Gene expression profile algorithm and test for determining prognosis of prostate cancer

1. A method of analyzing a biological sample containing cancer cells from a patient with prostate cancer, comprising:

determining a level of RNA transcripts of each of a set of genes consisting of: BGN, COL1A1, SFRP4, FLNC, GSN, GSTM2, TPM2, AZGP1, KLK2, FAM13C, SRD5A2, and TPX2, and one or more reference genes, in the biological sample,

normalizing the level of the RNA transcripts against the level of the one or more reference RNA transcripts from the sample to obtain normalized expression levels of the BGN, COL1A1, SFRP4, FLNC, GSN, GSTM2, TPM2, AZGP1, KLK2, FAM13C, SRD5A2, and TPX2 RNA transcripts,

assigning the RNA transcripts to gene groups selected from a cellular organization gene group, an androgen gene group, a stromal response gene group, and a proliferation gene group;

wherein the cellular organization group comprises FLNC, GSN, TPM2, and GSTM2, the androgen group comprises FAM13C, KLK2, AZGP1 and SRD5A2, the stromal response group comprises BGN, COL1A1, and SFRP4, and the proliferation group comprises TPX2, and

calculating one or more quantitative scores selected from (a) a stromal response group score obtained from normalized expression levels of the stromal response group genes wherein the stromal group score equals 0.527X BGN+0.457 X COL1A1+0.156 X SFRP4, (b) a cellular organization group score obtained from normalized expression levels of the cellular organization group genes wherein the cellular organization group score equals 0.163 X FLNC+0.504 X GSN+0.421 X TPM2+0.394 X GSTM2, (c) an androgen group score obtained from normalized expression levels of the androgen group genes wherein the androgen group score equals 0.634 X FAM13C+1.079 X KLK2+0.642 X AZGP1+0.997 X SRD5A2 threshold score where the SRD5A2 threshold score equals SRD5A2 if SRD5A2 is 5.5 or higher and equals 5.5 if SRD5A2 is less than 5.5, and (d) a TPX2 threshold score wherein the TPX2 threshold score equals TPX2 if TPX2 is 5.0 or higher and equals 5.0 if TPX2 is less than 5.0, wherein the gene symbols represent the normalized gene expression levels of the RNA transcripts of the respective genes.

2. The method of claim 1 , wherein the biological sample is a tissue sample.

3. The method of claim 2 , wherein the tissue sample is fixed, paraffin-embedded, or fresh, or frozen.

4. The method of claim 1 , wherein the level of one or more RNA transcripts is determined by quantitative RT-PCR.

5. The method of claim 1 , further comprising creating a report providing the one or more quantitative score results.

6. The method of claim 1 , wherein the one or more reference transcripts comprise RNA transcripts from one or more of ARF1, ATP5E, CLTC, GPS1, and PGK1.

7. A method of treating a prostate cancer patient, comprising:

administering active surveillance to the patient; wherein the patient was previously determined to have a low or intermediate risk of adverse pathology, non-organ-confined disease, high-grade disease, or high-grade or non-organ confined disease according to an analysis comprising:

determining a level of RNA transcripts of each of a set of genes consisting of: BGN, COL1A1, SFRP4, FLNC, GSN, GSTM2, TPM2, AZGP1, KLK2, FAM13C, SRD5A2, and TPX2, and one or more reference genes, in a biological sample from the patient,

normalizing the level of the RNA transcripts against the level of the one or more reference RNA transcripts from the sample to obtain normalized expression levels of the BGN, COL1A1, SFRP4, FLNC, GSN, GSTM2, TPM2, AZGP1, KLK2, FAM13C, SRD5A2, and TPX2 RNA transcripts,

comparing the normalized expression levels to gene expression data in reference prostate cancer samples, wherein increased normalized expression levels of BGN, COL1A1, SFRP4, and TPX2 correlate with an increased likelihood of adverse pathology, non-organ-confined disease, high-grade disease, or high-grade or non-organ confined disease, and wherein increased normalized expression levels of FLNC, GSN, GSTM2, TPM2, AZGP1, KLK2, FAM13C, and SRD5A2 correlate with a decreased likelihood of adverse pathology, non-organ-confined disease, high-grade disease, or high-grade or non-organ confined disease,

assigning the RNA transcripts to gene groups selected from a cellular organization gene group, an androgen gene group, a stromal response gene group, and a proliferation gene group; wherein the cellular organization group comprises FLNC, GSN, TPM2, and GSTM2, the androgen group comprises FAM13C, KLK2, AZGP1 and SRD5A2, the stromal response group comprises BGN, COL1A1, and SFRP4, and the proliferation group comprises TPX2,

calculating one or more quantitative scores for the patient, and

predicting the likelihood of one or more of adverse pathology, non-organ-confined disease, high-grade disease, or high-grade or non-organ-confined disease for the patient based on the one or more quantitative scores;

wherein the one or more quantitative scores are selected from a stromal response group score obtained from normalized expression levels of the stromal response group genes wherein the stromal group score equals 0.527 X BGN+0.457 X COL1A1+0.156 X SFRP4, a cellular organization group score obtained from normalized expression levels of the cellular organization group genes wherein the cellular organization group score equals 0.163 X FLNC+0.504 X GSN+0.421 X TPM2+0.394 X GSTM2, an androgen group score obtained from normalized expression levels of the androgen group genes wherein the androgen group score equals 0.634 X FAM13C+1.079 X KLK2+0.642 X AZGP1+0.997 X SRD5A2 threshold score where the SRD5A2 threshold score equals SRD5A2 if SRD5A2 is 5.5 or higher and equals 5.5 if SRD5A2 is less than 5.5, and a TPX2 threshold score wherein the TPX2 threshold score equals TPX2 if TPX2 is 5.0 or higher and equals 5.0 if TPX2 is less than 5.0, wherein the gene symbols represent the normalized gene expression levels of the RNA transcripts of the respective genes; and

wherein the stromal response group score and the proliferation group score positively correlate with an likelihood of adverse pathology, non-organ-confined disease, high-grade disease, and high-grade or non-organ confined disease, and wherein cellular organization group score and androgen group score negatively correlate with a likelihood of adverse pathology, non-organ-confined disease, high-grade disease, and high-grade or non-organ confined disease.

8. The method of claim 1 , wherein the method comprises determining the androgen group score.

9. The method of claim 7 , wherein the method comprises determining the androgen group score.

10. The method of claim 1 , wherein the method comprises determining the stromal group score.

11. The method of claim 7 , wherein the method comprises determining the stromal group score.

12. The method of claim 1 , wherein the method comprises determining the proliferation group score.

13. The method of claim 7 , wherein the method comprises determining the proliferation group score.