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Release Notes

Releases for the Interpretation Portal are bundled with NGIS releases, details of which can found here.

What's new in the Interpretation Portal?

Mira

Please be advised that after deployment, a final hard refresh is required to clear your browser cache. Subsequent deploys will not need this action.

April 2024:

  • Cancer sample and variant information is no longer shown in the Interpretation Portal to prevent redundancy with the Cancer DSS (INTPORTAL-1776, INTPORTAL-1775).
  • Prospective referrals, processed in the RD pipeline with Dragen v4, can now displayed in the Interpretation Portal (INTPORTAL-1744, CIPAPI-2145).
  • Users can now download STR plots from the Portal in SVG format instead of PNG (INTPORTAL-1744).
  • The Portal now supports the most recent gene panel updates for Test Directory v6 (IP-5377).
  • The HGVS field in the Summary of Findings HTML is now sourced from Cellbase (CIPAPI-941).
  • Editing the RoQ will no longer cause a referral to be moved to the "Reported Cases" tab if there's a newer RoQ in draft state (CIPAPI-1225).
  • The Portal has been upgraded to incorporate version 8.5.0 of GRM for GMS RD and 8.6.0 for Cancer referrals (IP-5416), this means that the Portal will support features of Tumour Only referrals (CIPAPI-2011) when these arrive.
  • BSVI has been decommissioned, as a result, users will no longer be able to access it.
Lyra Hotfix

Februrary 2024:

  • Resolves a bug related to the submission of Reporting Outcomes Questionnaires that were auto-populated for VUS variants (INTPORTAL-1805)
Lyra

December 2023:

  • The first stage of the Reporting Outcommes Questionnaires (ROQs) improvements has been completed. The Portal now ofers a new feature to auto-populate certain questions from the ROQ with the information previously entered during decision-making in Congenica. Learn more here (INTPORTAL-1645).
  • The gnomAD link from the Interpretation Browser now navigates to v4.0.0 (INTPORTAL-1788).
  • The SNP check has been removed from the Case Dispatch Workflow. Refer to the SMS Help Page for more information.
Kraz

November 2023:

  • The Portal now offers the ability to interpret cases using the Cancer DSS. For more details on the impact on the Portal, please refer to the Cancer DSS Quickstart Guide.
  • We have updated the PanelApp URLs. All links from the Portal will now redirect to https://panelapp.genomicsengland.co.uk/.
  • The Genomics England address displayed in the Portal has been updated to reflect the current information.
Jabbah

September 2023:

  • The default score for the Exomiser filter has been changed to =>0.75 from >0.75 (INTPORTAL-1690).
  • The Download TSV file button for the SNV table now displays the list of variants (INTPORTAL-1716).
  • The sort order for CVA Classifications is now working as expected; Pathogenic > Likely Pathogenic > Conflicting Classifications > VUS > Likely Benign > Benign > Unclassified (INTPORTAL-1707).
  • The CVA links to variants and ClinVar annotations are now loaded to variants when using the Add variants from VCF feature (IP-5207).
  • Now, after using the Add variants from VCF feature, the user sees the Filter Tiered Variants filter engaging with the selected gene and only the variants for this selected gene are visible in the SNV variant table (INTPORTAL-1704).
Izar Increments

May 2023:

  • Enables link out to Cancer Bridge DSS along side link to BSVI

  • Fixes Exomiser variant soring bug in the Interpretation Browser

  • Security vulnerability and cellbase client updates in the backend (SMS and CIP-API)

  • Updated link out:

    • Improved DECIPHER links for CNVs on the CNV call level table. Now there is one for the phenotype and one for the genome browser
    • Added links to Splice AI, OMIM and VarSome from variants on the SNV table

  • Fixed Test Tumour Diagnosis Date displaying incorrectly

  • Added a visual aid to quickly discriminate between rare and more common CNVs (gains and losses) based on population frequency

    • Loss columns: CNVs with a LOSS frequency % less than 0.5% are shaded in red. CNVs with a LOSS frequency % greater than or equal to 0.5% are not shaded red
    • Gain columns: CNVs with a GAIN frequency % less than 1% are shaded in red. CNVs with a GAIN frequency % greater than or equal to 1% are not shaded red

July 2023:

  • Session Management - Learn more about the changes here
Izar - March 2023

  • Performance improvements returning CVA annotations to the Interpretation Browser (INTPORTAL-1460)

  • Known Pathogenic Variant Prioritisation (KPVP) updates to the Interpretation Browser (IP-4603)

Bioinformatics Pipeline updates will mean known pathogenic variants from ClinVar, that previously may have been filtered out, will now be prioritised by Genomics England Tiering.

To support interpretation of KPVP results, the Interpretation Browser has added a new "ClinVar Classifications" column that allows users to more easily review and access ClinVar annotations.

For further information on KPVP please see here.

And for a full demo of Izar release see the recording here

Image

Hercules Increment - January 2023
  • The Interpretation Browser now contains links to DECIPHER, gnomAD and UCSC
  • Variant read depth is displayed in the Interpretation Browser
  • There's a new variant copy button that copies variant details into Alamut format for easier pasting
  • The STR sorting has been improved and there is a new STR filter
  • When users filter variants based on Exomiser score the default filter value has changed to 0.75
  • See here for more info on these changes
Grace - November 2022
  • The Interpretation Portal is now displaying Tier Null STRs. More information here, including a demo video.
  • The warning that FMR1 variants are not reported in STR report events has been updated to only be shown if FMR1 variants are indeed not reported, so that users don't incorrectly assume FMR1 STRs are not reported. More information here.
  • A new scenario has been included in The Diagnostic Discovery video to help users navigate through cases with non-PASS variants. Watch it here.
  • The landing page of the Portal Help Page now displays an introductory video to the Interpretation Portal's role in the GMS. Watch it here.
  • New files associated with cancer referrals available for download. Including, annotated VCF for small variants, germline CNV/SV VCF, somatic CNV/SV CSV, BAF for tumour samples. Please refer to the Cancer Genome Analysis Guide for further information

Coming Up Next!

Upgrade to Cellbase v5 (IP-5149)

Currently, our system relies on Cellbase v4 to gather annotations across various components of the Portal. With the upcoming upgrade to Cellbase v5, the Portal will seamlessly transition to the latest database versions utilized within the NGIS.

If you have any feedback please get in touch with our service desk at ge-servicedesk@genomicsengland.co.uk quoting the INTPORTAL-XXXX

Last update: 2024-05-17