Methods of classifying, diagnosing, stratifying and treating cancer patients and their tumors

A method of classifying a tumor comprising the steps of:

• providing a tumor sample;
• detecting expression or activity of a gene encoding the polypeptide of SEQ ID NO:2 in the sample;
• and
• classifying the tumor as belonging to a tumor subclass based on the results of the detecting step.

A method of classifying a tumor comprising the steps of:

• providing a tumor sample;
• detecting expression or activity of a gene encoding the polypeptide of SEQ ID NO:3 in the sample;
• and
• classifying the tumor as belonging to a tumor subclass based on the results of the detecting step.

A method of classifying a tumor comprising the steps of:

• providing a tumor sample;
• detecting expression or activity of at least two genes selected from the group consisting of:
• a gene encoding the polypeptide of SEQ ID NO:1, SEQ ID NO:2, and SEQ ID NO:3 in the sample;
• and
• classifying the tumor as belonging to a tumor subclass based on the results of the detecting step.

A method of testing a subject comprising the steps of:

• providing a sample isolated from a subject;
• detecting expression or activity of a gene encoding the polypeptide of SEQ ID NO:1 in the sample;
• and
• providing diagnostic, prognostic, or predictive information based on the detecting step.

A method of testing a subject comprising the steps of:

• providing a sample isolated from a subject;
• detecting expression or activity of a gene encoding the polypeptide of SEQ ID NO:2 in the sample;
• and
• providing diagnostic, prognostic, or predictive information based on the detecting step.

A method of testing a subject comprising the steps of:

• providing a sample isolated from a subject;
• detecting expression or activity of a gene encoding the polypeptide of SEQ ID NO:3 in the sample;
• and
• providing diagnostic, prognostic, or predictive information based on the detecting step.

A method of testing a subject comprising the steps of:

• providing a sample isolated from the subject;
• detecting expression or activity of at least two genes selected from the group consisting of:
• a gene encoding the polypeptide of SEQ ID NO:1, SEQ ID NO:2, and SEQ ID NO:3 in the sample;
• and
• providing diagnostic, prognostic, or predictive information based on the detecting step.

A method of testing a subject comprising the steps of:

• providing a sample isolated from a subject;
• detecting expression or activity of a gene encoding the polypeptide of SEQ ID NO:1 in the sample;
• and
• stratifying the subject for a clinical trial based on the detecting step.

A method of testing a subject comprising the steps of:

• providing a sample isolated from a subject;
• detecting expression or activity of a gene encoding the polypeptide of SEQ ID NO:2 in the sample;
• and
• stratifying the subject for a clinical trial based on the detecting step.

A method of testing a subject comprising the steps of:

• providing a sample isolated from a subject;
• detecting expression or activity of a gene encoding the polypeptide of SEQ ID NO:3 in the sample;
• and
• stratifying the subject for a clinical trial based on the detecting step.

A method of testing a subject comprising the steps of:

• providing a sample isolated from the subject;
• detecting expression or activity of at least two genes selected from the group consisting of:
• a gene encoding the polypeptide of SEQ ID NO:1, SEQ ID NO:2, and SEQ ID NO:3 in the sample;
• and
• stratifying the subject for a clinical trial based on the detecting step.

A method of testing a subject comprising the steps of:

• providing a sample isolated from a subject;
• detecting expression or activity of a gene encoding the polypeptide of SEQ ID NO:1 in the sample;
• and
• selecting a treatment based on the detecting step.

A method of testing a subject comprising the steps of:

• providing a sample isolated from a subject;
• detecting expression or activity of a gene encoding the polypeptide of SEQ ID NO:2 in the sample;
• and
• selecting a treatment based on the detecting step.

A method of testing a subject comprising the steps of:

• providing a sample isolated from a subject;
• detecting expression or activity of a gene encoding the polypeptide of SEQ ID NO:3 in the sample;
• and
• selecting a treatment based on the detecting step.

A method of testing a subject comprising the steps of:

• providing a sample isolated from the subject;
• detecting expression or activity of at least two genes selected from the group consisting of:
• a gene encoding the polypeptide of SEQ ID NO:1, SEQ ID NO:2, and SEQ ID NO:3 in the sample;
• and
• selecting a treatment based on the detecting step.

A method of testing a compound or a combination of compounds for activity against tumors comprising steps of:

• obtaining or providing tumor samples taken from subjects who have been treated with the compound or combination of compounds, wherein the tumors fall within a tumor subclass;
• comparing the response rate of tumors that fall within the tumor subclass and have been treated with the compound with the overall response rate of tumors that have been treated with the compound or combination of compounds or with the response rate of tumors that do not fall within the subclass and have been treated with the compound or combination of compounds;
• and
• identifying the compound or combination of compounds as having selective activity against tumors in the tumor subclass if the response rate of tumors in the subclass is greater than the overall response rate or the response rate of tumors that do not fall within the subclass.

A method of testing a compound or a combination of compounds for activity against tumors comprising steps of:

• treating subjects in need of treatment for tumors with the compound or combination of compounds;
• comparing the response rate of tumors that fall within a tumor subclass with the overall response rate of tumors or with the response rate of tumors that do not fall within the subclass;
• and
• identifying the compound or combination of compounds as having selective activity against tumors in the tumor subclass if the response rate of tumors in the subclass is greater than the overall response rate or the response rate of tumors that do not fall within the subclass.

A method of testing a compound or a combination of compounds for activity against tumors comprising steps of:

• treating subjects in need of treatment for tumors with the compound or combination of compounds or with an alternate compound, wherein the tumors fall within a tumor subclass;
• comparing the response rate of tumors treated with the compound or combination of compounds with the response rate of tumors treated with the alternate compound;
• and
• identifying the compound or combination of compounds as having superior activity against tumors in the tumor subclass, as compared with the alternate compound, if the response rate of tumors treated with the compound or combination of compounds is greater than the response rate of tumors treated with the alternate compound.