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Cohort Analysis

Cohort Analysis

From the Cohorts menu in the left hand navigation, select a cohort created in Create Cohort to begin a cohort analysis.

Query Details

The query details can be accessed by clicking the triangle next to Show Query Details. The query details displays the selections used to create a cohort. The selections can be edited by clicking the pencil icon in the top right.

Charts

  1. 1.
    Charts will be open by default. If not, click Show Charts.
  2. 2.
    Use the gear icon in the top-right to change viewable chart settings.
  3. 3.
    There are four charts available to view summary counts of attributes within a cohort as histogram plots.
  4. 4.
    Click Hide Charts to hide the histograms.

Subjects

  1. 1.
    By Default, the Subjects tab is displayed.
  2. 2.
    The Subjects tab with all Subjects list is displayed below Charts with a link to each Subject by ID and other high-level information. By clicking a subject ID, you will be brought to the data collected at the Subject level.
  3. 3.
    Search for a specific subject, but typing the Subject ID into the Search Subjects text box.
  4. 4.
    Get all details available on a subject by clicking the hyperlinked Subject ID in the Subject list.

Marker Frequency

  1. 1.
    Click the Marker Frequency tab, then click the Gene Expression tab.
  2. 2.
    Down-regulated genes are displayed in blue and Up-regulated genes are displayed in red.
  3. 3.
    A frequency in the Cohort is displayed and the Matching number/Total is also displayed in the chart.
  4. 4.
    Genes can be searched by using the Search Genes text box.

Genes

  1. 1.
    You are brought to the Gene tab under the Gene Summary sub-tab.
  2. 2.
    Select a Gene by typing the gene name into the Search Genes text box.
  3. 3.
    A Gene Summary will be displayed that lists information and links to public resources about the selected gene.
  4. 4.
    Click the Variants tab and Show legend and filters if it does not open by default.
  5. 5.
    Below the interactive legend you see a set of analysis tracks: Needle Plot, Primate AI, Pathogenic variants, and Exons.
  6. 6.
    The Needle Plot allows toggling the plot by gnomAD frequency and Sample Count. Select Sample Count in the Plot by legend above the plot.
  7. 7.
    Hover over the Variant to see details about the Variant from public resources and counts of variants in the selected cohort by disease category.
  8. 8.
    Use the Exon zoom bar from each end of the Amino Acid sequence to zoom in on the gene domain to better separate observations.
  9. 9.
    The Pathogenic Variant Track shows pop up details with pathogenicity calls, phenotypes, submitter and a link to the ClinVar entry is seen by hovering over the purple triangles.
  10. 10.
    The Gene Expression tab shows known gene expression data from tissue types in GTEx.
  11. 11.
    The Genetic Burden Test will only be available for de novo variants only.

Correlation

Clinical vs. Clinical Attribute Comparison – Bubble Plot

  1. 1.
    Click the Correlation Tab.
  2. 2.
    In X-axis category, select Clinical.
  3. 3.
    In X-axis Attribute, select a clinical attribute.
  4. 4.
    In Y-axis category, select Clinical.
  5. 5.
    In Y-Axis Attribute, select another clinical attribute.
  6. 6.
    You will be shown a bubble plot comparing the first clinical attribute on the x-axis to second attributes on the y-axis.
  7. 7.
    The size of the bubbles correspond to the number of subjects falling into those categories.

Molecular vs. Molecular Attribute Comparison – Bubble Plot

To see a breakdown of Somatic Mutations vs. RNA Expression levels perform the following steps:
Note this comparison is for a Cancer case.
  1. 1.
    Click the Correlation Tab.
  2. 2.
    In X-axis category, select Somatic.
  3. 3.
    In X-axis Attribute, select a gene.
  4. 4.
    In Y-axis category, select RNA expression.
  5. 5.
    In Y-Axis Attribute, type a gene and leave Reference Type, NORMAL.
  6. 6.
    Click Continuous to see violin plots of compared variables.

Clinical vs. Molecular Attribute Comparison – Bubble Plot

Note this comparison is for a Cancer case.
  1. 1.
    Click the Correlation Tab.
  2. 2.
    In X-axis category, select Somatic.
  3. 3.
    In X-axis Attribute, type a gene name.
  4. 4.
    In Y-axis category, select Clinical.
  5. 5.
    In Y-Axis Attribute, select a clinical attribute.

Molecular Breakdown

  1. 1.
    Click the Molecular Breakdown Tab.
  2. 2.
    In Enter a clinical Attribute, and select a clinical attribute.
  3. 3.
    In Enter a gene, select a gene by typing a gene name.
  4. 4.
    You are shown a stacked bar-chart by the clinical attribute selected values on the Y-axis.
  5. 5.
    For each attribute value the bar represents the % of Subjects with RNA Expression, Somatic Mutation, and Multiple Alterations.

CNV

If there is Copy Number Variant data in the cohort:
  1. 1.
    Click the CNV tab.
  2. 2.
    A graph will show CNV a Sample Percentage on the Y-axis and Chromosomes on the X-axis.
  3. 3.
    Any value above Zero is a copy number gain, and any value below Zero is a copy number loss.
  4. 4.
    Click Chromosome: to select a specific chromosome position.

Subject Export for Analysis in ICA Bench

ICA allows for integrated analysis in a computation workspace. You can export your cohorts definitions and, in combination with molecular data in your ICA Project Data, perform, for example, a GWAS analysis.
  1. 1.
    Confirm the VCF data for your analysis is in ICA Project Data.
  2. 2.
    From within your ICA Project, Start a Bench Workspace -- See Bench for more details.
  3. 3.
    Navigate back to ICA Cohorts.
  4. 4.
    Create a Cohort of subjects of interest using Create a Cohort.
  5. 5.
    From the Subjects Tab click the Export icon on the top-right of the subject list. The file will be downloaded to your browser. Rename the file to something useful for subsequent work.
  6. 6.
    Create another cohort if needed for your Research and complete the last 2 steps.
  7. 7.
    Navigate to your Project Data by clicking Data from the left hand navigation panel.
  8. 8.
    Drag and Drop the files exported from the Cohorts module into the gray box at the top of the file/folder list.
  9. 9.
    Navigate to the Bench workspace created in the second step.
  10. 10.
    After the workspace has started up, click Access.
  11. 11.
    Find the /Project/ folder in the Workspace file navigation.
  12. 12.
    This folder will contain your cohort files created along with any pipeline output data needed for your workspace analysis.