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Results Found: 123

  • A Molecular Taxonomy of Urothelial Carcinoma

    Authors
    Sjödahl, Gottfrid
    Lauss, Martin
    Lindgren, David
    Höglund, Mattias
    Description

    Gene expression profiles from 308 UC used to define seven molecular subtypes using step-by-step partitions and a bootstrap approach. Total RNA from fresh-frozen resection samples of 308 urothelial carcinomas was hybridized to the Illumina HumanHT-12 V3.0 expression beadchip arrays (Illumina Inc) at the SCIBLU Genomics Centre at Lund University Sweden.

    Subject
    Gene Expression Profiling
    Urinary Bladder Neoplasms
    Access Rights
    Free to All

  • Acral Melanoma (TGEN, Genome Res 2017): Whole exome sequencing and transcriptome analysis of 34 Acral Melanoma patients (33 with matched normals)

    Authors
    Liang, Winnie S.
    Hendricks, William
    Kiefer, Jeffrey
    Schmidt, Jessica
    22 more author(s)...
    Description

    This dataset contains summary data visualizations and clinical data from a comprehensive genomic and transcriptomic analysis of 34 acral lentiginous melanomas (ALM). The study was conducted to analyze ALM, a rare sun-shielded melanoma subtype of cutaneous melanoma (CM) which is associated with worse survival than other CM in an effort to delineate non-UV oncogenic mechanisms. The clinical data includes mutation count, information about mutated genes, patient demographics, disease status, therapeutic details and copy number alterations among other relevant data points.

    Subject
    Chromosome Aberrations
    DNA Mutational Analysis
    Melanoma/genetics
    Melanoma/pathology
    Transcriptome
    Access Rights
    Free to All

  • Acute Myeloid Leukemia (TCGA, Firehose Legacy)

    Description

    TCGA Acute Myeloid Leukemia. Source data from GDAC Firehose. Previously known as TCGA Provisional. This dataset contains summary data visualizations and clinical data from a broad sampling of 200 carcinomas from 200 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 about mutated genes, patient demographics, sample type, disease code, Abnormal Lymphocyte Percent, Atra Exposure, Basophils Cell Count, Blast Count, Cytogenetic abnormality type, and FAB. The dataset includes Next-Generation Clustered Heat Maps (NG-CHM) viewable via an embedded NG-CHM Heat Map Viewer, provided my MD Anderson Cancer Center, which provides a graphical environment for exploration of clustered or non-clustered heat map data. The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.

    Subject
    DNA Mutational Analysis
    Leukemia, Myeloid, Acute
    Access Rights
    Free to All

  • Acute Myeloid Leukemia (TCGA, PanCancer Atlas) data

    Description

    This dataset contains summary data visualizations and clinical data from a broad sampling of over 200 acute myeloid leukemias. The data was gathered as part of the PanCancer Atlas initiative, which aims to answer big, overarching questions about cancer by examining the full set of tumors characterized in the robust TCGA dataset. The clinical data includes mutation count, information about mutated genes, patient demographics, disease status, tumor typing, and chromosomal gain or loss. The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.

    Subject
    DNA Mutational Analysis
    Leukemia, Myeloid, Acute
    Access Rights
    Free to All

  • Adenoid Cystic Carcinoma Project (J Clin Invest 2019)

    Description

    Multi-Institute Cohort of 1045 Adenoid Cystic Carcinoma patients. This dataset contains summary data visualizations and clinical data from a broad sampling of 1045 adenoid cystic carcinomas. The data was gathered in support of an article in the Journal of Clinical Investigation. The clinical data includes mutation count, information about mutational analysis, patient demographics, survival status, and tumor type (based on the opensource OncoTree ontology developed at MSK). The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.

    Subject
    Carcinoma, Adenoid Cystic
    Access Rights
    Free to All

  • Adrenocortical Carcinoma (TCGA, Firehose Legacy)

    Description

    TCGA Adrenocortical Carcinoma; raw data at the NCI; source mutation data from GDAC Firehose. This dataset contains summary data visualizations and clinical data from a broad sampling of 92 adrenocortical carcinomas. 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 about mutated genes, patient demographics, Adjuvant Postoperative Pharmaceutical Therapy Administered Indicator, tumor typing, disease status, Atypical Mitotic Figures, Capsular Invasion, Ct scan preop results, Cytoplasm Presence Less Than Equal 25 Percent, and Days to Sample Collection. The dataset includes Next-Generation Clustered Heat Maps (NG-CHM) viewable via an embedded NG-CHM Heat Map Viewer, provided my MD Anderson Cancer Center, which provides a graphical environment for exploration of clustered or non-clustered heat map data. The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.

    Subject
    Adrenocortical Carcinoma
    DNA Mutational Analysis
    Access Rights
    Free to All

  • Adrenocortical Carcinoma (TCGA, PanCancer Atlas) data

    Description

    This dataset contains summary data visualizations and clinical data from a broad sampling of 91 adrenocortical carcinomas. The data was gathered as part of the PanCancer Atlas initiative, which aims to answer big, overarching questions about cancer by examining the full set of tumors characterized in the robust TCGA dataset. The clinical data includes mutation count, information about mutated genes, patient demographics, disease status, tumor typing, and chromosomal gain or loss. The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.

    Subject
    Adrenocortical Carcinoma
    DNA Mutational Analysis
    Access Rights
    Free to All

  • Ampullary Carcinoma (Baylor College of Medicine, Cell Reports 2016).

    Description

    Exome sequencing analysis of 160 cancers arising in the periampullary region, 62 of these clearly arising from either the bile duct (n = 44) or the duodenum (n = 18) and 98 for which the epithelium of origin could not be clearly defined morphologically (AMPCA). This dataset contains summary data visualizations and clinical data from a sampling of 160 samples of ampullary adenocarcinomas from Baylor College of Medicine Elkins Pancreatic Center, Australian Pancreatic Cancer Genome Initiative, MD Anderson Cancer Center, and the Technical University of Dresden. The clinical data includes Patient ID, Sample ID, Mutation Count, Percent Intestinal, Associated Adenoma, Cllularity based on allele frequency, Data Source, Days to Last Followup, Immunohistochemistry Subtype, Morphology Other Features, Morphology Subtype, Neoplasm Histologic, Grade Note, Overall Survival (Months), Overall Survival Status, Patient's Vital Status, PB Blast Percentage, and Primary Tumor Site.

    Subject
    Ampulla of Vater
    Carcinoma
    Access Rights
    Free to All

  • An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression

    Authors
    Albanese, Steven Kyle
    Parton, Daniel Lawrence
    Isik, Mehtap
    Rodriguez-Laureano, Lucelenie
    7 more author(s)...
    Description

    Source code, assay data, full expression results for all ABL1 constructs, wild-type kinases, and ABL1 and SRC mutants, plasmid libraries, and other supporting material for the generation of a library of human kinase domain constructs for automated bacterial expression. From the publication abstract, "Kinases play a critical role in cellular signaling and are dysregulated in a number of diseases, such as cancer, diabetes, and neurodegeneration. Therapeutics targeting kinases currently account for roughly 50% of cancer drug discovery efforts. The ability to explore human kinase biochemistry and biophysics in the laboratory is essential to designing selective inhibitors and studying drug resistance. Bacterial expression systems are superior to insect or mammalian cells in terms of simplicity and cost effectiveness but have historically struggled with human kinase expression. Following the discovery that phosphatase coexpression produced high yields of Src and Abl kinase domains in bacteria, we have generated a library of 52 His-tagged human kinase domain constructs that express above 2 μg/mL of culture in an automated bacterial expression system utilizing phosphatase coexpression (YopH for Tyr kinases and lambda for Ser/Thr kinases). Here, we report a structural bioinformatics approach to identifying kinase domain constructs previously expressed in bacteria and likely to express well in our protocol, experiments demonstrating our simple construct selection strategy selects constructs with good expression yields in a test of 84 potential kinase domain boundaries for Abl, and yields from a high-throughput expression screen of 96 human kinase constructs. Using a fluorescence-based thermostability assay and a fluorescent ATP-competitive inhibitor, we show that the highest-expressing kinases are folded and have well-formed ATP binding sites. We also demonstrate that these constructs can enable characterization of clinical mutations by expressing a panel of 48 Src and 46 Abl mutations."

    Subject
    Bacteria/metabolism
    Binding sites
    Escherichia coli/metabolism
    Phosphorylation
    Protein Structure, Secondary
    Protein-Tyrosine Kinases
    Proto-Oncogene Proteins c-abl
    src-Family Kinases
    Access Rights
    Free to All
    Fee Required

  • Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytoma (MSKCC, Neuro Oncol 2017): Genomic characterization using next generation sequencing (NGS) in 22 Anaplastic Oligodendroglioma and Anaplastic Oligoastrocytomas.

    Authors
    Thomas, Alissa A.
    Abrey, Lauren E.
    Terziev, Robert
    Raizer, Jeffrey J.
    24 more author(s)...
    Description

    This dataset contains summary data visualizations and sequencing data of anaplastic oligodendroglioma (AO) and anaplastic oligoastrocytoma (AOA) tumors following a trial using induction temozolomide (TMZ) followed by myeloablative high-dose chemotherapy (HDC) with autologous stem-cell transplant (ASCT) as a potential strategy to defer radiotherapy. The clinical data includes mutation count, information about mutated genes, patient demographics, disease progression among other relevant data points. The data set also includes copy-number segment data downloadable as .seg files and viewable via the Integrative Genomics Viewer.

    Subject
    Brain Neoplasms
    Chemoradiotherapy
    DNA Mutational Analysis
    Oligodendroglioma
    Temozolomide
    Access Rights
    Free to All

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