The PHC is a powerful tool that allows omics data files to be stored and indexed into the database so users can view and perform a deeper analysis of an individual subject's genomic test results against data from external databases using the Omics Explorer and other parts of the PHC platform.
The process consists of uploading the test files into the Files folder of the PHC. Users can use the Automated Ingestion to upload larger amounts of genomic data. When adding data for a small number of subjects, users can use the Omics Add Data to associate the files with the correct subject for ingestion and indexing. The single subject's omics test data can then be viewed in Omics Explorer which can be accessed from the Subjects tab from the left panel of PHC. For more information regarding adding omics data to the PHC see data processing.
|Type of Omics Data||Location of Omics Data in PHC|
|Single subject's Omics Data||Omics Explorer|
|Omics Data of subjects in a project||Insights modules (mutations across the entire project can be viewed in Needle plots or Oncoprint)|
|Ingestion/index status of Omics test files and associated files||Omics-Dashboard|
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 (such as dbSNP, gnomAD, and ClinVar) along with our annotation of variants using our own knowledge base.
The Omics Explorer allows users to view a subject’s genetic test data along with annotations from external germline and somatic variant databases in an easy to navigate format. Two different ways to view the data include:
- The Omics Summary shows the subject's individual tests stacked in one table for easy viewing.
- The Filtered View allows the user to view the subject's sequence types (Germline/Somatic) and the different variant types separately and filtered to fine tune the data viewed.
The Omics Dashboard shows the status of all Omics Tests and associated data records within a project.
Omics Add Data¶
Add Data allows you to associate genomic files with a subject and have them added/indexed into the PHC database for filtering and viewing in Omics Explorer and Subject Viewer.
Omics Tests (option under the Omics tab) allows you to view the genomic tests that have been indexed/ingested into the PHC. You can filter by subject or test status.
Omics Test Detail¶
Omics Test Detail shows all the variant & sequence types reported in the test in one Variant Sets table, as well as information about when the test occurred, was uploaded, and was ingested.
Automated Ingestion - Ingests test files from different vendors.
Data Processing - Analyzes Omics data for deep analysis.
Nightly Upload - Automates data ingestion.
Variant Detail - Displays information about a specific variant.