Prepare Metadata Sheets

In ICA Cohorts, metadata describe any subjects and samples imported into the system in terms of attributes, including:
  • subject:
    • demographics such as age, sex, ancestry;
    • phenotypes and diseases;
    • biometrics such as body height, body mass index, etc.;
    • 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, among others.
You can use these attributes while creating a cohort to define the cases and/or controls that you want to include.
During import, you will be asked to upload a metadata sheet as a tab-delimited (TSV) file. An example sheet is available for download on the Import files page in the ICA Cohorts UI.
A metadata sheet will need to contain at least these four columns per row:
  • Subject ID - identifier referring to individuals; use the column header "SubjectID".
  • Sample ID - identifier for a sample. Sample IDs need to match the corresponding column header in VCF/GVCFs; each subject can have multiple samples, these need to be specified in individual rows for the same SubjectID; use the column header "SampleID".
  • Biological sex - can be "Female (XX)", "Female", or simply "F"; "Male (XY)", "Male", "M"; "X (Turner's)"; "XXY (Klinefelter)"; "XYY"; "XXXY" or "Not provided". Use the column header "DM_Sex" (demographics).
  • Sequencing technology - can be "Whole genome sequencing", "Whole exome sequencing", "Targeted sequencing panels", or "RNA-seq"; use the column header "TC" (technology).
A description of all attributes and data types currently supported by ICA Cohorts can be found here: ICA_Cohorts_Supported_Attributes.xlsx
You can download an example of a metadata sheet, which contains some samples from The Cancer Genome Atlas (TCGA) and their publicly available clincal attributes, here: ICA_Cohorts_Example_Metadata.tsv