Links

Create a Cohort

ICA Cohorts lets you create a research cohort of subjects and associated samples based on the following criteria:
  • Project: include subjects that are part of any ICA Project that you own or that is shared with you;
  • Subject:
    • Demographics such as age, sex, ancestry.
    • Phenotypes and diseases.
    • Biometrics such as body height, body mass index.
    • Pathological classification, tumor stages, etc.
    • Family and patient medical history.
  • Sample:
    • Sample type such as FFPE.
    • Tissue type.
    • Sequencing technology: Whole genome DNA-sequencing, RNAseq, single-cell RNAseq, etc.
  • Molecular attributes:
    • Samples with a somatic mutation in one or multiple, specified genes.
    • Samples with a germline variant of a specific type in one or multiple, specified genes.
    • Samples over- or under-expressed in one or multiple, specified genes.
    • Samples with a copy number gain or loss involving one or multiple, specified genes.

Include/Exclude

  • As attributes are added to the 'Selected Condition' on the right-navigation panel, you can choose to include or exclude the criteria selected.
    • Select a criteria from 'Subject' or 'Molecular' attributes by filling in the appropriate checkbox on the respective attribute selection pages.
    • When selected, the attribute will appear in the right-navigation panel.
    • You can use the 'Include' / 'Exclude' dropdown next to the selected attribute to have that attribute included or excluded in your query.
    • Note: This feature is not available on the 'Project' level selections as there is no overlap between subjects in datasets.
    • Note: Using exclusion criteria does not account for NULL values. For example, if the Super-population 'Europeans' is excluded, subjects will be in your cohort even if they do not contain this data point.
Once you selected Create Cohort, the above data are organized in tabs such as Project, Subject, and Molecular. Each tab then contains the aforementioned sections, among others, to help you identify cases and/or controls for further analysis. Navigate through these tabs, or search for an attribute by name to directly jump to that tab and section, and select attributes and values that are relevant to describe your subjects and samples of interest. Assign a new name to the cohort you created, and click Apply to save the cohort.

Duplicate a Cohort Definition

  • After creating a Cohort, select the Duplicate icon.
  • A copy of the Cohort definition will be created and tagged with "_copy".

Delete a Cohort Definition

  • Deleting a Cohort Definition can be accomplished by clicking the Delete Cohort icon.
  • This action cannot be undone.

Sharing a Cohorts within an ICA Project

After creating a Cohort, users can set a Cohort bookmark as Shared. By sharing a Cohort, the Cohort will be available to be applied across the project by other users with access to the Project. Cohorts created in a Project are only accessible at scope of the user. Other users in the project cannot see the cohort created unless they use this sharing functionality.

Share Cohort Definition

  • Create a Cohort using the directions above.
  • To make the Cohort available to other users in your Project, click the Share icon.
  • The Share icon will be filled in black and the Shared Status will be turned from Private to Shared.
  • Other users with access to Cohorts in the Project can now apply the Cohort bookmark to their data in the project.

Unshare a Cohort Definition

  • To unshare the Cohort, click the Share icon.
  • The icon will turn from black to white, and other users within the project will no longer have access to this cohort definition.

Archive a Cohort Definition

  • A Shared Cohort can be Archived.
  • Select a Shared Cohort with a black Shared Cohort icon.
  • Click the Archive Cohort icon.
  • You will be asked to confirm this selection.
  • Upon archiving the Cohort definition, the Cohort will no longer be seen by other users in the Project.
  • The archived Cohort definition can be unarchived by clicking the Unarchive Cohort icon.
  • When the Cohort definition is unarchived, it will be visible to all users in the Project.