NGIS Production Environment: Congenica Incident Notification
Investigating - SERVICE:
NGIS Congenica Portal

SEVERITY:
3

GEL REF:
GEL-308530

DESCRIPTION:
Some tiered variants missing in the Congenica Portal

SUMMARY OF IMPACT:
We are aware of an issue in Congenica where it appears that in some referrals not all tiered variants are being displayed. We have raised the issue with Congenica and will update when we have more information.

In the meantime, you can assess tiered variants in either the Interpretation Browser or the New Interpretation Browser

These guides can help you with the workaround options:
Interpret your referral without a DSS
New Interpretation Portal Guide

We apologise for any inconvenience this may be causing you.
Nov 24, 2025 - 09:50 GMT
Uptime over the past 90 days. View historical uptime.
General_Service_Updates_Genomics_England Operational
90 days ago
100.0 % uptime
Today
NGIS_Production_Environment Degraded Performance
90 days ago
99.48 % uptime
Today
General_Service_Updates_NGIS_Production ? Operational
90 days ago
99.72 % uptime
Today
NGIS_PROD_Test_Selection Operational
90 days ago
100.0 % uptime
Today
NGIS_PROD_Test_Ordering Operational
90 days ago
99.24 % uptime
Today
NGIS_PROD_SFTP Operational
90 days ago
99.24 % uptime
Today
NGIS_PROD_M.I.Portal Operational
90 days ago
99.24 % uptime
Today
NGIS_PROD_Interpretation_Portal Operational
90 days ago
99.24 % uptime
Today
NGIS_PROD_CIP-API Operational
90 days ago
99.24 % uptime
Today
NGIS_PROD_CVA Operational
90 days ago
99.24 % uptime
Today
NGIS_PROD_IGV Operational
90 days ago
99.21 % uptime
Today
NGIS_PROD_Congenica Degraded Performance
90 days ago
100.0 % uptime
Today
NGIS_PROD_Cancer_DSS Operational
90 days ago
100.0 % uptime
Today
NGIS_UAT_Environment Operational
90 days ago
99.53 % uptime
Today
General_Service_Updates_NGIS_UAT ? Operational
NGIS_UAT_Test_Selection Operational
90 days ago
100.0 % uptime
Today
NGIS_UAT_Test_Ordering Operational
90 days ago
99.24 % uptime
Today
NGIS_UAT_SFTP Operational
90 days ago
99.93 % uptime
Today
NGIS_UAT_M.I.Portal Operational
90 days ago
99.24 % uptime
Today
NGIS_UAT_Interpretation_Portal Operational
90 days ago
99.24 % uptime
Today
NGIS_UAT_CIP_API Operational
90 days ago
99.24 % uptime
Today
NGIS_UAT_CVA Operational
90 days ago
99.24 % uptime
Today
NGIS_UAT_IGV Operational
90 days ago
99.24 % uptime
Today
NGIS_UAT_Congenica Operational
90 days ago
100.0 % uptime
Today
NGIS_UAT_Cancer_DSS Operational
90 days ago
100.0 % uptime
Today
Third Party Integrator Operational
90 days ago
100.0 % uptime
Today
Third Party Integrator - Production Operational
90 days ago
100.0 % uptime
Today
Third Party Integrator - UAT Operational
90 days ago
100.0 % uptime
Today
Third Party Integrator - SIT Operational
90 days ago
100.0 % uptime
Today
100K_Applications Operational
90 days ago
100.0 % uptime
Today
100K_Interpretation_Portal Operational
90 days ago
100.0 % uptime
Today
100K_CIP-API Operational
90 days ago
100.0 % uptime
Today
100K_SNP Operational
90 days ago
100.0 % uptime
Today
100K_Congenica Operational
90 days ago
100.0 % uptime
Today
100K_MI_Portal Operational
90 days ago
100.0 % uptime
Today
General_Service_Updates_100K_Applications Operational
90 days ago
100.0 % uptime
Today
100K_Labkey Operational
90 days ago
100.0 % uptime
Today
100K_Open_Clinica Operational
90 days ago
100.0 % uptime
Today
Cloud_RE Operational
90 days ago
100.0 % uptime
Today
General_Service_Updates_Cloud_RE ? Operational
90 days ago
100.0 % uptime
Today
CloudOS Operational
90 days ago
100.0 % uptime
Today
VDI Operational
90 days ago
100.0 % uptime
Today
AWS_Workspace Operational
90 days ago
100.0 % uptime
Today
Research_Environment Operational
90 days ago
99.74 % uptime
Today
General_Service_Updates_Research_Environment Operational
90 days ago
100.0 % uptime
Today
RE_Confluence ? Operational
90 days ago
100.0 % uptime
Today
RE_Labkey Operational
90 days ago
100.0 % uptime
Today
RE_Data_Discovery_Portal Operational
90 days ago
100.0 % uptime
Today
RE_High_Performance_Compute_HPC_HELIX Operational
90 days ago
100.0 % uptime
Today
RE_Participant_Explorer Operational
90 days ago
97.67 % uptime
Today
RE_Research_Portal Operational
90 days ago
100.0 % uptime
Today
RE_IVA Operational
90 days ago
100.0 % uptime
Today
RE_Airlock_MFT Operational
90 days ago
100.0 % uptime
Today
Atlassian_Suite Operational
90 days ago
100.0 % uptime
Today
GE_Jira_Service_Desk Operational
90 days ago
100.0 % uptime
Today
GE_Jira Operational
90 days ago
100.0 % uptime
Today
GE_Confluence Operational
90 days ago
100.0 % uptime
Today
PanelApp Operational
90 days ago
100.0 % uptime
Today
Generation Study (Newborns) Operational
90 days ago
100.0 % uptime
Today
Generation Study Portal Operational
90 days ago
100.0 % uptime
Today
Generation Study Website Operational
90 days ago
100.0 % uptime
Today
Generation Study CRM Operational
90 days ago
100.0 % uptime
Today
Variant Review Tool Operational
90 days ago
100.0 % uptime
Today
Newborns Pipeline Operational
90 days ago
100.0 % uptime
Today
Tableau Operational
90 days ago
99.88 % uptime
Today
Tableau_Production_Internal Operational
90 days ago
99.76 % uptime
Today
Tableau_Production_External (Coming Soon) ? Operational
90 days ago
100.0 % uptime
Today
Aspera Operational
90 days ago
100.0 % uptime
Today
Aspera ? Operational
90 days ago
100.0 % uptime
Today
GitLab Operational
90 days ago
99.93 % uptime
Today
GitLab Operational
90 days ago
99.93 % uptime
Today
Artifactory Operational
90 days ago
100.0 % uptime
Today
Artifactory ? Operational
90 days ago
100.0 % uptime
Today
WEKA Storage Platform Operational
90 days ago
100.0 % uptime
Today
WEKA ? Operational
90 days ago
100.0 % uptime
Today
Colt Operational
90 days ago
100.0 % uptime
Today
Lumen Internet Connectivity ? Operational
90 days ago
100.0 % uptime
Today
Manage Engine Operational
90 days ago
100.0 % uptime
Today
Manage Engine (Self-Service) ? Operational
90 days ago
100.0 % uptime
Today
Manage Engine (AD Manager Plus) ? Operational
90 days ago
100.0 % uptime
Today
Semarchy Operational
90 days ago
100.0 % uptime
Today
Semarchy Master Data Management ? Operational
90 days ago
100.0 % uptime
Today
Quantum ObjectStore Operational
90 days ago
100.0 % uptime
Today
Quantum ObjectStore Operational
90 days ago
100.0 % uptime
Today
Miro Application Operational
Miro Log in ability Operational
Miro Mail System Operational
Miro Web Site Operational
Operational
Degraded Performance
Partial Outage
Major Outage
Maintenance
Major outage
Partial outage
No downtime recorded on this day.
No data exists for this day.
had a major outage.
had a partial outage.

No incidents or maintenance related to this downtime.

Scheduled Maintenance

Research Environment - Maintenance Notification - IVA and OpenCGA Nov 26, 2025 14:00-16:00 GMT

Dear Researchers,

We would like to inform you of a planned upgrade to IVA and OpenCGA. The applications will not be available during the maintenance period.

Maintenance period: The applications will be unavailable Wednesday, 26 November 2025 from 14:00(GMT) to 16:00 (GMT).

Once the upgrade is complete, you will be able to use the application as usual.

We appreciate your understanding and apologise for any inconvenience caused.

Best Wishes,
Genomics England
Posted on Nov 20, 2025 - 12:34 GMT

Research Environment - Maintenance Notification - CloudOS Nov 27, 2025 05:00-09:00 GMT

Dear research user,

We would like to inform you of a planned update in the Lifebit Platform on Thursday, 27 November 2025 from 5:00 (GMT) to 09:00 (GMT).

The change will affect the Cohort Browser Platform Module.

This means that during the change window the Cohort Browser module will be unavailable.
You will not be able to
- load cohorts
- view old cohorts

Any workflows or analyses already running will not be affected.

We recommend that you avoid logging into CloudOS during this time.

In the unlikely event that you experience any issues, please raise a ticket through Genomics England Service Desk.

We apologise in advance for any inconvenience caused by this upgrade.

Best wishes,
Genomics England
Posted on Nov 20, 2025 - 12:45 GMT

NGIS Production Environment: Congenica Case Deletion - 04 December 2025 Dec 4, 2025 09:00-17:00 GMT

Dear Congenica User,

This is a reminder that GEL will be deleting cases from Congenica on a regular basis. The cases that will be marked for deletion will be the ones that have been closed for 2 weeks in the Interpretation Portal, this is regardless of the amount of time that it has been in Congenica. Closed is defined as the report/summary of findings and exit questionnaire being completed by the user.

The next set of deletions will take place on the Thursday, 04 December 2025.

If you wish to keep a case in Congenica, we advise that you inform the Genomics England Service Desk at least 3 days in advance of the 2 week mark for your case.
Posted on Nov 21, 2025 - 15:59 GMT
Nov 24, 2025

Unresolved incident: NGIS Production Environment: Congenica Incident Notification.

Nov 23, 2025

No incidents reported.

Nov 22, 2025

No incidents reported.

Nov 21, 2025
NGIS Production Environment: Congenica Case Deletion - 20 November 2025
Completed - The scheduled maintenance has been completed.
Nov 21, 15:57 GMT
Scheduled - Dear Congenica User,

This is a reminder that GEL will be deleting cases from Congenica on a regular basis. The cases that will be marked for deletion will be the ones that have been closed for 2 weeks in the Interpretation Portal, this is regardless of the amount of time that it has been in Congenica. Closed is defined as the report/summary of findings and exit questionnaire being completed by the user.

The next set of deletions will take place on the Thursday, 20 November 2025.

If you wish to keep a case in Congenica, we advise that you inform the Genomics England Service Desk at least 3 days in advance of the 2 week mark for your case.
Nov 6, 17:23 GMT
Nov 20, 2025
NGIS UAT Environment: Regulus and Cancer DSS v6.14.0 Release Notification
Completed - The scheduled maintenance has been completed.
Nov 20, 14:35 GMT
In progress - Scheduled maintenance is currently in progress. We will provide updates as necessary.
Nov 20, 10:00 GMT
Scheduled - Dear all,

We would like to inform you of planned software releases for the NGIS UAT environment.

Regulus and Cancer DSS v6.14.0 will be released on Thursday, 20 November 2025 from 10.00 (GMT) - 18.00 (GMT).

The Regulus Release Note and the Cancer DSS v6.14.0 Release Note are available in the 'GEL Release Documentation' folder in NHS Futures.

The main changes in the Regulus release are:
- Move to numeric tiering for CNVs
- Split annotation and tiering
- Bug fixes
- Tech improvements and supporting changes for RD

The main changes in the Cancer DSS v6.14.0 release are:
- MNV and HGVS small variant annotation limitation alert
- Coverage plot resolution improvements

Please note that all NGIS applications in the NGIS UAT environment would be unavailable during the stated timeframe.

There will be no impact to the NGIS production environment.
Nov 18, 15:34 GMT
Nov 19, 2025
NGIS Production Environment: Maintenance Notification
Completed - Dear all,

We are pleased to notify you that the planned maintenance in the NGIS production environment has been successfully completed.

We have deployed the patch to production Congenica portal to fix the connection issue users were experiencing accessing OMIM through Congenica.

All NGIS applications are now available.
Nov 19, 18:59 GMT
In progress - Scheduled maintenance is currently in progress. We will provide updates as necessary.
Nov 19, 17:00 GMT
Scheduled - Dear all,

We would like to inform you of an outage on the NGIS production environment, to implement some planned changes. The outage will be on Wednesday, 19 November 2025 from 17:00 (GMT) to 21:00 (GMT).

Please note that the NGIS applications will be unavailable in the NGIS production environment during the advised timeframe.

If you have any queries about what changes will be implemented in the planned window please contact the Genomics England Service Desk.
Nov 12, 13:24 GMT
Genomics England: Incident Notification
Resolved - SERVICE:
JIRA Service Desk, Confluence and JIRA

SEVERITY:
2

GEL REF:
GEL-307847

DESCRIPTION:
JIRA Service Desk, JIRA and Confluence access issues

SUMMARY OF IMPACT:
Genomics England's JIRA Service Desk and Confluence access is now fully restored following the resolution of the global Cloudflare incident.

We apologise for any inconvenience this may have caused you.
Nov 19, 07:26 GMT
Monitoring - SERVICE:
JIRA Service Desk, Confluence and JIRA

SEVERITY:
2

GEL REF:
GEL-307847

DESCRIPTION:
JIRA Service Desk, JIRA and Confluence access issues

SUMMARY OF IMPACT:
Clouflare have implemented a fix which has restored access to Genomics England's JIRA Service Desk and Confluence. We are currently monitoring the applications until Cloudflare services are fully resolved.

All NGIS applications are currently unimpacted.
Nov 18, 13:59 GMT
Investigating - SERVICE:
JIRA Service Desk, Confluence and JIRA

SEVERITY:
2

GEL REF:
GEL-307847

DESCRIPTION:
JIRA Service Desk, JIRA and Confluence access issues

SUMMARY OF IMPACT:
We are currently experiencing an outage to Genomics England's JIRA Service Desk and Confluence, which cannot be accessed currently. This is due to the ongoing global outage of Cloudflare.

All NGIS applications are currently unimpacted.

If you want to raise any issues with Genomics England Service Desk on 0808 281 9535 or email ge-servicedesk@genomicsengland.co.uk.
We apologise for any inconvenience this may cause you.
Nov 18, 12:04 GMT
Nov 18, 2025
Research Environment - Maintenance Notification - CloudOS Data Release
Completed - The scheduled maintenance has been completed.
Nov 18, 18:00 GMT
In progress - Scheduled maintenance is currently in progress. We will provide updates as necessary.
Nov 18, 09:00 GMT
Scheduled - Dear users,

We would like to inform you of a planned release being deployed for CloudOS.

SW 5.11 Uracil Release will be deployed on Tuesday, 18 November 2025 between 09:00 (GMT) and 18:00 (GMT).

Please note that we cannot ensure the normal functionality of the CloudOS application during this time.

This release will include a number of new features for CloudOS, including:
Advanced Analytics
- Instantly link job directories, logs, or results to interactive sessions with the `--link` flag, removing manual S3 path copying.
User Login
- Users are automatically logged out at midnight local time for secure session resets without affecting daytime work.
Workspace Management
- Members can now view their compute and storage costs in the dashboard, previously admin-only, with monthly summaries and breakdowns.
Procurement Management
- Procurement Admins receive procurement event notifications via email and the bell icon, with customizable preferences from Account Settings.
Organisation Management
- Organisation Admins can now search workspace and group dropdowns when configuring SCIM for easier navigation.
TargetID
- Specify custom variant sets for Regenie Step 2 in GWAS analyses to focus on predefined variants.

You may need to clear your browser cache within the AWS Workspace to see the changes that have been applied in the release.

If you have any issues following this release, please let us know by raising a Service Desk ticket.

We apologise in advance for any inconvenience caused by this upgrade.

Best wishes,
Genomics England
Nov 14, 16:31 GMT
Research Environment - Maintenance Notification - CloudOS
Completed - The scheduled maintenance has been completed.
Nov 18, 17:00 GMT
In progress - Scheduled maintenance is currently in progress. We will provide updates as necessary.
Nov 18, 09:00 GMT
Scheduled - Dear research user,

We would like to inform you of planned maintenance for Tuesday, 18 November 2025 from 09:00 (GMT) to 17:00 (GMT).

The Research Environment (RE) accessed with registration code wslhr+9BK4PR will be discontinued.

This is the previous generation of our RE and we will be closing it down. Users will no longer be able to access the RE using this registration code after this date.

Most users are already using the current RE and this change will not affect them.

If you are using the old code, to access the current RE, you need to use registration code wslhr+WJH7W9. Your username and password remain the same.

All users' home directories from the old RE are already synchronised to their existing home directory under the new code, at ~/cloudre_home/

The synchronisation process occurs every day at 00:00 (midnight), so any files saved to your home drive on the old RE will be synchronised to the new location nightly.

If you have any trouble using registration code wslhr+WJH7W9, please contact Genomics England Service Desk.

Best Wishes,
Genomics England
Nov 5, 11:29 GMT
Nov 17, 2025

No incidents reported.

Nov 16, 2025
NGIS Production Environment: Congenica V4 Release
Completed - Dear all,

We are pleased to notify you that the Congenica V4 code release was successfully deployed to the NGIS production environment.

Congenica in the NGIS production environment is now available to use.

Please note we have been informed by Congenica there is an issue identified accessing OMIM through the Congenica portal currently, which is unrelated to the code release. We will send further communication about this issue next week.
Nov 16, 09:52 GMT
In progress - Scheduled maintenance is currently in progress. We will provide updates as necessary.
Nov 15, 18:00 GMT
Update - Dear all,

Further to our communication to you last week, we would like to remind you of the planned software release to Congenica in the NGIS Production environment. Congenica version 4.0 will be released on Saturday, 15 November 2025 from 18:00 (GMT) to 12:00 (GMT) on Sunday, 16 November 2025.

The Congenica 4.0 Release Notes are available in the Release Notes folder in NHS Futures.

The main changes in this release are:
- Migration to Ensembl v109 and related database changes
- Automated update of Gene Panels

Please note that Congenica in the NGIS production environment will be unavailable during the advised timeframe. All other NGIS applications are unaffected.
Nov 12, 13:27 GMT
Scheduled - Dear all,

We would like to inform you of a planned software release to Congenica in the NGIS Production environment. Congenica version 4.0 will be released on Saturday, 15 November 2025 from 18:00 (GMT) to 12:00 (GMT) on Sunday, 16 November 2025.

The Congenica 4.0 Release Notes are available in the Release Notes folder in NHS Futures.

The main changes in this release are:
- Migration to Ensembl v109 and related database changes
- Automated update of Gene Panels

Please note that Congenica in the NGIS production environment will be unavailable during the advised timeframe. All other NGIS applications are unaffected.
Nov 4, 14:37 GMT
Nov 15, 2025
Nov 14, 2025
[GEL Internal Communication] Atlassian: Jira Service Desk Essential Maintenance
Completed - The scheduled maintenance has been completed.
Nov 14, 18:30 GMT
In progress - Scheduled maintenance is currently in progress. We will provide updates as necessary.
Nov 14, 18:00 GMT
Scheduled - We will be undergoing scheduled maintenance during this time.
Nov 10, 11:11 GMT
Genomics England JIRA Service Desk: Maintenance Notification
Completed - The scheduled maintenance has been completed.
Nov 14, 18:30 GMT
In progress - Scheduled maintenance is currently in progress. We will provide updates as necessary.
Nov 14, 18:00 GMT
Scheduled - Dear all,

Genomics England JIRA Service Desk will be unavailable from 18:00 (GMT) to 18:30 (GMT), Friday, 14 November 2025 to implement a fix to a bug that was identified.

During the advised timeframe please email ge-servicedesk@genomicsengland.co.uk and your issues will then be logged when the system is available again.

We apologise any inconvenience this may cause you.
Nov 10, 12:01 GMT
Nov 13, 2025

No incidents reported.

Nov 12, 2025
Research Environment - Maintenance Notification - CloudOS update
Completed - The scheduled maintenance has been completed.
Nov 12, 09:00 GMT
In progress - Scheduled maintenance is currently in progress. We will provide updates as necessary.
Nov 12, 05:00 GMT
Scheduled - Dear research user,

We would like to inform you of a planned update in the Lifebit Platform on Wednesday, 12 November 2025 from 5:00 (GMT) to 09:00 (GMT).

The change will affect the Cohort Browser Platform Module.

This means that during the change window the Cohort Browser module will be unavailable. You will not be able to
-load cohorts
-view old cohorts

Any workflows or analyses already running will not be affected.

We recommend that you avoid logging into CloudOS during this time.

In the unlikely event that you experience any issues, please raise a ticket through Genomics England Service Desk.

We apologise in advance for any inconvenience caused by this upgrade.

Best wishes,
Genomics England
Nov 5, 14:55 GMT
Nov 11, 2025

No incidents reported.

Nov 10, 2025

No incidents reported.

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