitivity for oxaliplatin is MRPL16.

### Claim 579 (depends on 578)

The method of claim 578, wherein said one or more biomarkers of resistance to 5-FU is selected from the group consisting of: NT5E, CNN3, ACTN1, FLNA, ATP2B4, CYR61, LGALS1, RHOC, RAB32, and TMEM158.

### Claim 580 (depends on 578)

The method of claim 578, wherein the method further comprises calculating a difference score for the subject by subtracting the mean expression level of MRPL16 from the mean expression levels of said one or more biomarkers of resistance to 5-FU.

### Claim 581 (depends on 552)

The method of claim 552, further comprising determining the expression level of one or more additional biomarkers, wherein said one or more additional biomarkers is selected from the group consisting of: carcinoembryonic antigen (CEA), BRAF, KRAS, Fas-ligand, p53, Ki-67, thymidylate-synthase, dihydropyrimidine dehydrogenase, thymidine phosphorylase, microsatellite instability (MIS), and 18q allelic loss of heterozygosity (LOH18q):

### Claim 582 (depends on 552)

The method of claim 552, wherein said method further comprises, prior to step (a) or (b), amplifying said nucleotides of said one or more biomarkers of resistance and/or said one or more biomarkers of sensitivity from said tumor samples,
wherein, optionally, prior to said amplification, said nucleotides are subjected to reverse transcription.

### Claim 583 (depends on 552)

The method of claim 552, wherein step (a) and (b) are performed using the same tumor sample or two or more different tumor samples.

### Claim 584 (depends on 552)

The method of claim 552, wherein the tumor sample is:
(a) formalin-fixed paraffin embedded (FFPE) tissue; and/or
(b) fresh frozen tissue; and/or
(c) obtained from a tumor or a tumor biopsy.

### Claim 585 (depends on 552)

The method of claim 552, wherein the cancer has been resected from said subject.

### Claim 586 (depends on 552)

The method of claim 552 wherein said cancer is selected from the group consisting of: colorectal cancer, leukemia, myeloma, myelodysplastic syndrome, lymphoma, cervical cancer, prostate cancer, esophageal cancer, melanoma, glioma, pancreatic cancer, ovarian cancer, gastrointestinal stromal tumor, sarcoma, breast cancer, ER-positive cancer, bladder cancer, head and neck cancer, lung cancer, metastatic cancer, oral cavity cancer, uterine cancer, testicular cancer, skin cancer, thyroid cancer, brain cancer, stomach cancer, intra-epithelial cancer, bone cancer, biliary tract cancer, eye cancer, liver cancer, larynx cancer, kidney cancer, gastric cancer, blastoma, polycythemia vera, chordoma, synovioma, mesothelioma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, cystadenocarcinoma, bile duct carcinoma, choriocarcinoma, epithelial carcinoma, ependymoma, pinealoma, acoustic neuroma, schwannoma, meningioma, pituitary adenoma, nerve sheath tumor, cancer of the small intestine, cancer of the endocrine system, cancer of the penis, cancer of the urethra, cutaneous or intraocular melanoma, a gynecologic tumor, solid tumors of childhood, and neoplasms of the central nervous system.

### Claim 587 (depends on 586)

The method of claim 586, wherein:
(a) said colorectal cancer is selected from the group consisting of: adenocarcinoma, gastrointestinal carcinoid tumor, primary colorectal lymphoma, leiomyosarcoma, colorectal melanoma, and squamous cell carcinoma; or
(b) said breast cancer is medullary carcinoma; or
(c) said leukemia is acute myeloid leukemia, acute lymphoid leukemia, chronic myeloid leukemia, chronic lymphocytic leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroleukemia, or chronic leukemia; or
(d) said myeloma is multiple myeloma; or
(e) said lymphoma is diffuse large B-cell lymphoma, cutaneous T-cell lymphoma, peripheral T-cell lymphoma, Hodgkin's lymphoma, non-Hodgkin's lymphoma, Waldenstrom's macroglobulinemia, or lymphocytic lymphoma; or
(f) said glioma is oligodendroglioma; or
(g) said pancreatic cancer is adenosquamous carcinoma, signet ring cell carcinoma, hepatoid carcinoma, colloid carcinoma, islet cell carcinoma, or pancreatic neuroendocrine carcinoma; or
(h) said ovarian cancer is ovarian adenocarcinoma or embryonal carcinoma; or
(i) said sarcoma is fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, leiomyosarcoma, Ewing's sarcoma, or rhabdomyosarcoma; or
(j) said head and neck cancer is squamous cell carcinoma of the head and neck; or
(k) said lung cancer is non-small cell lung carcinoma, large cell carcinoma, bronchogenic carcinoma, or papillary adenocarcinoma; or
(l) said testicular cancer is seminoma or embryonal carcinoma; or
(m) said skin cancer is squamous cell carcinoma or basal cell carcinoma; or
(n) said thyroid cancer is papillary carcinoma or medullary carcinoma; or
(o) said brain cancer is astrocytoma or craniopharyngioma; or
(p) said liver cancer is hepatocellular carcinoma or hepatoma; or
(q) said kidney cancer is renal cell carcinoma or Wilms tumor; or
(r) said blastoma is nephroblastoma, medulloblastoma, hemangioblastoma, neuroblastoma, or retinoblastoma.

### Claim 588 (depends on 575)

The method of claim 575, wherein:
(a) the level of expression of said NT5E is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 94, 1015, 1016, 1683, 2064, 2207, 2316, 2446, 2714, or 2778; and/or
(b) the level of expression of said CNN3 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 95, 1157, 1476, or 1847; and/or
(c) the level of expression of said ACTN1 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 96, 934, 2203, 2469, 2737, 2816, or 2817; and/or
(d) the level of expression of said FLNA is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 97, 1387, 1490, 1542, 1621, 1773, 1867, 1902, 1960, 2048, 2051, 2347, or 2348; and/or
(e) the level of expression of said ATP2B4 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 98, 1498, 1845, 2056, 2284, 2285, 2523, or 2627; and/or
(f) the level of expression of said APRT is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 1 or 1201; and/or
(g) the level of expression of said GSR is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 2, 907, 1148, 1722; and/or
(h) the level of expression of said TUFM is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 3 or 1146; and/or
(i) the level of expression of said MRPS2 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 4 or 839; and/or
(j) the level of expression of said MTHFD2 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 5 or 1189; and/or
(k) the level of expression of said PRF1 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 209, 2314, 2315, or 2881; and/or
(l) the level of expression of said GZMB is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 210, 1681, or 1682; and/or
(m) the level of expression of said PTPRC is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 211, 212, 1020, 1632, 1675, 1998, 1999, 2535, 2636, or 2797; and/or
(n) the level of expression of said PTPRCAP is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 213, 1645, or 1646; and/or
(o) the level of expression of said CCND1 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 354, 1592, 1593, 1679, 1727, 1752, 1817, 2013, or 2640; and/or
(p) the level of expression of said LGALS3 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 355, 1299, 1334, 1335, or 2069; and/or
(q) the level of expression of said INPP4B is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 356, 919, 1453, 1616, 1617, 2199, 2386, 2625, or 2626; and/or
(r) the level of expression of said TMEM97 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 357, 966, 2532, or 2566; and/or
(s) the level of expression of said TCF7L2 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 358, 955, 1536, 1852, 2081, 2099, 2171, 2192, 2219, 2539, 2575, 2665, or 2880; and/or
(t) the level of expression of said MRPL16 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 399 or 1144; and/or
(u) the level of expression of said ANP32A is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 400, 1921, 2357, 2358, 2736, 2799, or 2800; and/or
(v) the level of expression of said SRSF2 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 401; and/or
(w) the level of expression of said PDSS1 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 402, 862, or 2058; and/or
(x) the level of expression of said PRIM1 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 403, 2266, or 2267; and/or
(y) the level of expression of said LPP is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 579, 984, 1031, 1437, 1693, 1731, 1828, 1831, 1872, 2040, 2063, 2104, 2109, 2119, 2123, 2160, 2197, 2400, 2401, 2618, 2784, 2852, or 2853; and/or
(z) the level of expression of said RHOC is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 580; and/or
(aa) the level of expression of said CAPN2 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 581, 1521, 1552, 1900, 1965, 2154, 2233, 2234, or 2826; and/or
(bb) the level of expression of said FLNA is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 582, 584, 587, 1387, 1490, 1542, 1621, 1773, 1867, 1902, 1960, 2048, 2051, 2347, or 2348; and/or
(cc) the level of expression of said WDR1 is detected and wherein the single-stranded nucleic acid molecule is a probe capable of detecting a nucleic acid having the sequence of SEQ ID NO. 583, 894, 1135, 1136, 1390, 2194, 2335, 2506, 2839, or 2862; and/or

### Claim 589 (depends on 588)

The method of claim 588, wherein:
(a) said probe for NT5E comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 94, 1015, 1016, 1683, 2064, 2207, 2316, 2446, 2714, or 2778; and/or
(b) said probe for CNN3 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 95, 1157, 1476, or 1847; and/or
(c) said probe for ACTN1 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 96, 934, 2203, 2469, 2737, 2816, or 2817; and/or
(d) said probe for FLNA comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 97, 1387, 1490, 1542, 1621, 1773, 1867, 1902, 1960, 2048, 2051, 2347, or 2348; and/or
(e) said probe for ATP2B4 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 98, 1498, 1845, 2056, 2284, 2285, 2523, or 2627; and/or
(f) said probe for APRT comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 1 or 1201; and/or
(g) said probe for GSR comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 2, 907, 1148, 1722; and/or
(h) said probe for TUFM comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 3 or 1146; and/or
(i) said probe for MRPS2 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 4 or 839; and/or
(j) said probe for MTHFD2 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 5 or 1189; and/or
(k) said probe for PRF1 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 209, 2314, 2315, or 2881; and/or
(l) said probe for GZMB comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 210, 1681, or 1682; and/or
(m) said probe for PTPRC comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 211, 212, 1020, 1632, 1675, 1998, 1999, 2535, 2636, or 2797; and/or
(n) said probe for PTPRCAP comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 213, 1645, or 1646; and/or
(o) said probe for CCND1 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 354, 1592, 1593, 1679, 1727, 1752, 1817, 2013, or 2640; and/or
(p) said probe for LGALS3 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 355, 1299, 1334, 1335, or 2069; and/or
(q) said probe for INPP4B comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 356, 919, 1453, 1616, 1617, 2199, 2386, 2625, or 2626; and/or
(r) said probe for TMEM97 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 357, 966, 2532, or 2566; and/or
(s) said probe for TCF7L2 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 358, 955, 1536, 1852, 2081, 2099, 2171, 2192, 2219, 2539, 2575, 2665, or 2880; and/or
(t) said probe for MRPL16 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 399 or 1144; and/or
(u) said probe for ANP32A comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 400, 1921, 2357, 2358, 2736, 2799, or 2800; and/or
(v) said probe for SRSF2 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 401; and/or
(w) said probe for PDSS1 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 402, 862, or 2058; and/or
(x) said probe for PRIM1 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 403, 2266, or 2267; and/or
(y) said probe for LPP comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 579, 984, 1031, 1437, 1693, 1731, 1828, 1831, 1872, 2040, 2063, 2104, 2109, 2119, 2123, 2160, 2197, 2400, 2401, 2618, 2784, 2852, or 2853; and/or
(z) said probe for RHOC comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 580; and/or
(aa) said probe for CAPN2 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 581, 1521, 1552, 1900, 1965, 2154, 2233, 2234, or 2826; and/or
(bb) said probe for FLNA comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 582, 584, 587, 1387, 1490, 1542, 1621, 1773, 1867, 1902, 1960, 2048, 2051, 2347, or 2348; and/or
(cc) said probe for WDR1 comprises a sequence comprising at least 5 continuous nucleotides and at least 75% identity to a sequence complementary to SEQ ID NO. 583, 894, 1135, 1136, 1390, 2194, 2335, 2506, 2839, or 2862.

### Claim 590

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.