Frequently Asked Questions¶
What are tags?
Tags are a designated field in the Interpretation Portal, used to alert users to specific issues that may impact analysis. Managed by the CIP-API or the bio-operations team, tags highlight deviations or potential concerns. For example, a tag may notify users if specific variants are unavailable in the Decision Support System (DSS).
What are the email notifications?
The Interpretation Portal’s Email Notifications provide daily alerts to GLHs about cases with status changes in the last 24 hours that may require attention. Two distinct emails are sent: one for routine referrals and another for urgent referrals.
Each email includes a table with key case details: - Referral ID - Status (matching the Portal tab) - Requesting and Interpreting Organizations - Clinical Indication - Type (e.g., Cancer or Rare Disease)
To update recipient email addresses or add new ones, please submit a Service Desk ticket.
What do the warnings or error messages mean?
Error or warning messages in the Interpretation Portal are not necessarily indicative of system errors.
- N/A message under “NHS ID”, “Full Name”, “Date of Birth”, and “Patient Choice” columns indicates that the portal is unable to connect to TOMS at that time. This is expected behavior when the data is unavailable.
- Message A: Appears when Genomics Testing Consent cannot be populated from TOMS.
- Message B: Appears when the Interpretation Portal is unable to connect to TOMS and populate the case with PID.
- Message C: Appears when the Interpretation Portal is unable to connect to TOMS and populate the case notes.
- Message D: Appears when the Interpretation Portal is unable to connect to TOMS and populate the case with PID.
- Message E: Appears when the Interpretation Portal is unable to connect to TOMS and populate the case with PID.
In the Referral Grid, where cases are categorized by status tabs, a message may appear stating: "Unable to retrieve patient data." This indicates that the portal cannot connect to TOMS and populate the case with PID.
What are Interpretation Services?
Interpretation Services are applications or algorithms used in the Genomics England Interpretation Platform to help users determine the molecular basis of their patients' conditions.
Each service applied to a referral produces an Interpreted Genome, which is essentially a prioritized list of variants identified by the algorithm.
The Rare Disease Interpretation Browser allows users to review the results of these services and select primary findings for the case.
For more details on Tiering and Exomiser, the current interpretation services, please refer to the Genomics England Rare Disease Genome Analysis Guide v2.0.
Note: When the Exomiser score for a variant is 0, it may appear missing in the Interpretation Portal, but the variant will have an Exomiser ranking. GLHs are required to review variants with Exomiser ranks 1-3 and any variant with a score above 0.75. This issue affects both the 100,000 Genomes Project and GMS cases and will be rectified in the future. Currently, you can check the Exomiser score for a variant in the payload of a case, downloadable via the 'Payload' button on the case page.
Why can't I see the Genomic and Data checks on the Rare Disease Referral page?
The Genomics England WGS pipeline for Rare Disease performs a QC check of the reported sex against the genetic sex.
In previous versions of the Interpretation Portal, the outcome of this check was visible. However, since the check must pass for the WGS pipeline to run (and thus the referral register in the Portal), this information was deemed unnecessary and has been removed.
What are Decision Support Systems?
Decision Support Systems (DSS) enable users to review and report on cases in the Genomics England Interpretation Platform. They facilitate multidisciplinary teams (MDTs) and allow users to explore beyond variants highlighted by Interpretation Services.
For more detailed information, please refer to the application-specific DSS user guides.
What is CVA?
The Clinical Variant Ark (CVA) is Genomics England's comprehensive knowledge base designed for comparing cases with similar phenotypic and genotypic profiles. It offers a detailed overview of the prioritized variants identified by Interpretation Services. Additionally, CVA includes linked Summary of Findings, Reported Outcomes Questionnaires, and Variant Interpretation Logs.
For access to CVA, please visit: CVA Portal.
What is CellBase?
CellBase supports the annotation of thousands of genomic features by integrating biological information about genomic features, proteins, gene expression regulation, functional annotation, genomic variation, and systems biology.
As well as providing annotations for the tiering interpretation service, the Interpretation Browser uses CellBase to provide additional variant annotations. See the Interpretation Browser for more information.
Why is my referral flagged?
Please refer to the Referral Flags page for more information on why your referral might be flagged.
What Exomiser score is shown in the report events table?
The Interpretation Browser displays the "combined" Exomiser score, calculated using a logistic regression model to combine the phenotype and variant scores.
If you need the individual variant and phenotype scores for a variant, you can download the payload and find them in the "vendorSpecificScores" section of the Exomiser interpreted genome.
For more details on Exomiser Interpreted Genomes, please refer to the Exomiser Service Documentation.
Why is read depth information not shown for my variant?
Read depth information is displayed in the Interpretation Browser as reported by the associated interpretation services. For more information, see the Read Depth section.
How does the Exomiser filter work?
The Exomiser filter in the Interpretation Browser is a "greater than" filter. By default, it filters variants with a combined Exomiser score greater than 0.75.
What are the CVA classifications?
CVA classifications shown in the Interpretation Browser summarize the classifications assigned to variants in the reporting outcomes questionnaires. They do NOT include any classifications added to variants in DSS that do not end up in a Summary of Findings. These can be viewed in the Variant Interpretation Logs accessible via the CVA Portal.
What does the shading in the Interpretation Portal mean?
- Yellow-shaded referrals in the case grid: Indicate that draft work has been saved for the case, meaning you have started working on it but have not yet finished.
- Green-shaded variants in the interpretation browser: Indicate variants that were either added from the VCF file or called by Exomiser but have not yet been validated. These require your review to determine clinical significance.
How do I update a previous interpretation with new findings?
For instructions on updating a previous interpretation with new findings, see here.