Using the built in Geno Browser

The data preview tab in the cohort browser allows you to view data in tabular form. You can add or remove fields as columns.

To add columns, select the icon on the top right corner of the table, that shows customize columns when you hover.

Select + Add Columns. This will open the tab to select the list of fields.

Here we have added Gene Name from genomic sample, followed by classification, mutation type and variant effect from Variant.

To filter down via specific genes in a tabular format, select Gene Name. This will give an option to either sort by ascending or descending, or you can search for a gene of interest.

Select Search column à Type BRCA and press enter.

The tabular format will update and return a list of BRCA genes along with their mutation type, classification (actionable or VUS) and variant effect.

You can remove columns by selecting Clear All Columns or by individual columns by selecting the – sign next to the column name.

The cohort browser also allows to add genotype filters.

Select the + sign next to the genomic sample filter.

This will open the list of fields tab. Under the Geno tab, you have options to filter by Gene/ Effect or by Variant ID

The Gene/Effect allows you to filter by variant type, zygosity, variant effects and gene/gene range.

The Variant ID tab allows you to filter by the variant id of interest.

The Cohort Filter allows you to add as many filters as possible.

The Genomic tab in the cohort browser shows variants that are present in the current cohort filter.

This tab includes a lollipop chart that displays allele frequency and the tabular format for these variants.

To understand the genomic cohort browser,

Type any gene of interest on the right end corner. Here, we have entered TP53 gene.

This will display a lollipop chart of the allele frequency for TP53 gene.

When you hover around on one of the blue points, it gives you the reference, alternate, type, position, and allele frequency information.

Below the lollipop chart is the allele frequency chart in tabular format. This involves location, rsid, reference, alternate, type, consequence, cohort allele frequency (allele frequency calculated based on the current selection), Population allele frequency (allele frequency in the entire dataset), GnomAD allele frequency (allele frequency of the allele from the GnomAD dataset).

By select any of the RSID, it leads you to the NIH page that gives you dbsnp details of the variant.