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Results Found: 30
  • MSK-IMPACT Clinical Sequencing Cohort (MSKCC, Nat Med 2017): Targeted sequencing of 10,000 clinical cases using the MSK-IMPACT assay

    Description

    This dataset contains summary data visualizations and clinical data from the targeted sequencing of 10,000 clinical cases using the MSK-IMPACT assay. The clinical data includes mutation count, information about mutated genes, tumor mutational burden calculations, tissue site from which the sample was derived, tumor purity among other relevant data points. The data set also includes copy-number segment...

    Subject
    Adenocarcinoma
    Adenocarcinoma of Lung
    Adenocarcinoma, Mucinous
    Breast Neoplasms
    Carcinoma, Ductal, Breast
    Carcinoma, Hepatocellular
    Carcinoma, Lobular
    Carcinoma, Non-Small-Cell Lung
    Carcinoma, Renal Cell
    Carcinoma, Squamous Cell
    Carcinosarcoma
    Cholangiocarcinoma
    Colonic Neoplasms
    Colorectal Neoplasms
    Cystadenocarcinoma, Serous
    DNA Mutational Analysis
    Gallbladder Neoplasms
    Glioblastoma
    Liposarcoma
    Lung Neoplasms
    Lymphoma, Follicular
    Melanoma
    Mesothelioma
    Neoplasms, Squamous Cell
    Neurofibroma
    Oligodendroglioma
    Osteosarcoma
    Ovarian Neoplasms
    Pancreatic Neoplasms
    Prostatic Neoplasms
    Rectal Neoplasms
    Sarcoma
    Sarcoma, Synovial
    Squamous Cell Carcinoma of Head and Neck
    Stomach Neoplasms
    Thyroid Cancer, Papillary
    Urinary Bladder Neoplasms
    Uterine Neoplasms
    Uveal Neoplasms
    Access Rights
    Free to All
  • Organ-specific in situ transcriptomics of MDA231 cells identified by Flura-seq

    Alternate Title(s)
    Flura-seq identifies organ-specific adaptations in metastasis-initiating cells
    Authors
    Basnet, Harihar
    Tian, Lin
    Massagué, Joan
    Description

    Summary from the GEO: "Metastasis-initiating cells dynamically adapt to the distinct microenvironments of different organs, but these early adaptations are poorly understood due to the limited sensitivity of in situ transcriptomics. We developed fluorouracil-labeled RNA sequencing (Flura-seq) for in situ analysis with unprecedented sensitivity. Flura-seq utilizes cytosine deaminase (CD) to convert...

    Subject
    Brain Neoplasms
    Breast Neoplasms
    Gene Expression Profiling
    Lung Neoplasms
    Transcriptome
    Access Rights
    Free to All
  • Flura-Seq Identifies In Situ Transcriptomes of Micrometastases

    Authors
    Basnet, Harihar
    Macalinao, Danilo Reynaldo Galindez
    Massagué, Joan
    Description

    Summary from the GEO: "Understanding the biology of rare cell populations in the context of their microenvironment requires an accurate analysis of the transcriptomes of these cells as expressed in situ. We developed fluorouracil-tagged RNA sequencing (Flura-seq) to characterize the transcriptomes of small cell subpopulations from a whole organ in model systems. The method utilizes cytosine deaminase...

    Subject
    Brain Neoplasms
    Breast Neoplasms
    Gene Expression Profiling
    Lung Neoplasms
    Transcriptome
    Transforming Growth Factor beta
    Access Rights
    Free to All
  • Thoracic PDX (MSK, Provisional): Targeted sequencing of thoracic PDX lines to characterize genetic alterations in 139 tumor/normal pairs via MSK-IMPACT.

    Description

    This dataset contains summary data visualizations and clinical data from a broad 183 samples of thoracic tumors from 77 patients. The data was generated by the Charles Rudin Lab, utilizing the MSK-IMPACT targeted sequencing test. The clinical data includes tumor type (based on the opensource OncoTree ontology developed at MSK), mutation count, information about mutated genes, patient demographics,...

    Subject
    Adenocarcinoma of Lung
    Carcinoma, Non-Small-Cell Lung
    DNA Mutational Analysis
    Lung Neoplasms
    Mesothelioma
    Access Rights
    Free to All
  • NCI-60 Cell Lines (NCI, Cancer Res 2012): Whole-exome sequencing of 67 samples by NCI-60 cell line project

    Description

    This dataset contains summary data visualizations and clinical data from 67 samples from 67 patients as part an NCI-60 cell line project to compile NCI-60 cell line high-throughput and high-content data into CellMiner, a genomic and pharmacologic database created by the National Cancer Center Institute. The clinical data includes deidentified patient and sample IDs, mutation counts, detailed cancer...

    Subject
    Adenocarcinoma
    Brain Neoplasms
    Breast Neoplasms
    Carcinoma, Renal Cell
    Colorectal Neoplasms
    DNA Mutational Analysis
    Leukemia, Myeloid
    Lung Neoplasms
    Melanoma
    Ovarian Neoplasms
    Prostatic Neoplasms
    Access Rights
    Free to All
  • Lung Squamous Cell Carcinoma (TCGA, Firehose Legacy)

    Description

    TCGA Lung Squamous Cell Carcinoma. Source data from GDAC Firehose. Previously known as TCGA Provisional. This dataset contains summary data visualizations and clinical data from a broad sampling of 511 carcinomas from 511 patients. The data was gathered as part of the Broad Institute of MIT and Harvard Firehose initiative, a cancer analysis pipeline. The clinical data includes mutation count, information...

    Subject
    Carcinoma, Non-Small-Cell Lung
    Carcinoma, Squamous Cell
    DNA Mutational Analysis
    Lung Neoplasms
    Access Rights
    Free to All
  • Non-Small Cell Cancer (MSKCC, Cancer Discov 2017): Targeted sequencing of 860 patients with metastatic lung adenocarcinoma

    Description

    This dataset contains the summary data visualizations and clinical data from targeted sequencing of 915 samples from 860 patients with metastatic lung adenocarcinoma. Clinical data includes: Number of Samples Per Patient, Mutation Count, Fraction Genome Altered, Diagnosis Age, Sex, Primary/Metastasis Sample Type, Chemotherapy, Clinical Trial, Driver Mutations, Durable Clinical Benefit, Gene Panel,...

    Subject
    Adenocarcinoma
    Adenocarcinoma of Lung
    Carcinoma, Non-Small-Cell Lung
    Lung Neoplasms
    Access Rights
    Free to All
  • Non-Small Cell Lung Cancer (MSK, Cancer Cell 2018): Whole-exome sequencing of 75 tumor/normal NSCLC pairs treated with PD-1 plus CTLA-4 blockade

    Description

    This dataset contains the summary data visualizations and clinical data from whole-exome sequencing of 75 tumor/normal NSCLC pairs treated with PD-1 plus CTLA-4 blockade from 75 patients. Clinical data includes: Mutation Count, Sex, Histology, Age (yrs), Best Overall Response, Durable Clinical Benefit, ECOG performance status, HLA_A1 allele, HLA_A2 alleles, HLA_B1 alleles, HLA_B2 alleles, HLA_C1 alleles,...

    Subject
    Carcinoma, Non-Small-Cell Lung
    Immune Checkpoint Inhibitors
    Lung Neoplasms
    Access Rights
    Free to All
  • Lung Adenocarcinoma (MSKCC, 2020): Targeted sequencing of 604 lung adenocarcinoma tumor/normal pairs via MSK-IMPACT

    Description

    This dataset contains the summary data visualizations and clinical data from targeted sequencing of 604 lung adenocarcinoma tumors from 604 patients via MSK-IMPACT. Clinical data includes: Mutation Count, Fraction Genome Altered, Sex, Age At Surgery, Clinical Nodal Status, CT Size, Diffusion lung capacity for carbon monoxide, FEV1, FGA Facets, Overall Survival Status, Pathologic Nodal Status Pathologic...

    Subject
    Adenocarcinoma
    Adenocarcinoma of Lung
    Lung Neoplasms
    Access Rights
    Free to All
  • Non-Small Cell Lung Cancer (MSKCC, J Clin Oncol 2018): IMPACT sequencing of 240 NSCLC tumor/normal pairs treated at MSKCC with anti-PD-(L)1 based therapy.

    Description

    This dataset contains the summary data visualizations and clinical data from IMPACT sequencing of 240 NSCLC tumor/normal pairs treated at MSKCC with anti-PD-(L)1 based therapy from 240 patients. Clinical data includes: Cancer Type, Mutation Count, Fraction Genome Altered, Sex, Durable Clinical Benefit, FGA, Gene Panel, IRB, Lines of treatment, Mutation Rate, Oncotree Code, PD-L1 Score (%), Smoker,...

    Subject
    Adenocarcinoma of Lung
    Carcinoma, Large Cell
    Carcinoma, Non-Small-Cell Lung
    Carcinoma, Squamous Cell
    Lung Neoplasms
    Access Rights
    Free to All