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study view add arm-level CNA chart in TCGA shows ancestry data #2119

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inodb opened this issue Nov 10, 2023 · 3 comments
Open

study view add arm-level CNA chart in TCGA shows ancestry data #2119

inodb opened this issue Nov 10, 2023 · 3 comments

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@inodb
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inodb commented Nov 10, 2023

Go to TCGA Pancan studies, click arm-level tab and click the dropdown

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@inodb inodb changed the title CNA in TCGA shows ancestry data study view add arm-level CNA chart in TCGA shows ancestry data Nov 10, 2023
@dippindots dippindots self-assigned this Jan 9, 2025
@dippindots dippindots transferred this issue from cBioPortal/cbioportal Jan 9, 2025
@dippindots dippindots removed their assignment Jan 9, 2025
@dippindots
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@cBioPortal/curation This is a data issue related to study acc_tcga_pan_can_atlas_2018, Gene Ancestry data has a wrong
genericAssayType as "ARMLEVEL_CNA", please see https://www.cbioportal.org/api/molecular-profiles/acc_tcga_pan_can_atlas_2018_genetic_ancestry

{
  "molecularAlterationType": "GENERIC_ASSAY",
  "genericAssayType": "ARMLEVEL_CNA",
  "datatype": "LIMIT-VALUE",
  "name": "Genetic Ancestry",
  "description": "Genetic ancestries were determined using five different methods as described in Carrot-Zhang et al (2020). These consensus calls were created based on the ancestral population that received the majority of assignments for each patient. The original data is <a href=\"https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020\">here</a>.",
  "showProfileInAnalysisTab": true,
  "patientLevel": false,
  "molecularProfileId": "acc_tcga_pan_can_atlas_2018_genetic_ancestry",
  "studyId": "acc_tcga_pan_can_atlas_2018",
  "study": {
    "name": "Adrenocortical Carcinoma (TCGA, PanCancer Atlas)",
    "description": "Adrenocortical Carcinoma TCGA PanCancer data. The original data is <a href=\"https://gdc.cancer.gov/about-data/publications/pancanatlas\">here</a>. The publications are <a href=\"https://www.cell.com/pb-assets/consortium/pancanceratlas/pancani3/index.html\">here</a>.",
    "publicStudy": true,
    "pmid": "29625048,29596782,29622463,29617662,29625055,29625050,29617662,32214244,29625049,29850653,36334560",
    "citation": "TCGA, Cell 2018",
    "groups": "PUBLIC;PANCAN",
    "status": 0,
    "importDate": "2024-12-19 17:17:35",
    "readPermission": true,
    "studyId": "acc_tcga_pan_can_atlas_2018",
    "cancerTypeId": "acc",
    "referenceGenome": "hg19"
  }
}

@ritikakundra
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@dippindots fixed the data. Will reimport the study.

@dippindots
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@ritikakundra Thanks for the quick fix!

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