Cancer biomarkers and classifiers and uses thereof

A system for analyzing a cancer, comprising:

• (a) a probe set comprising a plurality of target sequences, wherein
• (i) the plurality of target sequences hybridizes to one or more targets selected from Table 2B, Table 16 or SEQ ID NOs:1-1440;
• or
• (ii) the plurality of target sequences comprises one or more target sequences selected from Table 2B, Table 16 or SEQ ID NOs:1-1440;
• and
• (b) a computer model or algorithm for analyzing an expression level and/or expression profile of the target hybridized to the probe in a sample from a subject suffering from a cancer.

A method of diagnosing cancer in an individual in need thereof, comprising:

• (a) obtaining an expression profile from a sample obtained from the individual, wherein the expression profile comprises one or more targets selected from Table 2B, Table 16 or SEQ ID NOs:1-1440;
• (b) comparing the expression profile from the sample to an expression profile of a control or standard;
• and
• (c) diagnosing a cancer in the individual if the expression profile of the sample (i) deviates from the control or standard from a healthy individual or population of healthy individuals, or (ii) matches the control or standard from an individual or population of individuals who have or have had the cancer.

A method of predicting whether an individual is susceptible to developing a cancer, comprising:

• (a) obtaining an expression profile from a sample obtained from the individual, wherein the expression profile comprises one or more targets selected from Table 2B, Table 16 or SEQ ID NOs:1-1440;
• (b) comparing the expression profile from the sample to an expression profile of a control or standard;
• and
• (c) predicting the susceptibility of the individual for developing a cancer based on (i) the deviation of the expression profile of the sample from a control or standard derived from a healthy individual or population of healthy individuals, or (ii) the similarity of the expression profiles of the sample and a control or standard derived from an individual or population of individuals who have or have had the cancer.

A method of predicting an individual's response to a treatment regimen for a cancer, comprising:

• (a) obtaining an expression profile from a sample obtained from the individual, wherein the expression profile comprises one or more targets selected from Table 2B, Table 16 or SEQ ID NOs:1-1440;
• (b) comparing the expression profile from the sample to an expression profile of a control or standard;
• and
• (c) predicting the individual's response to a treatment regimen based on (a) the deviation of the expression profile of the sample from a control or standard derived from a healthy individual or population of healthy individuals, or (b) the similarity of the expression profiles of the sample and a control or standard derived from an individual or population of individuals who have or have had the cancer.

A method of prescribing a treatment regimen for a cancer to an individual in need thereof, comprising:

• (a) obtaining an expression profile from a sample obtained from the individual, wherein the expression profile comprises one or more targets selected from Table 2B, Table 16 or SEQ ID NOs:1-1440;
• (b) comparing the expression profile from the sample to an expression profile of a control or standard;
• and
• (c) prescribing a treatment regimen based on (i) the deviation of the expression profile of the sample from a control or standard derived from a healthy individual or population of healthy individuals, or (ii) the similarity of the expression profiles of the sample and a control or standard derived from an individual or population of individuals who have or have had the cancer.