Omics Filtered View¶
With the Omics Summary toggled OFF, the Omics Explorer displays the Filtered View where the data for Somatic and Germline Variants are broken down into their own tabs. Users can use the Filters on the left side of the Omics Explorer to help sort the data displayed in the Omics Explorer table.
Select from the following:
- Short (single changes in the DNA i.e., 1 base change)
- Structural (rearrangement of the DNA i.e., translocation and inversion)
- Copy Number (duplications or deletions of a large region)
- Expression (RNA sequencing)
Filters are only available in the Omics Filtered View (in either the Somatic or Germline tabs). Filters are found on the left side of the Omics Explorer page. These filters correspond to the columns in the table. The available filters vary depending on which Variant Type (see below) is selected. Any selected filters will only apply to the sequence type and the variant type (i.e., filtering on the Somatic Short Variants). Filters search across all transcripts, not just the canonical transcript.
If no filters are selected, the Omics Explorer Table will show all variants within the specific test (Germline vs Somatic) and Variant Type (short, structural, copy number, expression).
Once you add a filter, a chip with the filter name gets added above the Omics Explorer Table (see image below). You can remove the filter by deselecting it in the filter list on the left or clicking the “x” on the filter chip. You can also clear all the filters selected with the Clear All button at the top of the filters panel (see image below).
Filter selections within a category are “ORed”. For example, under the Coding Effect filter category, selecting Frameshift and Splice region will return results that match Frameshift OR Splice Region.
Filter selections across categories are “ANDed”. For example, if we go to the Coding Effect filter category and select Missense and then go to the Zygosity filter category and select Heterozygous, the filtered results will match both the Missense Coding Effect filter AND the Heterozygous Zygosity filter.
Saved Filters are pre-saved and often complex filtering criteria that users can access with the ease of a dropdown menu. Saved Filters are created by users with the
Layout AdminABAC privilege. This dropdown menu can be found on the left side of the Omics Explorer.
Create a Saved Filter¶
- Select the filtering criteria
Click the Save button beneath the Saved Filters dropdown menu.
In the window that opens, name your filter and give it a description (optional)
This filter will now be available in the Saved Filters dropdown
Filter and Saved Filter Tools¶
Save - This button allows you (if you have the
Layout AdminABAC privilege) to save/modify a filter.
If you load a Saved Filter from the dropdown menu and add more filters to that base, the Saved Filter dropdown will now say "Modified".
While users with the
Layout AdminABAC privilege can save this modified filter as a new filter with a new name, only the filter owner or a project admin can update an existing filter (saving it with the same name) created by another user.
Reset - Clicking the Reset button will remove any added filters and restore the Saved Filter
Clear All - Clicking this button removes all selected filters, including Saved Filters. This will cause the Omics Explorer table to display all unfiltered data.
Delete a Saved Filter¶
Only users with the
Layout AdminABAC privilege or the filter creator can delete a Saved Filter.
Click on the Saved Filters settings icon to open the Manage Saved Filters page
On the Manage Saved Filters page that opens, click the trash can icon beside the filter you wish to remove
List of Filters¶
The list of filters available varies depending on which Variant Type (Short, Structural, Copy Number, or Expression) is selected. Once a filter is selected, a chip is placed above the Omics Explorer table.
Gene Sets - This is a list of genes. By default, a selection of gene sets auto-populates into every project. Gene sets are defined and created in the Knowledge tab of the PHC by users with any of these ABAC privilege:
Once a gene set is created, it will show up automatically in this filter list. Here is the default list:
- ACMG 59
- DNA Repair
- FoundationOne CDx
- FoundationOne Heme
- FoundationOne Liquid
- PharmGKB PGx VIP
- Sanger Cancer Genes Tier1 v86
- Sanger Cancer Germline v86
- Sanger Oncogenes v86
- Sanger Tumor Suppressors v86
Gene - (separate multiples with a comma) Use the search box to search the populated gene list or manually enter the gene(s) you wish to filter on.
- Populated List - Begin typing the gene name to search from our populated list pulled from the HGNC database. A list with any matches will populate, along with the full gene name as well as any aliases for that gene.
- Manual Entry - You can manually enter the gene name, then hit "enter". This option exists for 2 reasons:
- To allow users to locate gene names that are in the data but are not in the populated list
- To list multiple genes (separate the genes with a comma)
Cancer Knowledge Base (CKB) checkbox
Coding Effect - These are the types of mutations that affect the RNA and protein coding (this shows up in the Variant Class column of the Omics Explorer Table)
Splice region - Using the SnpEff annotation tool, a
splice_region_variantcan be one of the following:
Splice site - A variant in one of the canonical splicing donor or acceptor base pairs [GT/AG] at the exon/intron boundary. See SnpEff annotation tool for more info.
- Start lost
Protein Changes (add – separate with comma) - This data will be seen under the AA Change(Amino Acid) Column of the Omics Explorer table
- Chromosome 1
- Chromosome 2
- Chromosome 3
- Chromosome 4
- Chromosome 5
- Chromosome 6
- Chromosome 7
- Chromosome 8
- Chromosome 9
- Chromosome 10
- Chromosome 11
- Chromosome 12
- Chromosome 13
- Chromosome 14
- Chromosome 15
- Chromosome 16
- Chromosome 17
- Chromosome 18
- Chromosome 19
- Chromosome 20
- Chromosome 21
- Chromosome 22
- Chromosome M
- Chromosome X
- Chromosome Y
Position – Position refers to the numeric chromosome position (enter value)
- COSMIC Minimum Count – (enter value) This refers to how often a mutation has been seen in the COSMIC (Catalog of Somatic Mutations in Cancer) external database. Typing a "1" in the search box would let you know if anything had ever been found in COSMIC. The result would be seen under the Omics Explorer table column, COSMIC Count.
- COSMIC IDS – This is the numeric COSMIC ID of a mutation. This ID number links to the COSMIC website. Enter a value in the box (multiples separated by a comma).
- dbSNP rs IDs – This ID number will link out to the dbSNP (database of Single Nucleotide Polymophism) website. Enter a value in the box (multiples separated by a comma).
- ClinVar Significance checkboxes
- Pathogenic or Likely Pathogenic
- Uncertain significance
- Benign or Likely Benign
- Conflicting interpretations
- Risk factor
- Drug Response
- Not provided
- ClinVar Review Status checkboxes (can select multiple)
- Practice Guideline
- Reviewed By Expert Panel
- Criteria Provided, Multiple Submitters, No Conflicts
- Criteria Provided, Single Submitter
- Criteria Provided, Conflicting Interpretations
- No Assertion Criteria Provided
- No Assertion Provided
- No Interpretation for the Single Variant
Pop Freq (gnomAD database) - (search via value boxes) This numeric value (found under the Genome Frequency column of the Omics Explorer table), is brought in by the gnomAD database and tells how frequent a variant is in the genome.
- >=Allele Frequency - add a value between 0.0 and 1.0 (if blank it's treated as 0)
- <=Allele Frequency - add a value between 0.0 and 1.0 (if blank it's treated as 0)
Note: If you set this filter then go back and change the values, it will not add a new filter, instead, it will replace the previous Pop Freq values.
Maximum Across Populations - (value boxes) The frequency of a variant is often variable across racial ancestral populations (i.e. European, Asian, African, etc.) and the overall average frequency does not always reflect whether the variant is rare or common within each subpopulation. The ‘Max Across Populations’ represents the single highest frequency the variant is found across all racial ancestral populations (regardless of which population). This is most helpful to filter for variants that are rare across all populations, for example, by setting the filter to ( >= Min ‘0’ and <= Max ‘0.001’).
- >=Allele Frequency
- <=Allele Frequency
- Gene Class - This data is brought in from a public tool
- Protein Coding
- Micro RNA
- Short ncRNA
- Long ncRNA
- T Cell Receptor
- Reference - In cases where a particular genetic assay shows if it matches the reference genome, this checkbox allows you to search for those matches
- Variant Quality
- Variant Allele Freq - Value boxes
- >=Allele Frequency
- <=Allele Frequency
- Combined in Silico Prediction
- Select % Damaging or Damaging Rank Score
- Individual In Silico Predictors
- Predictor – Select between FATHMM, SIFT, MUT Taster
Variant Count – Tells how many variants meet the selected filters. Anything over 999 is annotated as 999+. However, infinite scrolling allows you to see all the variants in the Omics Explorer table