Methods for assessing proliferation and anti-folate therapeutic response
OwnerJoel EISNER, Michael MILBURN +4inventors
InventorsJoel EISNER, Michael MILBURN, Gregory M. MAYHEW, Myla LAI-GOLDMAN, Jianping SUN, Charles M. PEROU
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Abstract
Provided herein is an antifolate predictive response signature for use in determining the response of a subject suffering from cancer to antifolate therapy. Also provided are methods and compositions for determining proliferation in a sample obtained from a subject suffering from cancer through the use of a proliferation gene signature as well as methods for predicting response of a subject suffering from cancer based on an assessment of proliferation in a sample obtained from the subject.
Claims90
A method of detecting a biomarker in a sample obtained from a patient suffering from cancer, the method comprising measuring the nucleic acid expression level of a plurality of biomarkers selected from Table 1 using an amplification, hybridization and/or sequencing assay.
The method of any one of the above claims, wherein the plurality of biomarkers comprises at least 8 biomarkers, at least 16 biomarkers, at least 24 biomarkers, at least 32 biomarkers, at least 40 biomarkers or at least 48 biomarkers of Table 1.
A method of determining whether a patient suffering from cancer is likely to respond to treatment with an antifolate agent, the method comprising,
- determining an antifolate predictive response signature of a sample obtained from a patient suffering from cancer;
- and
- based on the antifolate predictive response signature, assessing whether the patient is likely to respond to treatment with an antifolate agent, wherein a positive antifolate predictive response signature predicts that the patient is likely to respond to the treatment with an antifolate agent.
A method for selecting a patient suffering from cancer for an antifolate agent, the method comprising, determining an antifolate predictive response signature of a sample obtained from a patient suffering from cancer;
- and selecting the patient for treatment with an antifolate agent if the antifolate response signature is positive.
A method of treating cancer in a patient, the method comprising:
- measuring the expression level of a plurality of classifier biomarkers in a sample obtained from a patient suffering from cancer, wherein the plurality of classifier biomarkers are selected from a set of classifier biomarkers listed in Table 1, wherein the measured expression levels of the plurality of classifier biomarkers provide an antifolate predictive response signature for the sample;
- and
- administering an antifolate agent based on presence of a positive antifolate predictive response signature.
A system for determining an antifolate predictive response signature of a sample obtained from a subject suffering from cancer, the system comprising:
- (a) one or more processors;
- and
- (b) one or more memories operatively coupled to at least one of the one or more processors and having instructions stored thereon that, when executed by at least one of the one or more processors, cause the system to
- (i) detect an expression level of each of a plurality of classifier biomarkers from Table 1;
- (ii) compare the expression levels of each of the plurality of classifier biomarkers from Table 1 to the expression levels of each of the plurality of classifier biomarkers from Table 1 in a control;
- and
- (iii) classifying the sample as TRU, PP, or PI based on the results of the comparing step.
Dependencies are inferred from the claim text.