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Results Found: 18
  • Validation of dedifferentiated liposarcoma (DDLS) cell lines with the original tumors via copy number alteration analysis [sequencing]

    Authors
    Okada, Tomoyo
    Gularte-Mérida, Rodrigo
    Shen, Yawei
    Singer, Samuel
    Description

    Summary from GEO: "We validated patient's tumor-derived cell lines of liposarcoma by analysing copy number alterations using aCGH or WGS and comparing with the original tumor tissues." Overall design from GEO: "Examination of copy number alterations for 2 cell lines, one of the original tumor, one PDX-tumor and its original tumor."

    Subject
    Cell Line, Tumor
    DNA Copy Number Variations
    Liposarcoma
    Access Rights
    Free to All
  • Validation of dedifferentiated liposarcoma (DDLS) cell lines with the original tumors via copy number alteration analysis [array]

    Authors
    Okada, Tomoyo
    Gularte-Mérida, Rodrigo
    Shen, Yawei
    Singer, Samuel
    Description

    Summary from GEO: "We validated patient's tumor-derived cell lines of liposarcoma by analysing copy number alterations using aCGH or WGS and comparing with the original tumor tissues." Overall design from GEO: "Examination of copy number alterations for 2 cell lines, one of the original tumor, one PDX-tumor and its original tumor."

    Subject
    Cell Line, Tumor
    DNA Copy Number Variations
    Liposarcoma
    Access Rights
    Free to All
  • Table S6 from Phase II Clinical Trial of Everolimus in a Pan-Cancer Cohort of Patients with mTOR Pathway Alterations

    Authors
    Adib, Elio
    Klonowska, Katarzyna
    Giannikou, Krinio
    Do, Khanh T.
    15 more author(s)...
    Description

    Description from Figshare: "Table S6. Copy number alterations (CNAs) in cancer genes identified by whole exome sequencing (WES) and/or initial panel sequencing. Each sheet is a different tumor sample."

    Subject
    Clinical Trial, Phase II
    DNA Copy Number Variations
    Everolimus
    High-Throughput Nucleotide Sequencing
    Neoplasms/drug therapy
    TOR Serine-Threonine Kinases
    Access Rights
    Free to All
  • Supplementary Table 4 from Next-Generation Sequencing of Pulmonary Large Cell Neuroendocrine Carcinoma Reveals Small Cell Carcinoma–like and Non–Small Cell Carcinoma–like Subsets

    Authors
    Rekhtman, Natasha
    Pietanza, Maria C.
    Hellmann, Matthew D.
    Naidoo, Jarushka
    16 more author(s)...
    Description

    Description from Figshare: "Supplementary Table 4: Complete list of mutations and copy number alterations detected by MSK-IMPACT in 45 LCNECs"

    Subject
    Carcinoma, Neuroendocrine
    Carcinoma, Non-Small-Cell Lung
    DNA Copy Number Variations
    Lung Neoplasms
    Mutation/genetics
    Small Cell Lung Carcinoma
    Access Rights
    Free to All
  • Supplementary Table S1 from Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung

    Authors
    Concepcion, Carla P.
    Ma, Sai
    LaFave, Lindsay M.
    Bhutkar, Arjun
    19 more author(s)...
    Description

    Description from Figshare: "Mutations and copy number alterations in PDX models used in this study"

    Subject
    Adenocarcinoma of Lung
    Cell Lineage
    DNA Copy Number Variations
    Lung Neoplasms
    Neoplasm Metastasis
    Access Rights
    Free to All
  • CoMMpass IA19: Data from "Gene interaction network analysis in multiple myeloma detects complex immune dysregulation associated with shorter survival"

    Description

    The Multiple Myeloma Research Foundation (MMRF) runs a multi-site longitudinal clinical registry study of patients newly diagnosed with MM. This project is called CoMMpass, and collects both clinical and genomic information periodically. Researchers used interim analysis 19 (IA19) for their conclusions in "Gene interaction network analysis in multiple myeloma detects complex immune dysregulation...

    Subject
    Clinical Trial
    DNA Copy Number Variations
    Genomics
    Multiple Myeloma
    RNA-Seq
    Whole Genome Sequencing
    Access Rights
    Free to all with registration
  • Code from "Gene interaction network analysis in multiple myeloma detects complex immune dysregulation associated with shorter survival"

    Authors
    Simhal, Anish Kumar
    Description

    Code associated with the manuscript for "Gene interaction network analysis in multiple myeloma detects complex immune dysregulation associated with shorter survival." Includes data and instructions, R scripts, lab notebooks, and high resolution images.

    Subject
    DNA Copy Number Variations
    Multiple Myeloma
    RNA-Seq
    Software
    Access Rights
    Free to All
  • JaBbA (Junction Balance Analysis)

    Authors
    Imielinski, Marcin
    Description

    Description from GitHub: "JaBbA builds a genome graph based on junctions and read depth from whole genome sequencing, inferring optimal copy numbers for both vertices (DNA segments) and edges (bonds between segments). It can be used for discovering various patterns of structural variations. If you use JaBbA in your work, please cite: Distinct Classes of Complex Structural Variation Uncovered across...

    Subject
    DNA Copy Number Variations
    Genomics
    Mutation/genetics
    Neoplasms/genetics
    Whole Genome Sequencing
    Access Rights
    Free to All
  • AscatNGS

    Authors
    Raine, Keiran
    Menzies, Andy
    Alcantara, Raul
    Beal, Simon
    Description

    Description from GitHub: "AscatNGS contains the Cancer Genome Projects workflow implementation of the ASCAT copy number algorithm for paired end sequencing. We do not offer support for WXS analysis, please contact the authors of ASCAT here. For details of the underlying algorithm please see the ASCAT site. "

    Subject
    Algorithms
    Data Analysis
    DNA Copy Number Variations
    High-Throughput Nucleotide Sequencing
    Access Rights
    Free to All
  • cgpBattenberg

    Authors
    Raine, Keiran
    Beal, Kathryn
    Dentro, Stefan
    Chapman, Brad
    1 more author(s)...
    Description

    Description from GitHub: "An installation helper, perl wrapper and the R program Battenberg which detects subclonality and copy number in matched NGS data."

    Subject
    Data Analysis
    DNA Copy Number Variations
    Electronic Data Processing
    High-Throughput Nucleotide Sequencing
    Access Rights
    Free to All