Materials and methods for determining diagnosis and prognosis of prostate cancer

A method for determining the prognosis of a subject diagnosed as having prostate cancer, comprising:

• (a) providing a prostate tissue sample from said subject;
• (b) measuring the level of expression for prostate cancer signature genes in said sample;
• (c) comparing said measured expression levels to reference expression levels for said prostate cancer signature genes;
• and
• (d) if said measured expression levels are not significantly greater or less than said reference expression levels, identifying said subject as having a relatively better prognosis than if said measured expression levels are significantly greater or less than said reference expression levels, or if said measured expression levels are significantly greater or less than said reference expression levels, identifying said subject as having a relatively worse prognosis than if said measured expression levels are not significantly greater or less than said reference expression levels.

A method for identifying a subject as having or not having prostate cancer, comprising:

• (a) providing a prostate tissue sample from said subject, wherein said sample comprises prostate stromal cells;
• (b) measuring expression levels for one or more genes in said stromal cells, wherein said one or more genes are prostate cancer signature genes;
• (c) comparing said measured expression levels to reference expression levels for said one or more genes, wherein said reference expression levels are determined in stromal cells from non-cancerous prostate tissue;
• and
• (d) if said measured expression levels are significantly greater or less than said reference expression levels, identifying said subject as having prostate cancer, and if said measured expression levels are not significantly greater or less than said reference expression levels, identifying said subject as not having prostate cancer.

A method for determining a prognosis for a subject diagnosed as having prostate cancer, comprising:

• (a) providing a prostate tissue sample from said subject, wherein said sample comprises prostate stromal cells;
• (b) measuring expression levels for one or more genes in said stromal cells, wherein said one or more genes are prostate cancer signature genes;
• (c) comparing said measured expression levels to reference expression levels for said one or more genes, wherein said reference expression levels are determined in stromal cells from non-cancerous prostate tissue;
• and
• (d) if said measured expression levels are not significantly greater or less than said reference expression levels, identifying said subject as having a relatively better prognosis than if said measured expression levels are significantly greater or less than said reference expression levels, or if said measured expression levels are significantly greater or less than said reference expression levels, identifying said subject as having a relatively worse prognosis than if said measured expression levels are not significantly greater or less than said reference expression levels.

A method for identifying a subject as having or not having prostate cancer, comprising:

• (a) providing a prostate tissue sample from said subject;
• (b) measuring expression levels for one or more prostate cell-type predictor genes in said sample;
• (c) determining the percentages of tissue types in said sample based on said measured expression levels;
• (d) measuring expression levels for one more prostate cancer signature genes in said sample;
• (e) determining a classifier based on said percentages of tissue types and said measured expression levels;
• and
• (f) if said classifier falls into a predetermined range of prostate cancer classifiers, identifying said subject as having prostate cancer, or if said classifier does not fall into said predetermined range, identifying said subject as not having prostate cancer.

A method for determining a prognosis for a subject diagnosed with and treated for prostate cancer, comprising:

• (a) providing a prostate tissue sample from said subject;
• (b) measuring expression levels for one or more prostate tissue predictor genes in said sample;
• (c) determining the percentages of tissue types in said sample based on said measured expression levels;
• (d) measuring expression levels for one more prostate cancer signature genes in said sample;
• (e) determining a classifier based on said percentages of tissue types and said measured expression levels;
• and
• (f) if said classifier falls into a predetermined range of prostate cancer relapse classifiers, identifying said subject as being likely to relapse, or if said classifier does not fall into said predetermined range, identifying said subject as not being likely to relapse.

A method for identifying the proportion of two or more tissue types in a tissue sample, comprising:

• (a) using a set of other samples of known tissue proportions from a similar anatomical location as said tissue sample in an animal or plant, wherein at least two of said other samples do not contain the same relative content of each of the two or more cell types;
• (b) measuring overall levels of one or more gene expression or protein analytes in each of said other samples;
• (c) determining the regression relationship between the relative proportion of each tissue type and the measured overall levels of each gene expression or protein analyte in said other samples;
• (d) selecting one or more analytes that correlate with tissue proportions in said other samples;
• (e) measuring overall levels of one or more of said analytes in step (d) in said tissue sample;
• (f) matching the level of each analyte in said tissue sample with the level of said analyte in step (d) to determine the predicted proportion of each tissue type in said tissue sample;
• and
• (g) selecting among predicted tissue proportions for said tissue sample obtained in step
• (0 using either the median or average proportions of all the estimates.

A method for comparing the levels of two or more analytes predicted by one or more methods to be associated with a change in a biological phenomenon in two sets of data each containing more than one measured sample, comprising:

• (a) selecting only analytes that are assayed in both sets of data;
• (b) ranking said analytes in each set of data using a comparative method such as the highest probability or lowest false discovery rate associated with the change in the biological phenomenon;
• (c) comparing a set of analytes in each ranked list in step (b) with each other, selecting those that occur in both lists, and determining the number of analytes that occur in both lists and show a change in level associated with the biological phenomenon that is in the same direction;
• and
• (d) calculating a concordance score based on the probability that said number of comparisons would show the observed number of change in the same direction, at random.