Omics Filtered View¶
In the blue header at the top of the Omics Explorer there is an Omics Summary toggle button allowing you to switch between a summary view and a filtered view of the omics data. With this toggled OFF, the Omics Explorer displays the Filtered View where the data for Somatic and Germline Variants are broken down into their own tabs, and users can use the Filters on the left side of the page to help fine tune the data displayed in the Omics Explorer table.
Somatic Variant vs Germline Variant¶
Somatic and Germline Variants are often referred to as sequence types.
Somatic Variant – A somatic mutation is a variant that is added later (such as a cancer from smoking). Somatic mutations occur in a single body cell and cannot be inherited. The tumor RNA and DNA are sequenced from a tumor sample.
Germline Variant – A germline mutation (such as a BRCA mutation) comes from the germ cells (egg and sperm), is found in every cell of the body, and can be passed down to offspring. This DNA is sequenced from blood or saliva.
Within the Somatic and Germline tabs, you can view the variant types within those sequence types.
Select from the following:
- Short (single nucleotide variants or short insertions and deletions in the DNA such as ~ 1-20 base changes) This option has the most annotations and the most filters.
- Structural (for example, fusions, translocations and inversions) There are fewer data columns associated with Structural Variants. Also, there will often be two genes listed together under the Gene column.
- Copy Number (duplications or deletions of a large region)
Expression (RNA sequencing) This variant looks at close to 20,000 genes in the genome and shows expression for all of those - which is too many to scroll through. You can click the carrot to change the sort order of the column (ascending/descending) as shown in the clip below. But this sort order is not for the full 20,000 genes, it is only for what has been loaded into the table at that moment in time.
To perform the ascending/descending listing of Expression across all 20,000 genes, not just what is in the table, use the Expression Rank Order filter and select either:
- Order by highest expressed
- Order by lowest expressed
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. Selected filters only apply to the sequence type and the variant type (such as 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. The filter can be removed by deselecting it in the filter list on the left of the page 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.
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”. We illustrate this in the clip below. By adding a Coding Effect/ Missense filter and then adding a Zygosity/Heterozygous filter, the filtered results shown in the table 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 from the filters on the left side of the page.
Click the Save button (see above image) beneath the Saved Filters dropdown menu.
In the window that opens, name your filter and give it a description (optional)
To set this as the Default Filter, users must have one of the following ABAC privileges:
Toggle the Set as default filter switch on (see image above). This applies a single filter automatically for the selected sequence and variant combination (such as Somatic + Short). The default filter applies to the whole project. To remove a default filter, the filter must be deleted or replaced by a new filter.
This filter will now be available in the Saved Filters dropdown.
Filter and Saved Filter Tools¶
The three tools (shown in the image below) allow users to save a filter, reset to the currently loaded filter, or clear all filters.
Save - Users with the
Layout AdminABAC privilege can click this button 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 removes any added filters and restores 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 Admin ABAC privilege or the filter creator can delete a Saved Filter.
To 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 iconbeside 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 (That is, European, Asian, African, and so on) 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
- JAX Clinical Knowledgebase
- In JAX - Displays any variant that has an annotation in the JAX knowledgebase in any transcript
- Protein Effect (multiple can be selected)
- Gain of Function
- Gain of Function - Predicted
- Loss of Function
- Loss of Function - Predicted
- No Effect
- No Effect - Predicted
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.