Update - SERVICE:
NGIS Tumor Samples
SEVERITY:
2
GEL REF:
GEL-206086
DESCRIPTION:
Tumor samples failing a non-contractual T>G metric
SUMMARY OF IMPACT:
This is a reminder that this incident is still being investigated by Ilumina and please be vigilant when analysing cases
.
We have been notified by Illumina that a subset of tumour samples have been failing a non-contractual T>G metric and the issue is currently being investigated by Illumina. We have confirmation from Illumina that the issue is not connected to the T>G issue we experienced last year. Any samples with the failed metric have been re-sequenced.
There are 9 cases where T>G fraction is still exceeding cut-off after re-sequencing. We have contacted affected GLHs with a list of samples with any next steps options. Upon inspecting sequencing data in IGV we believe a larger number of cases can be impacted to a lesser degree. We recommend reviewing any reportable variants in IGV to exclude clinical reporting of false positive variants.
Oct 02, 2023 - 09:47 BST
NGIS Tumor Samples
SEVERITY:
2
GEL REF:
GEL-206086
DESCRIPTION:
Tumor samples failing a non-contractual T>G metric
SUMMARY OF IMPACT:
This is a reminder that this incident is still being investigated by Ilumina and please be vigilant when analysing cases
.
We have been notified by Illumina that a subset of tumour samples have been failing a non-contractual T>G metric and the issue is currently being investigated by Illumina. We have confirmation from Illumina that the issue is not connected to the T>G issue we experienced last year. Any samples with the failed metric have been re-sequenced.
There are 9 cases where T>G fraction is still exceeding cut-off after re-sequencing. We have contacted affected GLHs with a list of samples with any next steps options. Upon inspecting sequencing data in IGV we believe a larger number of cases can be impacted to a lesser degree. We recommend reviewing any reportable variants in IGV to exclude clinical reporting of false positive variants.
Oct 02, 2023 - 09:47 BST
Investigating - SERVICE:
NGIS Tumor Samples
SEVERITY:
2
GEL REF:
GEL-206086
DESCRIPTION:
Tumor samples failing a non-contractual T>G metric
SUMMARY OF IMPACT:
We have been notified by Illumina that a subset of tumour samples have been failing a non-contractual T>G metric and the issue is currently being investigated by Illumina. We have confirmation from Illumina that the issue is not connected to the T>G issue we experienced last year.
Any samples with the failed metric have been re-sequenced. There are 8 cases where T>G fraction is still exceeding cut-off after re-sequencing. We have contacted affected GLHs with a list of samples with any next steps options.
Upon inspecting sequencing data in IGV we believe a larger number of cases can be impacted to a lesser degree. We recommend reviewing any reportable variants in IGV to exclude clinical reporting of false positive variants.
Sep 19, 2023 - 09:33 BST
NGIS Tumor Samples
SEVERITY:
2
GEL REF:
GEL-206086
DESCRIPTION:
Tumor samples failing a non-contractual T>G metric
SUMMARY OF IMPACT:
We have been notified by Illumina that a subset of tumour samples have been failing a non-contractual T>G metric and the issue is currently being investigated by Illumina. We have confirmation from Illumina that the issue is not connected to the T>G issue we experienced last year.
Any samples with the failed metric have been re-sequenced. There are 8 cases where T>G fraction is still exceeding cut-off after re-sequencing. We have contacted affected GLHs with a list of samples with any next steps options.
Upon inspecting sequencing data in IGV we believe a larger number of cases can be impacted to a lesser degree. We recommend reviewing any reportable variants in IGV to exclude clinical reporting of false positive variants.
Sep 19, 2023 - 09:33 BST
Identified - The issue has been identified and the fix needs to be implemented.
Aug 04, 2023 - 11:38 BST
Aug 04, 2023 - 11:38 BST
Investigating - Dear Researcher,
We are aware that Ensembl is currently not available due to network problems.
Our teams are working on the issue as a matter of urgency and will update you as soon as we have more information.
We apologise for any inconvenience caused.
Best wishes,
Genomics England
Jun 30, 2023 - 18:03 BST
We are aware that Ensembl is currently not available due to network problems.
Our teams are working on the issue as a matter of urgency and will update you as soon as we have more information.
We apologise for any inconvenience caused.
Best wishes,
Genomics England
Jun 30, 2023 - 18:03 BST
General_Service_Updates_Genomics_England
Operational
NGIS_Production_Environment
Operational
General_Service_Updates_NGIS_Production
?
Operational
NGIS_PROD_Test_Selection
Operational
NGIS_PROD_Test_Ordering
Operational
NGIS_PROD_SFTP
Operational
NGIS_PROD_M.I.Portal
Operational
NGIS_PROD_Sample_Matching_Service
Operational
NGIS_PROD_Interpretation_Portal
Operational
NGIS_PROD_CIP-API
Operational
NGIS_PROD_CVA
Operational
NGIS_PROD_IGV
Operational
NGIS_PROD_SNP
Operational
NGIS_PROD_BSVI
Operational
NGIS_PROD_Congenica
Operational
NGIS_PROD_Cancer_Bridge_DSS
Operational
NGIS_UAT_Environment
Operational
General_Service_Updates_NGIS_UAT
?
Operational
NGIS_UAT_Test_Selection
Operational
NGIS_UAT_Test_Ordering
Operational
NGIS_UAT_SFTP
Operational
NGIS_UAT_M.I.Portal
Operational
NGIS_UAT_Sample_Matching_Service
Operational
NGIS_UAT_Congenica
Operational
NGIS_UAT_Interpretation_Portal
Operational
NGIS_UAT_Bertha
Operational
NGIS_UAT_CIP_API
Operational
NGIS_UAT_SNP
Operational
NGIS_UAT_BSVI
Operational
NGIS_UAT_Cancer_Bridge_DSS
Operational
Third Party Integrator
Operational
Third Party Integrator - Production
Operational
Third Party Integrator - UAT
Operational
Third Party Integrator - SIT
Operational
100K_Applications
Operational
100K_Interpretation_Portal
Operational
100K_CIP-API
Operational
100K_SNP
Operational
100K_Congenica
Operational
100K_MI_Portal
Operational
General_Service_Updates_100K_Applications
Operational
Cloud_RE
Operational
General_Service_Updates_Cloud_RE
?
Operational
CloudOS
Operational
VDI
Operational
AWS_Workspace
Operational
Research_Environment
Operational
General_Service_Updates_Research_Environment
Operational
RE_Inuvika
?
Operational
RE_Confluence
?
Operational
RE_Labkey
Operational
RE_Data_Discovery_Portal
Operational
RE_High_Performance_Compute_HPC_HELIX
Operational
RE_Participant_Explorer
Operational
RE_Research_Portal
Operational
RE_IVA
Operational
RE_Airlock_MFT
Operational
Atlassian_Suite
Operational
GE_Jira_Service_Desk
Operational
GE_Jira
Operational
GE_Confluence
Operational
PanelApp
Operational
Generation Study (Newborns)
Operational
Generation Study Portal
Operational
Generation Study Website
Operational
Generation Study CRM
Operational
Variant Review Tool
Operational
Tableau
Operational
Tableau_Production_Internal
Operational
Tableau_Production_External (Coming Soon)
?
Operational
Aspera
Operational
Aspera
?
Operational
GitLab
Operational
GitLab
Operational
Artifactory
Operational
Artifactory
?
Operational
WEKA Storage Platform
Operational
WEKA
?
Operational
Lumen
Operational
Lumen Internet Connectivity
?
Operational
Manage Engine
Operational
Manage Engine (Self-Service)
?
Operational
Manage Engine (AD Manager Plus)
?
Operational
Semarchy
Operational
Semarchy Master Data Management
?
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.
Scheduled Maintenance
Subject: Research Environment - Data Discovery discontinuation: Date moved forward
Apr 29, 2024 09:00-10:00 BST
Dear Researcher,
It has become necessary to discontinue the Data Discovery application earlier than planned. Therefore, it will no longer be available in the Research Environment from Monday, 29 April 2024. We understand this may be disruptive for some researchers, and we apologise for any inconvenience it may cause.
If you are using Data Discovery, please transition to alternative tools. For most use cases, Participant Explorer will provide an excellent alternative.
You can find more information about Participant Explorer in our user guide.
Please contact our Genomics England Service Desk via Service Desk Portal with description ‘Data Discovery EoL' if you are unable to meet your needs with alternative tools.
Best wishes,
Genomics England.
Posted on Apr 22, 2024 - 11:51 BST
It has become necessary to discontinue the Data Discovery application earlier than planned. Therefore, it will no longer be available in the Research Environment from Monday, 29 April 2024. We understand this may be disruptive for some researchers, and we apologise for any inconvenience it may cause.
If you are using Data Discovery, please transition to alternative tools. For most use cases, Participant Explorer will provide an excellent alternative.
You can find more information about Participant Explorer in our user guide.
Please contact our Genomics England Service Desk via Service Desk Portal with description ‘Data Discovery EoL' if you are unable to meet your needs with alternative tools.
Best wishes,
Genomics England.
Posted on Apr 22, 2024 - 11:51 BST
Research Environment - Application End of Life Notification: Data Discovery
Apr 29, 2024 10:00-11:00 BST
Update -
Dear Researcher,
We will be discontinuing the Data Discovery application in the Genomics England Research Environment on Wednesday, 22 May 2024. We understand this may be disruptive for some researchers, and we apologise for any inconvenience it may cause.
If you are currently using Data Discovery, we recommend that you begin transitioning to alternative tools as soon as possible. For most use cases, Participant Explorer will provide an excellent alternative. You can find more information about Participant Explorer in our user guide.
Please contact our Genomics England Service Desk via Service Desk Portal with description ‘Data Discovery EoL'
If this is your first time using the Service Desk Portal, you will need to create an account first. Please remember that your login credentials for the Service Desk Portal are different from those that you use to log into the Research Environment or Research Portal.
Our Portal is available 24/7, however please be aware that support hours are Mon-Fri 9am to 5.30pm (excluding Bank Holidays).
Best wishes,
Genomics England
Mar 04, 2024 - 16:19 GMT
We will be discontinuing the Data Discovery application in the Genomics England Research Environment on Wednesday, 22 May 2024. We understand this may be disruptive for some researchers, and we apologise for any inconvenience it may cause.
If you are currently using Data Discovery, we recommend that you begin transitioning to alternative tools as soon as possible. For most use cases, Participant Explorer will provide an excellent alternative. You can find more information about Participant Explorer in our user guide.
Please contact our Genomics England Service Desk via Service Desk Portal with description ‘Data Discovery EoL'
If this is your first time using the Service Desk Portal, you will need to create an account first. Please remember that your login credentials for the Service Desk Portal are different from those that you use to log into the Research Environment or Research Portal.
Our Portal is available 24/7, however please be aware that support hours are Mon-Fri 9am to 5.30pm (excluding Bank Holidays).
Best wishes,
Genomics England
Mar 04, 2024 - 16:19 GMT
Scheduled -
Dear Researcher,
We will be discontinuing the Data Discovery application in the Genomics England Research Environment on Wednesday, 22 May 2024. We understand this may be disruptive for some researchers, and we apologise for any inconvenience it may cause.
If you are currently using Data Discovery, we recommend that you begin transitioning to alternative tools as soon as possible. For most use cases, Participant Explorer will provide an excellent alternative. You can find more information about Participant Explorer in our user guide.
Please contact our Genomics England Service Desk via Service Desk Portal with description ‘Data Discovery EoL'
If this is your first time using the Service Desk Portal, you will need to create an account first. Please remember that your login credentials for the Service Desk Portal are different from those that you use to log into the Research Environment or Research Portal.
Our Portal is available 24/7, however please be aware that support hours are Mon-Fri 9am to 5.30pm (excluding Bank Holidays).
Best wishes,
Genomics England
Mar 04, 2024 - 16:16 GMT
We will be discontinuing the Data Discovery application in the Genomics England Research Environment on Wednesday, 22 May 2024. We understand this may be disruptive for some researchers, and we apologise for any inconvenience it may cause.
If you are currently using Data Discovery, we recommend that you begin transitioning to alternative tools as soon as possible. For most use cases, Participant Explorer will provide an excellent alternative. You can find more information about Participant Explorer in our user guide.
Please contact our Genomics England Service Desk via Service Desk Portal with description ‘Data Discovery EoL'
If this is your first time using the Service Desk Portal, you will need to create an account first. Please remember that your login credentials for the Service Desk Portal are different from those that you use to log into the Research Environment or Research Portal.
Our Portal is available 24/7, however please be aware that support hours are Mon-Fri 9am to 5.30pm (excluding Bank Holidays).
Best wishes,
Genomics England
Mar 04, 2024 - 16:16 GMT
NGIS Production Environment: Mira Release Notification (Test Ordering only)
Apr 30, 2024 17:00-22:00 BST
Dear all,
We would like to inform you of a planned software release for the Test Ordering Service in the NGIS production environment.
Mira - (NGIS version 1.48.0) will be released on Tuesday, 30 April 2024 from 17:00 (BST) to 22:00 (BST).
The Mira Release notes are available in the Forward Schedule of Change portal.
The main change in this release is:
- PDS (Personal Demographic Service) will replace current Inhealthcare patient look up
Please note that the Test Ordering will be unavailable in the NGIS production environment during the advised timeframe. All other applications in the NGIS production environment will be available.
The remaining Mira release changes will go in on Wednesday, 1 May.
Posted on Apr 23, 2024 - 15:59 BST
We would like to inform you of a planned software release for the Test Ordering Service in the NGIS production environment.
Mira - (NGIS version 1.48.0) will be released on Tuesday, 30 April 2024 from 17:00 (BST) to 22:00 (BST).
The Mira Release notes are available in the Forward Schedule of Change portal.
The main change in this release is:
- PDS (Personal Demographic Service) will replace current Inhealthcare patient look up
Please note that the Test Ordering will be unavailable in the NGIS production environment during the advised timeframe. All other applications in the NGIS production environment will be available.
The remaining Mira release changes will go in on Wednesday, 1 May.
Posted on Apr 23, 2024 - 15:59 BST
NGIS Production Environment: Mira and Cancer DSS Release Notification
May 1, 2024 13:00-21:00 BST
Dear all,
We would like to inform you of planned software releases for the NGIS production environment.
Mira - (NGIS version 1.48.7) and Cancer DSSv6.0.0 will be released on Wednesday, 01 May 2024 from 13:00 (BST) to 21:00 (BST).
The Mira and Cancer DSS Release notes are available in the Forward Schedule of Change portal.
The main changes in these releases are:
- Dragen v4 for RD - Tumour First / Germline Late
- PanelApp Data changes - GRM Update
- VIL Improvements
- Prioritise variants in known disease associated non-coding genes (non-MT)
- Removal of BSVI access from the Interpretation Portal
- Some accessibility changes, bug fixes for Cancer DSS and a move of the DSS to a new infrastructure
Please note that all NGIS applications except for Test Ordering will be unavailable in the NGIS production environment during the advised timeframe.
Posted on Apr 24, 2024 - 12:51 BST
We would like to inform you of planned software releases for the NGIS production environment.
Mira - (NGIS version 1.48.7) and Cancer DSSv6.0.0 will be released on Wednesday, 01 May 2024 from 13:00 (BST) to 21:00 (BST).
The Mira and Cancer DSS Release notes are available in the Forward Schedule of Change portal.
The main changes in these releases are:
- Dragen v4 for RD - Tumour First / Germline Late
- PanelApp Data changes - GRM Update
- VIL Improvements
- Prioritise variants in known disease associated non-coding genes (non-MT)
- Removal of BSVI access from the Interpretation Portal
- Some accessibility changes, bug fixes for Cancer DSS and a move of the DSS to a new infrastructure
Please note that all NGIS applications except for Test Ordering will be unavailable in the NGIS production environment during the advised timeframe.
Posted on Apr 24, 2024 - 12:51 BST
NGIS Production Environment: Congenica Case Deletion - 02 May 2024
May 2, 2024 09:00-17:00 BST
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, 02 May 2024.
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 Apr 19, 2024 - 11:23 BST
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, 02 May 2024.
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 Apr 19, 2024 - 11:23 BST