FAQs
What are the email notifications?
The Interpretation Portal’s Email Notifications serve as daily alerts for GLHs regarding 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 crucial case details: Referral ID, Status (matching the Portal tab), Requesting and Interpreting Organizations, Clinical Indication, and 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 may appear in the Interpretation Portal and these are not necessarily errors within the system.
In a particular case page, the N/A message, “NHS ID”, “Full Name”, “Date of Birth” and “Patient Choice” columns for this patient signify that the portal is unable to connect to TOMS at that point in time. This is expected behaviour when the data is unavailable.
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A) This message appears when the Genomics Testing Consent cannot be populated from TOMS
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B) This message appears when the Interpretation Portal is unable to connect to TOMS and populate the case with PID
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C) This message appears when the Interpretation Portal is unable to connect to TOMS and populate the case notes
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D) This message appears when the Interpretation Portal is unable to connect to TOMS and populate the case with PID
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E) This message appears when the Interpretation Portal is unable to connect to TOMS and populate the case with PID
In the Referral Grid, where the cases are separated by the status tabs a message may appear stating: “Unable to retrieve patient data”. This message appears when the portal is unable to connect to TOMS and populate the case with PID.
Find more information
What are Interpretation Services?
Interpretation Services are applications or algorithms that can be applied to referrals in the Genomics England Interpretation Platform that facilitate users in determining the molecular basis to their patient's conditions.
Each Interpretation Service applied to a referral produces an Interpreted Genome which is essentially a prioritised list of variants in the cases genome identified by the algorithm.
The Rare Disease Interpretation Browser enables users to review the results of Interpretation Services and select them as primary findings for the case.
For further details of Tiering and Exomiser – the two current interpretation services, please refer to the Genomics England Rare Disease Genome Analysis Guide v2.0
Please note that currently, when the Exomiser score for a variant is 0, the score will appear to be missing in the Interpretation Portal. The variant will, however, have an Exomiser ranking.
It is understood that GLHs are mandated to review variants with Exomiser ranks 1-3 and any variants with a rank
above 0.75. The rank for a variant can be checked, if missing from the Interpretation Portal user interface, in the
payload for the case. This issue where the score is missing has been confirmed to affect 100,000 Genomes Project and
GMS cases. This will be rectified in future to ensure that all scores, even if the score is 0, will be displayed in
the Interpretation Portal for variants.
At present, GLHs can check the Exomiser score for a variant in the payload of a case, downloadable via the 'Payload' button on the right hand side of the case page.
How do I sign up for email notifications about my GMS referrals?
NHS GLHs will receive an email alerting them to any referral status updates including an alert to review cases after they have been sent to their respective DSS. The results email alert will be sent to the generic email address for the GLH held by Genomics England. If you wish to update or change the results email address, please contact the Genomics England Service desk: ge-servicedesk@genomicsengland.co.uk or http://bit.ly/ge-servicedesk.
An email notification will also be sent to GLHs in the event of a SMS check failure.
What is the Sample Matching Service?
Please, note that as of the Lyra release, the Sample Matching Service (SMS) check has been removed from the Case Dispatch Relevant. Refer to the SMS Help Page for more information.
The SMS provides a sample identity check.
Through SNP genotyping, SMS ensures that Rare Disease samples delivered to Genomics England match patient samples at the GLH, i.e. the SMS will identify any sample swaps or data inconsistencies which arise in samples delivered to Genomics England.
GLHs will provide NGIS with a set of SNP genotypes that will be compared by Genomics England against the WGS data.
If a sample has passed the SMS check, a check-circle symbol will be shown by the Sample ID shown on the Rare
Disease Referral Overview page
A failure of this check will be shown as a red close-circle symbol and samples which have yet to be checked will be given the “pending” or “sync” symbol.
The SMS API is queried in real time for the case – it does not store data for any cases.
If you have any referrals with samples that fail the SMS check, they will move to the “Identity Check Failures” tab.
Referrals that have samples “pending” a SNP genotyping VCF upload from a GLH will be visible in the “Identity Check Pending” tab.
Please contact Genomics England service desk if you have any queries over cases in the SMS tabs.
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 it was possible to view the outcome of this check, however, because the check needed to pass for the WGS pipeline to run (and thus the referral register in the Portal) this information was not informative to users so was removed
What are Decision Support Systems?
DSS enable users to review and report on cases in the Genomics England Interpretation Platform. They facilitate MDTs and allow users to explore beyond variants highlighted by Interpretation Services. Please refer to the application-specific DSS user guides for further information.
What is CVA?
The Clinical Variant Ark (CVA) is the Genomics England knowledge base where cases can be compared against phenotypically and genotypically similar cases. For access to CVA please refer to: www.cva.genomicsengland.nhs.uk
What is CellBase?
CellBase supports annotation of many thousands of genomic features per second; it integrates biological information about genomic features and proteins, gene expression regulation, functional annotation, genomic variation and systems biology information.
As well as CellBase providing the annotations for the tiering interpretation service, the Interpretation Browser uses CellBase to provide additional variant annotations. See Interpretation Browser for more info
Why is my referral flagged?
Please see the please see the Referral Flags page for more information.
What Exomiser score is shown in the report events table?
The Interpretation Browser displays the "combined" Exomiser score which is calculated by a logistic regression model is used to combine the phenotype and variant scores
If you require the individual variant and phenotype scores for a variant you can download the payload and find it in the "vendorSpecificScores" of the exomiser interpreted genome
For further information on Exomiser Interpreted Genomes please see here
Why is read depth information not shown for my variant?
Read depth information is displayed in the Interpretation Browser as it is reported by the associated interpretation services. For further information see Read depth section here
How does the Exomiser filter work?
The Exomiser filter on the Interpretation Browser is a "greater than" filter, by default it will filter variants that have a combined Exomiser score greater than 0.75.
What are the CVA classifications?
CVA classifications shown on the Interpretation Browser are a summary of the classifications assigned to variants in the reporting outcomes questionnaires. They do NOT include any classifications that have been added to variants in Decision Support Systems that don't end up in a Summary of Findings - these can be seen in Variant Interpretation Logs which can be accessed in CVA Portal.
What does the shading in the Interpretation Portal mean?
Yellow-shaded referrals in the case grid indicate that some draft work has been saved for the case. This means that you have started working on the case, but you have not yet finished.
Green-shaded variants in the interpretation browser are variants that were either added from the VCF file or called by Exomiser but have not yet been validated. This means that you need to review these variants to determine if they are clinically significant.
How do I update a previous interpretation with new findings?
See here