Abstract: Expression of Forkhead-box protein A1 (FOXA1), a transcription factor important for the normal development of the prostate gland is thought to be controlled by steroid hormones and GATA-3. Expression of FOXA1, GATA-3 and androgen receptor (AR) was retrospectively analyzed by immunohistochemistry (IHC) in a series of 80 primary tumors and 28 metastatic prostate cancers including 15 matched paired samples. High nuclear FOXA1 expression was seen in 19% of primary tumors and 89% of metastatic tumors (p<0.0001). FOXA1 expression correlated positively with tumor size, extra-prostatic extension, angiolymphatic invasion, AR and metastasis but did not correlate with age, tumor stage, Gleason score, presence of PIN or multifocality, seminal vesicle or perineural invasion and status of surgical excision margins. Expression of GATA-3 was not seen in either normal epithelium or tumor. High FOXA1 expression is associated with development of metastatic prostate cancer.

Abstract: Biomarkers are provided for detecting, diagnosing and prognosing thymic cancer in individuals having or suspected of having thymic cancer. In addition, kits are provided for measuring expression levels or the presence of the biomarkers associated with thymic cancer for detecting, diagnosing and prognosing thymic cancer. Furthermore, methods are provided for detecting, diagnosing and prognosing thymic cancer in individuals having or suspected of having thymic cancer via the biomarkers.

Abstract: A genetic biomarker panel is provided for prognosing late onset ER+ breast cancer relapse, in a breast cancer survivor patient. Kits are also provided for measuring levels or the presence of an identified panel of genetic biomarkers. Methods are also provided for identifying a breast cancer survivor patient at a relatively high risk of suffering a breast cancer relapse within 8 years of diagnosis, and therefore suitable for treatment with an aggressive chemotherapeutic regimen. The method may also be used for identifying a breast cancer survivor patient not at high risk of suffering a breast cancer relapse within 8 years of diagnosis, and thus not suitable for treatment with an aggressive chemotherapeutic regimen. The genetic biomarker panel includes an oligonucleotide/nucleic acid sequence specific for the following genes: MKI67, SPAG5, ESPL1, PLK1, or a genetic panel for MKI67, SPAG5, ESPL1, PLK1 and PGR.

Abstract: A method for determining the likelihood of late ER? breast cancer disease relapse/recurrence is disclosed. Late ER+ breast cancer disease onset and/or recurrence is determined for a period of 5 to 20 years after an initial ER+ breast cancer disease onset in a patient. An ER+ breast cancer patient is assigned a risk score that is compared to a defined threshold value, and identifies the risk score as low risk or high risk for late breast cancer recurrence. A late ER+ breast cancer gene panel of 8 to 15 genes is provided. Subjects having a risk score greater than or equal to that of the threshold value are at a relatively high risk of recurrent disease, and are determined to benefit from aggressive therapeutic intervention, whereas subjects having a risk score less than the threshold value are at a relatively low risk of recurrent disease, and could forego treatment.

Abstract: Expression of Forkhead-box protein A1 (FOXA1), a transcription factor important for the normal development of the prostate gland is thought to be controlled by steroid hormones and GATA-3. Expression of FOXA1, GATA-3 and androgen receptor (AR) was retrospectively analyzed by immunohistochemistry (IHC) in a series of 80 primary tumors and 28 metastatic prostate cancers including 15 matched paired samples. High nuclear FOXA1 expression was seen in 19% of primary tumors and 89% of metastatic tumors (p<0.0001). FOXA1 expression correlated positively with tumor size, extra-prostatic extension, angiolymphatic invasion, AR and metastasis but did not correlate with age, tumor stage, Gleason score, presence of PIN or multifocality, seminal vesicle or perineural invasion and status of surgical excision margins. Expression of GATA-3 was not seen in either normal epithelium or tumor. High FOXA1 expression is associated with development of metastatic prostate cancer.

Abstract: A genetic biomarker panel is provided for prognosing late onset ER+ breast cancer relapse, in a breast cancer survivor patient. Kits are also provided for measuring levels or the presence of an identified panel of genetic biomarkers. Methods are also provided for identifying a breast cancer survivor patient at a relatively high risk of suffering a breast cancer relapse within 8 years of diagnosis, and therefore suitable for treatment with an aggressive chemotherapeutic regimen. The method may also be used for identifying a breast cancer survivor patient not at high risk of suffering a breast cancer relapse within 8 years of diagnosis, and thus not suitable for treatment with an aggressive chemotherapeutic regimen. The genetic biomarker panel includes an oligonucleotide/nucleic acid sequence specific for the following genes: MKI67, SPAG5, ESPL1, PLK1, or a genetic panel for MKI67, SPAG5, ESPL1, PLK1 and PGR.

Abstract: Biomarkers are provided for detecting, diagnosing and prognosing thymic cancer in individuals having or suspected of having thymic cancer. In addition, kits are provided for measuring expression levels or the presence of the biomarkers associated with thymic cancer for detecting, diagnosing and prognosing thymic cancer. Furthermore, methods are provided for detecting, diagnosing and prognosing thymic cancer in individuals having or suspected of having thymic cancer via the biomarkers.

Abstract: Expression of Forkhead-box protein A1 (FOXA1), a transcription factor important for the normal development of the prostate gland is thought to be controlled by steroid hormones and GATA-3. Expression of FOXA1, GATA-3 and androgen receptor (AR) was retrospectively analyzed by immunohistochemistry (IHC) in a series of 80 primary tumors and 28 metastatic prostate cancers including 15 matched paired samples. High nuclear FOXA1 expression was seen in 19% of primary tumors and 89% of metastatic tumors (p<0.0001). FOXA1 expression correlated positively with tumor size, extra-prostatic extension, angiolymphatic invasion, AR and metastasis but did not correlate with age, tumor stage, Gleason score, presence of PIN or multifocality, seminal vesicle or perineural invasion and status of surgical excision margins. Expression of GATA-3 was not seen in either normal epithelium or tumor. High FOXA1 expression is associated with development of metastatic prostate cancer.

Abstract: Aspects of the invention include methods for identifying patients with HER2+ cancers that are at a heightened risk for developing brain metastasis within three years of having been diagnosed with HER2+ cancer. Some embodiments are methods that include the steps of contacting at least a portion of the tumor tissue from patients with probes that interact with the products of a set of thirteen genes that are expressed in these patients at markedly higher levels than in similarly situated patients that are not a heightened risk for developing brain metastasis within this three year window. In some embodiments the tissue samples are assayed from the presence of RNA indicative of the expression of member of a set of 13 genes identified as being differentially expressed in patients with and without a heightened risk for developing brain metastasis.

Abstract: Methods and compositions based on FOXA1 expression to predict long-term disease-free survival in patients with breast cancer are disclosed. In ER+ positive patients, expression of FOXA1 is useful in identifying a subgroup of patients with a better prognosis. FOXA1 expression correlates with luminal subtype breast cancer, and serves as a clinical marker for luminal subtype breast cancer. Expression of FOXA1 is useful as a prognostic marker for an effective response tumors and as a predictive marker for a greater likelihood of response to an anti-hormonal therapy. Prognostic ability of FOXA1 in low-risk breast cancers is useful in treatment decision making.