The Omics Explorer allows users to view a subject’s genetic test data in an easy to navigate format. LifeOmic takes the raw test data (chromosome position and identified variant change) from the sequencing vendor and annotates it through our own annotation pipeline. Our knowledge base is called Gnosis and it is comprised of data from external databases (i.e., ncbi, ClinVar) along with our annotation of variants using our own knowledge base.
How to Access the Omics Explorer¶
To access the Omics Explorer:
- Navigate to the Subjects tab on the left of the PHC screen
- Locate the subject in the Subjects Table whose data you wish to view by:
- Selecting NO filters, which allows you to scroll through the list of all subjects in your project.
- Using filters to locate your subject.
- Select the checkbox beside their name then launch the Omics Explorer by either:
- Scrolling to the right and clicking on the Omics icon to launch the Omics Explorer
- Clicking on the subject (which launches Subject Viewer), then clicking the Omics Explorer icon in the top right-hand corner of the screen
Omics Explorer Layout¶
In the blue banner at the top of the Omics Explorer:
- Project name and subject name
- Basic demographics about the subject (living status, race, ethnicity, DOB, and age)
- Genetic tests dropdown menu (test data from genetic testing vendors are grouped as a “test”)
- Sequence Name (test) i.e., Ashion
- Sequence Type (refers to the type of test)
- Body Site – Where tissue sample came from (breast biopsy, saliva, blood, etc.)
- MSI – Microsatellite Instability (tells how genomically stable the cancer is)
- TMB – Tumor Mutation Burden (quantitative and qualitative measure of how many mutations have been identified in that tumor).
- Omics Summary toggle – This button switches views between seeing the Germline and Somatic Variant data together (Omics Summary toggled ON) or separately (Omics Summary is toggled OFF).
Somatic Variant/ Germline Variant tabs¶
- Variants Types
- 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)
Variant Match/Gene Match/Affects Alternate Transcripts¶
Variant Match (green dot) – refers to cancer knowledge base (CKB) and will show when you filter on CKB (seen in primarily in Somatic Variant tab).
If we click on a Variant Match and open the Variant Detail page and look at the Drug Associations, the Variant Matches are listed first as these are exact matches, followed by the Gene Matches which are listed to provide additional information.
Gene Match (purple dot) – refers to cancer knowledge base (CKB). The Gene Match means this gene is known to have a gene drug association which can be viewed on the Variant Detail page.
Affects Alternate Transcript (blue dot) –A blue colored dot on the table means there may be other information or different transcripts (RNAs) for this gene, but we are only displaying one transcript (canonical) to keep the table simple. To view the other transcripts/information, click on the row to open theVariant Detail page. Here you can scroll down to view the Alternate Transcripts.
Access to More Data¶
In the top right corner of the blue header are three buttons that allow users to access more information regarding the subject and their test data. - View Test Detail Button – Opens a new browser window with details of the test - View PDF in Files – If a lab report (pdf) from the sequencing lab is uploaded to the PHC, clicking this takes you to the Files User Interface so you can view the test files - Subject Viewer - Allows you to switch to the Subject Viewer screen
Hyperlinks in the Omics Explorer Data Table link to the public annotation source.
Somatic Variant vs Germline Variant¶
In the Omics Explorer, you can view a subjects Somatic Variant data as well as their Germline Variant data by easily clicking between two tabs (when Omics Summary is toggled off) - Somatic Variant – A somatic mutation is a variant that is added later (i.e., a cancer from smoking). Somatic mutations occur in a single body cell and cannot be inherited. It is the tumor RNA and DNA sequenced from a tumor sample.
- Germline Variant – A germline mutation (i.e., 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. It is DNA sequenced from your blood or saliva.
To view more information on the Somatic and Germline Variant tabs, click here.
Table Column Headers¶
In the Somatic Variant/Germline Variant view (Omics Summary is toggled off), most of the table column headers correspond with the filters on the left side of the Omics Explorer. Filters will only apply to the sequence type and the variant type (i.e., filtering on the Somatic Short Variants).
In the Omics Summary view (Omics Summary is toggled on), the first 6 table columns are the most likely to populate data (CKB-Variant Type). The other table columns are for short variants and will be blank if it doesn’t apply to that variant type.
List of Table Column Headers:¶
Most data in the Omics Explorer table is curated by LifeOmic except where noted below. - CKB – LifeOmic’s own internal database built from external sources (public data) - Gene – this hyperlink opens the ncbi site for that specific gene in a new window - AA Change – the protein change - NC Change - Position – this is the DNA position in the genome where the mutation happened. The hyperlink opens a genome browser in a new window i.e., ucsc - Variant Class - Somatic Expression - Somatic Copy Number - Somatic Structure
- Variant Allele Freq
- Genomes Freq
- Genomes HOM
- Exomes Freq
- Exomes HOM
- DBSNP RS ID
- ClinVar Significance
- ClinVar Disease
- COSMIC Status
- COSMIC Count
- Damaging %
- Damaging Rank Score
- MUT Taster
- Gene ID
- Transcript ID
- Gene Class
- Ref (provided by the sequencing result)
- Alt (provided by the sequencing result)
- Ref:Alt:Depth (provided by the sequencing result)
- VCF Qual (provided by the sequencing result)
- VCF Filter (provided by the sequencing result)
- Coding Effect
- EXON Number
- Min Freq
- Max Freq
- ClinVar ID
- ClinVar Review
- ClinVar Submission
- ClinVar Nearby
- COSMIC ID
- COSMIC Histology
- COSMIC Site
- COSMIC Nearby
Filters are only available in the Somatic Variant/Germline Variant view (Omics Summary is toggled off).