Interpretation Platform
The Interpretation Platform (IP) represents a suite of applications developed by Genomics England and Partners to facilitate the interpretation of Whole Genome Sequencing (WGS) data in the NHS Genomic Medicine Service.
This site provides IP users with an overview of the IP and links to application specific documentation.
Interpretation Platform Applications¶
CIP-API¶
Enables tracking of cases throughout their interpretation journey (from pipeline to outcomes questionnaire). The API also enables communication between GeL and its internal and external third party integrators (TPIs) (Pipeline, CVA, DSS, GEMs). It can be accessed programmatically through a REST API, while it acts as a backend to systems such as the Genomics England Interpretation Portal
Interpretation Portal¶
Provides a front end to the CIPAPI. Users can track where their case is within the GeL workflow, review the results of interpretation services, interpret the results and create a "report" and complete the Outcomes Questionnaire.
CVA¶
The Clinical Variant Ark (CVA) is a knowledgebase built from high quality clinically relevant associations between genotypes and phenotypes and captures all interpretations made in the 100k & GMS. It has a REST API and Web Front End (CVA Portal).
IGV¶
This is a JavaScript installation of the open source genome browser, IGV. Users use this to visualise variants in the context of the genome to review quality, the variant validity and help with interpretation
SMS¶
Provides a means for GLHs to conduct a sample identity check to ensure that Rare Disease samples delivered to Genomics England match patient samples at the GLH. Mitigates issues such as sample swaps. Beware the acronym, not to be confused with the Sample Messaging Service.
Cancer DSS¶
The Cancer Decision Support Services (Cancer DSS) used within the Portal provides more enhanced interpretation support than offered in the Interpretation Portal. There are more variant annotations and database links in addition to more advanced visualisation capabilities. New features will continue to appear in the Cancer DSS to support evidence gathering and classification in line with Somatic Variant Interpretation Guidelines (SVIG).
RD DSS¶
The Rare Disease Decision Support Services (RD-DSS) used within the Portal, Cognenica, provides more enhanced interpretation support than that offered in the Interpretation Portal. There are more advanced filtering and visualisation capabilities.
Other Genomics England Applications¶
Other applications developed (or implemented) by Genomics England but not covered by this documentation include
- PanelApp
- Gel Report Models
- CellBase - TBC
- HTSget - TBC
- TOMS - TBC
- Rare Disease Pipeline
- Cancer Pipeline
- Exomiser