Abstract: Methods and compositions are provided for diagnosing lung cancer in a mammalian subject by use of 7 or more selected genes, e.g., a gene expression profile, from the blood of the subject which is characteristic of disease. The gene expression profile includes 7 or more genes of Table I, Table II, Table III, Table IV or Table IX herein.

Abstract: Methods and compositions are provided for diagnosing lung cancer in a mammalian subject by use of 7 or more selected genes, e.g., a gene expression profile, from the blood of the subject which is characteristic of disease. The gene expression profile includes 7 or more genes of Table I, Table II, Table III, Table IV or Table IX herein.

Abstract: Methods and compositions are provided for diagnosing lung cancer in a mammalian subject by use of 10 or more selected genes, e.g., a gene expression profile, from the blood of the subject which is characteristic of disease. The gene expression profile includes 10 or more genes of Table I or Table II herein.

Abstract: Methods and compositions are provided for diagnosing lung cancer in a mammalian subject by use of 10 or more selected genes, e.g., a gene expression profile, from the blood of the subject which is characteristic of disease. The gene expression profile includes 10 or more genes of Table I or Table II herein.

Abstract: Methods and compositions are provided for diagnosing lung cancer in a mammalian subject by use of 7 or more selected genes, e.g., a gene expression profile, from the blood of the subject which is characteristic of disease. The gene expression profile includes 7 or more genes of Table I, Table II, Table III, Table IV or Table IX herein.

Abstract: The present invention relates to methods and systems for high risk screening, diagnosis, prognosis, and surveillance of lung cancer. Accordingly, in one aspect, the invention provides a method for diagnosing or evaluating whether a subject has, or is at risk of having, lung cancer such as NSCLS. The method comprises obtaining a first expression level of the AKAP4 gene of a population of cells from the blood of a test subject; and comparing the first expression level with a first predetermined reference value. A difference between the first expression level and first predetermined reference value correlates with a diagnosis or evaluation of a lung cancer.

Abstract: A multi-analyte composition for the diagnosis of lung cancer or lung disease comprises a ligand selected from a nucleic acid sequence, polynucleotide or oligonucleotide capable of specifically complexing with, hybridizing to, or identifying an mRNA gene transcript from a mammalian blood sample, and an additional ligand selected from a nucleic acid sequence, polynucleotide or oligonucleotide capable of specifically complexing with, hybridizing to, or identifying an miRNA of a gene from a mammalian blood sample. Each ligand and additional ligand binds to a different gene transcript or miRNA and the gene transcripts and miRNA identified form a characteristic profile of a stage of lung cancer or lung disease. Methods of using this composition for diagnosis and evaluation and methods for developing such compositions are described.

Abstract: The present invention relates to methods and systems for high risk screening, diagnosis, prognosis, and surveillance of lung cancer. Accordingly, in one aspect, the invention provides a method for diagnosing or evaluating whether a subject has, or is at risk of having, lung cancer such as NSCLS. The method comprises obtaining a first expression level of the AKAP4 gene of a population of cells from the blood of a test subject; and comparing the first expression level with a first predetermined reference value. A difference between the first expression level and first predetermined reference value correlates with a diagnosis or evaluation of a lung cancer.

Abstract: Compositions and methods described herein include somatic cells that are competent for reprogramming and malignant transformation and are characterized by a reduction of the levels of Sp100 in the cells, cells having markers of pluripotent stem cells, and methods for preparing same. Methods for reversably regulating aging or reprogramming to pluripotency in a somatic cell involve modulating the expression of Sp100 therein. Methods and compositions for retarding the growth of or suppressing unwanted cell proliferation involve expressing, inducing expression of, or upregulating, Sp100 in a targeted cell that is undergoing unrestricted proliferation or replication or increasing exposure to Sp100 in the environment or microenvironment of the targeted cell. Also disclosed are methods for treating a proliferative disease or condition by increasing expression or levels of Sp100 in the targeted cell or its environment.

Abstract: An isoform-level gene panel is disclosed that can accurately classify a glioblastoma subtype from a tumor sample. Such an isoform level gene panel comprises the 121 to 214 target isoforms identified in Table 1. Also disclosed are reagents for quantitively detecting the expression or activity of the target isoforms of Table 1 in a patient sample. For example, such ligands can be PCR primer and probes sets. This isoform-level gene panel and reagents for detection of the isoforms are useful in an isoform-level assay for diagnosis of the molecular subtype of a glioblastoma in a patient. The assay employs algorithms and a novel computer program that performs the functions of FIG. 8. In one aspect, the assay is a high-throughput format.

Abstract: An isoform-level gene panel is disclosed that can accurately classify a glioblastoma subtype from a tumor sample. Such an isoform level gene panel comprises the 121 to 214 target isoforms identified in Table 1. Also disclosed are reagents for quantitatively detecting the expression or activity of the target isoforms of Table 1 in a patient sample. For example, such ligands can be PCR primer and probes sets. This isoform-level gene panel and reagents for detection of the isoforms are useful in an isoform-level assay for diagnosis of the molecular subtype of a glioblastoma in a patient. The assay employs algorithms and a novel computer program that performs the functions of FIG. 8. In one aspect, the assay is a high-throughput format.

Abstract: A multi-analyte composition for the diagnosis of lung cancer or lung disease comprises a ligand selected from a nucleic acid sequence, polynucleotide or oligonucleotide capable of specifically complexing with, hybridizing to, or identifying an mRNA gene transcript from a mammalian blood sample, and an additional ligand selected from a nucleic acid sequence, polynucleotide or oligonucleotide capable of specifically complexing with, hybridizing to, or identifying an miRNA of a gene from a mammalian blood sample. Each ligand and additional ligand binds to a different gene transcript or miRNA and the gene transcripts and miRNA identified form a characteristic profile of a stage of lung cancer or lung disease. Methods of using this composition for diagnosis and evaluation and methods for developing such compositions are described.

Abstract: Methods and compositions are provided for diagnosing or detecting a condition, e.g., lung disease in a mammalian subject by use of a micro-RNA expression level or an expression level profile of multiple miRNA in the peripheral blood mononuclear cells (PBMC) of the subject which is characteristic of COPD or NSCLC. Detection of changes in expression in specific miRNA biomarkers from that of a reference sample or miRNA expression profile are correlated with non-small cell lung cancer (NSCLC) and/or COPD and permit differentiation among healthy subjects, subjects with COPD and subjects with adenocarcinoma or squamous cell carcinoma.

Abstract: An isoform-level gene panel is disclosed that can accurately classify a glioblastoma subtype from a tumor sample. Such an isoform level gene panel comprises the 121 to 214 target isoforms identified in Table 1. Also disclosed are reagents for quantitatively detecting the expression or activity of the target isoforms of Table 1 in a patient sample. For example, such ligands can be PCR primer and probes sets. This isoform-level gene panel and reagents for detection of the isoforms are useful in an isoform-level assay for diagnosis of the molecular subtype of a glioblastoma in a patient. The assay employs algorithms and a novel computer program that performs the functions of FIG. 8. In one aspect, the assay is a high-throughput format.

Abstract: Methods and compositions are provided for diagnosing or detecting a condition, e.g., lung disease in a mammalian subject by use of a micro-RNA expression level or an expression level profile of multiple miRNA in the peripheral blood mononuclear cells (PBMC) of the subject which is characteristic of COPD or NSCLC. Detection of changes in expression in specific miRNA biomarkers from that of a reference sample or miRNA expression profile are correlated with non-small cell lung cancer (NSCLC) and/or COPD and permit differentiation among healthy subjects, subjects with COPD and subjects with adenocarcinoma or squamous cell carcinoma.

Abstract: Compositions and methods described herein include somatic cells that are competent for reprogramming and malignant transformation and are characterized by a reduction of the levels of Sp100 in the cells, cells having markers of pluripotent stem cells, and methods for preparing same. Methods for reversably regulating aging or reprogramming to pluripotency in a somatic cell involve modulating the expression of Sp100 therein. Methods and compositions for retarding the growth of or suppressing unwanted cell proliferation involve expressing, inducing expression of, or upregulating, Sp100 in a targeted cell that is undergoing unrestricted proliferation or replication or increasing exposure to Sp100 in the environment or microenvironment of the targeted cell. Also disclosed are methods for treating a proliferative disease or condition by increasing expression or levels of Sp100 in the targeted cell or its environment.

Abstract: Methods and compositions are provided for diagnosing or detecting a condition, e.g., lung disease in a mammalian subject by use of a micro-RNA expression level or an expression level profile of multiple miRNA in the peripheral blood mononuclear cells (PBMC) of the subject which is characteristic of COPD or NSCLC. Detection of changes in expression in specific miRNA biomarkers from that of a reference sample or miRNA expression profile are correlated with non-small cell lung cancer (NSCLC) and/or COPD and permit differentiation among healthy subjects, subjects with COPD and subjects with adenocarcinoma or squamous cell carcinoma.

Abstract: A method of developing a gene expression profile indicative of the presence or stage of a selected a disease, disorder or genetic pathology in a mammalian subject employs penalized discriminant analysis with recursive feature elimination. A method of diagnosing a cancer in a mammalian subject includes the steps of examining a sample containing the subject's immune cells and detecting a variance in the expression of a statistically significant number of genes, e.g., at least 10 non-tumor genes from those same genes in a characteristic disease or healthy gene expression profile. A significant variance in expression of these genes when compared to a gene expression profile, preferably an average gene expression profile of a normal control, or significant similarities to an average gene profile of subjects with cancer, correlates with a specific type of cancer and/or location of tumor.

Abstract: The present invention is a method distinguishing between head and neck squamous cell carcinoma and lung squamous cell carcinoma. In particular, a 10-gene classifier has been identified which can be used to distinguish between primary squamous cell carcinoma of the lung and metastatic head and neck squamous cell carcinoma. These genes include CXCL13, COL6A2, SFTPB, KRT14, TSPYL5, TMP3, KLK10, MMP1, GAS1, and MYH2. A panel of one or more of these genes, or proteins encoded thereby, can be used for early diagnosis and selection of an appropriate therapeutic treatment.

Abstract: Novel DNA sequences located 5' to the chromosome 11p13 breakpoint are employed as diagnostic probes for breast cancers, T cell leukemias and WAGR associated with chromosome 11 abnormalities. Probe compositions and methods for diganostic assays are provided.