Abstract: Provided herein are methods of identifying treatment-response signatures, such as in a subject with prostate cancer (such as a human or veterinary subject). In particular examples, the methods can determine with high accuracy whether a subject is likely to respond to a treatment. The methods can be computer-implemented methods.

Abstract: Disclosed herein are methods of treating and identifying subjects with ER+ breast cancer that will or will not develop resistance of tamoxifen. In some examples such methods include measuring expression of adaptor-related protein complex 2, sigma-1 subunit (AP2S1) from the retrograde neurotrophin signaling pathway, cyclin-dependent kinase 2 (CDC2) from the loss of NLP from mitotic centrosomes pathway, general transcription factor IIIC subunit 3 (GTF3C3) from the RNA polymerase III transcription initiation from Type 2 promoter pathway, eukaryotic translation initiation factor 2-alpha kinase 3 (EIFA2AK3) from the EIF2 pathway, and leucyl-tRNA synthetase (LARS) from the valine, leucine and isoleucine biosynthesis pathway.

Abstract: The present technology is directed to methods for diagnosing metastasis, or assessing risk of metastasis, in a subject having cancer. The present technology is also directed to methods for treating a subject having metastatic cancer or an increased risk of cancer metastasis; through the development of gene signatures with prognostic value for determining metastasis in human patients undergoing AR therapy. When compared to controls, the expression level of the genes is highly correlative with the presence of metastasis, as well as the risk of future cancer metastasis. The present technology is also directed to biomarkers that can identify and categorize the needs of different patients for less or more aggressive therapy to prevent or treat metastatic disease outcome.

Abstract: Disclosed herein are methods of treating and identifying subjects with cancer that will respond to chemotherapy treatment. Exemplary methods can be used to treat or identify subjects with lung or colorectal cancer that will respond positively (or will not respond) to chemotherapy.

Abstract: Disclosed herein are systems and methods for identifying biomarkers. Biomarker identification can be achieved while increasing efficiency and decreasing data and computation complexity but maintaining accuracy. Such biomarker identification can be achieved by applying pathway enrichment analysis associated with differential gene expression and epigenomic regulation, such as DNA methylation.

Abstract: Methods for predicting the response of prostate cancer to androgen deprivation therapy (ADT) using a gene signature of five genes (CSPG5, FKBP6, FOSB, STMN1, and TTC27) is provided. Also provided are sets containing specific binding molecules for each of CSPG5, FKBP6, FOSB, STMN1, and TTC27 and kits containing such sets.

Abstract: Methods for predicting the response of prostate cancer to androgen deprivation therapy (ADT) using a gene signature of five genes (CSPG5, FKBP6, FOSB, STMN1, and TTC27) is provided. Also provided are sets containing specific binding molecules for each of CSPG5, FKBP6, FOSB, STMN1, and TTC27 and kits containing such sets.