Hypoxia-related gene signatures for cancer classification

A method for prognosing lung cancer, comprising:

• (1) determining in a lung cancer sample the expression levels of a plurality of biomarkers comprising at least three test biomarkers selected from:
• ADM, STC1, ALDOC, HIG2, ENO1, ERO1L, IL8, VEGFA, IGFBP3, SLC2A1, GPI, NDRG1, ANGTPL4, P4HA1, ANGPT2, and PGK1;
• (2) generating a test value by (a) weighting the determined expression levels of each biomarker in said plurality of biomarkers with a predefined coefficient, and (b) combining the weighted expressions to provide the test value, wherein the combined weight given to said at least three test biomarkers is at least 40% of the total weight given to the expression of all biomarkers in said plurality of biomarkers;
• and
• (3)(a) diagnosing a test patient in whose sample said test value exceeds a reference value as having a lower likelihood of progression-free survival or a greater likelihood of disease progression or recurrence relative to a reference lung cancer patient with a test value equal to or lower than said reference value;
• or (b) diagnosing a test patient in whose sample said test value does not exceed a reference value as having a greater likelihood of progression-free survival or a lower likelihood of disease progression or recurrence relative to a reference lung cancer patient with a test value greater than said reference value.

A method of treating lung cancer comprising:

• (1) determining in a lung cancer sample the expression levels of a plurality of biomarkers comprising at least three test biomarkers selected from:
• ADM, STC1, ALDOC, HIG2, ENO1, ERO1L, IL8, VEGFA, IGFBP3, SLC2A1, GPI, NDRG1, ANGTPL4, P4HA1, ANGPT2, and PGK1;
• (2) generating a test value by (a) weighting the determined expression levels of each biomarker in said plurality of biomarkers with a predefined coefficient, and (b) combining the weighted expressions to provide the test value, wherein the combined weight given to said at least three test biomarkers is at least 40% of the total weight given to the expression of all biomarkers in said plurality of biomarkers;
• and
• (3)(a) administering an aggressive treatment to a test patient in whose sample said test value exceeds a reference value;
• or (b) administering a non-aggressive treatment to a test patient in whose sample said test value does not exceed a reference value.

A system for prognosing lung cancer, comprising:

• (a) a sample analyzer for quantifying in a lung cancer sample expression levels of a plurality of biomarkers comprising at least three test biomarkers selected from:
• ADM, STC1, ALDOC, HIG2, ENO1, ERO1L, IL8, VEGFA, IGFBP3, SLC2A1, GPI, NDRG1, ANGTPL4, P4HA1, ANGPT2, and PGK1;
• (b) a first computer program for receiving expression level data quantified in (a) and generating a test value by (a) weighting the determined expression levels of each biomarker in said plurality of biomarkers with a predefined coefficient, and (b) combining the weighted expressions to provide the test value, wherein the combined weight given to said at least three test biomarkers is at least 40% of the total weight given to the expression of all biomarkers in said plurality of biomarkers;
• (c) a second computer program for classifying a test patient in whose sample said test value exceeds a reference value as having a lower likelihood of progression-free survival or a greater likelihood of disease progression or recurrence relative to a reference lung cancer patient with a test value equal to or lower than said reference value;
• or (b) diagnosing a test patient in whose sample said test value does not exceed a reference value as having a greater likelihood of progression-free survival or a lower likelihood of disease progression or recurrence relative to a reference lung cancer patient with a test value greater than said reference value;
• and
• (d) a display module for reporting the classification in (c).

A method for prognosing colorectal cancer, comprising:

• (1) determining in a colorectal cancer sample the expression levels of a plurality of biomarkers comprising at least three test biomarkers selected from:
• ADM, STC1, ALDOC, HIG2, ENO1, ERO1L, IL8, VEGFA, IGFBP3, SLC2A1, GPI, NDRG1, ANGTPL4, P4HA1, ANGPT2, and PGK1;
• (2) generating a test value by (a) weighting the determined expression levels of each biomarker in said plurality of biomarkers with a predefined coefficient, and (b) combining the weighted expressions to provide the test value, wherein the combined weight given to said at least three test biomarkers is at least 40% of the total weight given to the expression of all biomarkers in said plurality of biomarkers;
• and
• (3)(a) diagnosing a test patient in whose sample said test value exceeds a reference value as having a lower likelihood of progression-free survival or a greater likelihood of disease progression or recurrence relative to a reference colorectal cancer patient with a test value equal to or lower than said reference value;
• or (b) diagnosing a test patient in whose sample said test value does not exceed a first reference value as having a greater likelihood of progression-free survival or a lower likelihood of disease progression or recurrence relative to a reference colorectal cancer patient with a test value greater than said reference value.