Abstract: Techniques and systems for translating images of biological samples stained according to a first staining technique into images representing the biological samples stained according to a second staining technique. In various implementations, the first staining technique can include a histopathological staining technique and the second staining technique can include an immunofluorescence staining technique or an immunohistochemistry staining technique.

Abstract: The invention described in the application relates to a panel of gene expression markers for node-negative, ER-positive, HER2-negative breast cancer patients. The invention thus provides methods and compositions, e.g., kits and/or microarrays, for evaluating gene expression levels of the markers and methods of using such gene expression levels to evaluate the likelihood of relapse of a node-negative, ER-positive, HER2-negative breast cancer patient. Such information can be used in determining treatment options for patients.

Abstract: The present invention relates to DNA sequences from regions of copy number change on chromosome 20. The sequences can be used in hybridization methods for the identification of chromosomal abnormalities associated with various diseases.

Abstract: A signature of a condition of a live cell is established in an assay that allows distribution of the receptors on the cell surface in response to binding a ligand. The receptors can be optically detected and quantified to provide a value for the condition, Test drugs can be screened for therapeutic potential in the assay: a potentially efficacious drug is identified by an ability to modulate an established signature. The receptor distribution signature can be corroborated with an mRNA expression profile of several genes, indicating, for example, metastasis.

Abstract: Herein is described the use of a collection of 50 breast cancer cell lines to match responses to 77 conventional and experimental therapeutic agents with transcriptional, proteomic and genomic subtypes found in primary tumors. Almost all compounds produced strong differential responses across the cell lines produced responses that were associated with transcriptional and proteomic subtypes and produced responses that were associated with recurrent genome copy number abnormalities. These associations can now be incorporated into clinical trials that test subtype markers and clinical responses simultaneously.

Abstract: Disclosed herein are methods of determining a diagnosis or prognosis for a subject with a breast tumor. In one embodiment, the method includes determining an amount of EPS8-like 1 (EPS8L1) in the sample (such as an amount of EPS8L1 nucleic acid or protein) and comparing the amount of EPS8L1 in the sample to a control. The subject is determined to have a poor prognosis (such as decreased likelihood of survival) if the amount of EPS8L1 in the sample is increased compared to the control. In some embodiments, the methods further include administering a treatment to a subject determined to have a poor prognosis, such as administering an ErbB2-targeting therapy to the subject.

Abstract: The present invention relates to cDNA sequences from a region of amplification on chromosome 20 associated with disease. The sequences can be used in hybridization methods for the identification of chromosomal abnormalities associated with various diseases. The sequences can also be used for treatment of diseases.

Abstract: Developed here is a mitotic network comprising a signature of up to 54 genes, and including also sub-sets of genes within the signature, which can identify members by requiring higher correlation values for a signature gene. The present mitotic network provides for methods for prognosis and diagnosis of various cancers. The mitotic network is conserved across cancers exhibiting aberrant mitotic activity and several genes in the network act as therapeutic targets. Development of other inhibitors of mitosis can apply expression values of the genes in the mitotic network from patient tissue to select patients during clinical validation of the new drugs.

Abstract: Methods and systems for identifying a cancer patient suitable for treatment with a PARP inhibitor. A 6-gene, 7-gene and 8-gene predictor panels of genes that are predictive of patient resistance or sensitivity to PARP inhibitors such as Olaparib.

Abstract: This invention pertains to the discovery that an amplification of the CYP24 gene or an increase in CYP24 activity is a marker for the presence of, progression of, or predisposition to, a cancer (e.g., breast cancer). Using this information, this invention provides methods of detecting a predisposition to cancer in an animal. The methods involve (i) providing a biological sample from an animal (e.g. a human patient); (ii) detecting the level of CYP24 within the biological sample; and (iii) comparing the level of CYP24 with a level of CYP24 in a control sample taken from a normal, cancer-free tissue where an increased level of CYP24 in the biological sample compared to the level of CYP24 in the control sample indicates the presence of said cancer in said animal.

Abstract: This invention pertains to the discovery that an amplification of the CYP24 gene or an increase in CYP24 activity is a marker for the presence of, progression of, or predisposition to, a cancer (e.g., breast cancer). Using this information, this invention provides methods of detecting a predisposition to cancer in an animal. The methods involve (i) providing a biological sample from an animal (e.g. a human patient); (ii) detecting the level of CYP24 within the biological sample; and (iii) comparing the level of CYP24 with a level of CYP24 in a control sample taken from a normal, cancer-free tissue where an increased level of CYP24 in the biological sample compared to the level of CYP24 in the control sample indicates the presence of said cancer in said animal.

Abstract: Methods for identifying a cancer patient, such as a breast cancer patient, suitable for treatment with a 4-anilinoquinazoline kinase inhibitor, such as lapatinib, and an AKT inhibitor, comprising detecting modulated expression of HER2 (ERBB2) and SASH1 or protein encoded thereof and detecting PIK3CA mutation status. High levels of expression in HER2 and high levels of SASH1 and/or positive PIK3CA mutation status indicate a patient that is suitable for treatment with a 4-anilinoquinazoline kinase inhibitor, such as lapatinib and an AKT inhibitor.

Abstract: Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Abstract: The present invention relates to cDNA sequences from a region of amplification on chromosome 20 associated with disease. The sequences can be used in hybridization methods for the identification of chromosomal abnormalities associated with various diseases. The sequences can also be used for treatment of diseases.

Abstract: Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Abstract: Cancer markers may be developed to detect diseases characterized by increased expression of apoptosis-suppressing genes, such as aggressive cancers. Genes in the human chromosomal regions, 8q24, 11q13, 20q11-q13, were found to be amplified indicating in vivo drug resistance in diseases such as ovarian cancer. Diagnosis and assessment of amplification levels certain genes shown to be amplified, including PVT1, can be useful in prediction of poor outcome of patient's response and drug resistance in ovarian cancer patients with low survival rates. Certain genes were found to be high priority therapeutic targets by the identification of recurrent aberrations involving genome sequence, copy number and/or gene expression are associated with reduced survival duration in certain diseases and cancers, specifically ovarian cancer. Therapeutics to inhibit amplification and inhibitors of one of these genes, PVT1, target drug resistance in ovarian cancer patients with low survival rates is described.

Abstract: A method of analyzing biological material by exposing the biological material to a recognition element, that is coupled to a mass tag element, directing an ion beam of a mass spectrometer to the biological material, interrogating at least one region of interest area from the biological material and producing data, and distributing the data in plots.

Abstract: This invention pertains to the discovery that an amplification of the CYP24 gene or an increase in CYP24 activity is a marker for the presence of, progression of, or predisposition to, a cancer (e.g., breast cancer). Using this information, this invention provides methods of detecting a predisposition to cancer in an animal. The methods involve (i) providing a biological sample from an animal (e.g. a human patient); (ii) detecting the level of CYP24 within the biological sample; and (iii) comparing the level of CYP24 with a level of CYP24 in a control sample taken from a normal, cancer-free tissue where an increased level of CYP24 in the biological sample compared to the level of CYP24 in the control sample indicates the presence of said cancer in said animal.

Abstract: This invention provides targeted nanoclusters comprising multiple polyvalent nanoparticle core units or nanoscaffolds, each nanoparticle core unit attached to multiple targeting moieties and multiple detectable moieties. The nanoclusters find use in a broad range of analytical assays, diagnostic assays and as targeted therapeutics.

Abstract: Developed here is a mitotic network comprising a signature of up to 54 genes, and including also sub-sets of genes within the signature, which can identify members by requiring higher correlation values for a signature gene. The present mitotic network provides for methods for prognosis and diagnosis of various cancers. The mitotic network is conserved across cancers exhibiting aberrant mitotic activity and several genes in the network act as therapeutic targets. Development of other inhibitors of mitosis can apply expression values of the genes in the mitotic network from patient tissue to select patients during clinical validation of the new drugs.