Release Notes
v5.1.0
These Release Notes include new features, product limitations and known issues for Illumina Connected Insights v5.1.0, cloud-only.
New Features:
Ability to upgrade to new versions Illumina Connected Insights using user interface allowing users to control the time of transition and versions per each workgroup
Automated, guideline-based acute myeloid leukemia (AML) subtype classification feature that takes into account identified biomarkers (eg, by the DRAGEN Amplicon, DRAGEN WGS Somatic or other pipelines), a user-determined karyotype, and other parameters
Ability to add and report a user-determined karyotype determined by cytogenetic microarray or another method
Ability to add and report the blast count percentage, history of cytotoxic therapy exposure, history of myelodysplastic syndrome, and history of myeloproliferative neoplasm as parameters for AML classification feature or other purposes.
Automatic conversion of knowledge base specific assertion tiers to one standard (ASCO/AMP, ESCAT or user-defined) when including assertions to report
Added ISCN nomenclature for deletions, duplications, insertions, inversions, translocations and other variant classes
Ability to add a “virtual variant” - a variant that is not presented in the VCF file - if an additional variant is identified by an orthogonal method or to correct a variant calling issue (eg when two variants should be presented as one variant)
Ability to upload and display gene expression data (number of transcripts per million) generated by DRAGEN RNA (and pipelines including DRAGEN RNA), DRAGEN RNA Amplicon, DRAGEN Amplicon (via DRAGEN RNA Amplicon), DRAGEN TSO 500 (for cases with RNA samples).
Improved display of information for structural variants spanning multiple genes, eg arm-level CNVs:
Variants page lists all impacted genes in a tooltip
Biomarker page and report represent the entire event
Biomarker page includes knowledge base records for all impacted genes with search and filter functions to facilitate navigation
Added BAM tracks to Visualize tab plots (eg, fusion plots) on biomarker pages
Integration with desktop version of IGV
One-letter HGVS variant notations in addition to three-letter HGVS notations
Ability to quickly search and filter variants by gene symbol using a text box
Out-of-the-box compatibility with the following pipelines: DRAGEN Amplicon v4.3.13, DRAGEN Enrichment v4.3.13, DRAGEN Somatic Whole Genome v4.3.13, DRAGEN RNA v4.3.13
Out-of-the-box compatibility with DUX4 Rearrangement Caller in scope of DRAGEN Somatic Whole Genome v4.3 pipeline
Manual data upload from BaseSpace Sequence Hub for DNA Amplicon v2.1.1, RNA Amplicon v2.1.0 and DNA + RNA Amplicon v1.0.5
Improved reporting template (Pre-configured Demo Report Template (Version 2.1)) with several additions and updates for clarity:
Added Karyotype section
Added a new section for variants with only biological classification
Added reporting of gene expression
Updated report header structure
Updated display of structure variants
Updated Genomic Biomarkers section (TMB, MSI, GIS)
Updated Clinical trials section
Updated Methodology and Sources section
Updates to reduce white space
Streamlined JSON output file to facilitate report customization, eg, all sample metadata is now in one section
Updated billing logic:
Incorporated the number of genes when determining the sample size
Introduced new category – very small panels (< 25 genes)
For cases created by uploading the data from the local storage using Data Uploader, the Delete Case function now also deletes the case analysis data and metadata from the cloud storage on ICA.
Defect Repairs:
6614: Total depth and VAF are now calculated for RNA splice variants.
7284: Fixed an issue causing some recruiting clinical trials be omitted if their status changed from “suspended” to “recruiting”.
7514: Fixed an issue causing OncoKB assertions that have “Colorectal cancer excluded” in disease name to be displayed on Biomarker page, for example, a Level 1 record for BRAF V600E.
7399: Fixed an issue causing the platform, in extremely rare scenarios, to increment variant count by more than 1 if a large variant or splice variant overlaps with multiple variants in another case.
8413: Fixed an issue causing the column order change in the Variants tab not to be remembered after changing column width.
Known Issues:
940: Therapy packs (e.g., Orsythia 28 Day Pack) may fail validation when adding them to an assertion.
1298: Read order in the BAM track may change after zooming in the IGV viewer.
3409: CN calls produced by DRAGEN TruSight Oncology 500 v2.5.2+ Analysis Software with CN=2 or CN > 2 and annotated as <DEL> are not displayed.
3594: Command Line Interface logs may take long time to sync (up to 4 hours) and not reflect latest actions if exported before the sync is completed.
3660: The error notification for a failed Data Upload will be replaced with the successful upload of the subsequent run folder causing customer to lose the failure notification.
3723: The software will display two duplicating variants if they were called by two different pipelines, for example, a small variant caller and a structural variant caller.
3777: Users will not be able to upload NR transcripts into My Knowledge Base. CKB assertions will not be displayed for NR transcript variants.
3836: Biomarker page may not open and an error message “Variant not found in index” will be displayed when clicking on some events on the Genome View plot and the Variants page.
3934: Reopening an approved report does not trigger notification of assertion update even if there are updated assertions for the case.
3943: For DRAGEN RNA pipeline, RNA BAM track in IGV Web is not enabled by default for small variants and needs to be turned on manually.
5080: A case may move to “Has issues” status if its reprocessing is ongoing on one tab and a user tries to approve the report on another browser tab.
5133: User preferred transcripts for a gene may not be prioritized as expected if user uploads preferred transcripts file with incorrect gene-transcript pairs.
5263: A valid case can be ingested with a status “Has issues” again if it was originally ingested with “Has issues” and there was a failure with report automation.
5491: Coverage graph may not display findings if they use a different transcript rather than the one used to create the graph.
5494: In IGV Web, the SV variant track may show only one SV when multiple SVs are present in the same locus.
5599: Records from CIViC knowledge base for broad variant categories like “PTEN mutation” will match all variants for the given gene even when match is not appropriate. For example, it will match records for exon variants to intron variants.
6199: Data upload of analysis results generated by the DRAGEN WGS Somatic v4.2 pipeline fails when the pipeline was run on ICA starting with BAM files. A workaround is to download data locally first. Alternatively, users can manually create a sample sheet and upload it into the analysis output folder in ICA before the analysis is completed. When the analysis is complete, the output will be automatically uploaded into Connected Insights.
6200: Variant filtering based on SpliceAI score and gene name may return incorrect results due to use of different transcripts.
6231: Previewing Report template does not work on Safari browser.
6332, 6378: Fusion representation is impacted if one breakend is in chrM.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
6623: Oncogenicity prediction tool does not correctly calculate OP3 criterion for PIK3CA p.Met1? variant.
7336: When assertions from multiple knowledge sources are present on different transcripts of a variant, the default transcript may not be the transcript with the highest oncogenic classification.
8403: Annotations including CGC, ClinGen, OMIM, 1000 genomes, and custom annotations are not displayed or filterable for SV deletions and CNVs over 10 Mb in size. It can cause these events to be omitted when filtering by annotations. Review of genome view and Circos plots are recommended to identify these larger events (seen as a large deletion arc in the SV track or abnormal coverage in the coverage and CNV track) and also by filtering for SVs and CNVs with length over 10 Mb.
9374: Variant count is incorrect for copy number neutral variants
9169: For Classification & Risk Stratification Prediction, the AML with NPM1 mutation evidence map may show multiple risk stratification results are met if the related conditions are met. The result on the tile and in the generated report text is correct.
Product Limitations:
191: The software does not yet display records related to co-occurring variants.
895 and 1415: The software does not consider partial exclusion criteria while listing clinical trials, for example, the trial with the following criteria will be prioritized for all listed markers “Patients with known EGFR mutations (except exon 20 insertion), BRAF mutations (V600), MET Exon14 skipping or ALK or ROS1 translocations that can be treated with oral tyrosine kinase inhibitors are excluded”.
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Assertions created for variants uploaded with GRCh37 reference genome are not displayed for the same variants uploaded with the GRCh38 reference genome.
6099: Unable to create assertions for extremely large copy number variants or structural variants.
8561: Annotation of mitochondrial variants is not supported when using the longer genome reference for the mitochondrial genome (hg19), only the shorter genome reference for the mitochondrial genome (GRCh37) is supported.
Revision History
Version
Description of Change
00
Initial Release
v5.0.1
These Release Notes include new features, product limitations and known issues for Illumina Connected Insights v5.0.1, cloud-only.
New Features:
Compatibility with the following pipelines: DRAGEN TruSight Oncology 500 v2.5.3 (DRAGEN server), DRAGEN TruSight Oncology 500 v2.6.0 (DRAGEN server and ICA), DRAGEN TruSight Oncology 500 ctDNA v2.6.1 (DRAGEN server and ICA).
3986 (cloud): The following QC metrics generated by DRAGEN Amplicon pipelines v4.1, v4.2 and v4.3 are now automatically uploaded and available in the Pipeline & QC Configuration page for setting thresholds and adding to case overviews and reports: Aligned Bases in Target Region (Count), Average Alignment Coverage in Target Region, Uniformity of Coverage > 20% of Mean in Target Region (Percentage). Additionally, metric Q30 Bases (Count) is also available in the Pipeline & QC Configuration page.
Defect Repairs:
10810: Implemented measures to minimize case processing interruptions due to spikes in computational demand. In addition, the software will now display “Has Issues” status for impacted cases under such condition to indicate the need to re-process the case (software was not displaying any indication for error before)
Known Issues:
940: Therapy packs (e.g., Orsythia 28 Day Pack) may fail validation when adding them to an assertion.
1298: Read order in the BAM track may change after zooming in the IGV viewer.
3409: CN calls produced by DRAGEN TruSight Oncology 500 v2.5.2+ Analysis Software with CN=2 or CN > 2 and annotated as
<DEL>are not displayed.3594: Command Line Interface logs may take long time to sync (up to 4 hours) and not reflect latest actions if exported before the sync is completed.
3660: The error notification for a failed Data Upload will be replaced with the successful upload of the subsequent run folder causing to lose the failure notification.
3723: The software will display two duplicating variants if they were called by two different pipelines, for example, a small variant caller and a structural variant caller.
3777: Users will not be able to upload NR transcripts into My Knowledge Base. JAX-CKB assertions will not be displayed for NR transcript variants.
3836: Biomarker page may not open and an error message “Variant not found in index” will be displayed when clicking on some events on the Genome View plot and the Variants page.
3934: Reopening an approved report does not trigger notification of assertion update even if there are updated assertions for the case.
3943: For DRAGEN RNA pipeline, RNA BAM track in IGV is not enabled by default for small variants and needs to be turned on manually.
5080: A case may move to “Has issues” status if its reprocessing is ongoing on one tab and a user tries to approve the report on another browser tab.
5133: User preferred transcripts for a gene may not be prioritized as expected if user incorrect gene-transcript pairs when uploading the file with user preferred transcripts.
5263: A valid case can be ingested with a status “Has issues” again if it was originally ingested with “Has issues” and there was a failure with report automation.
5491: Coverage graph may not display findings if they use a different transcript rather than the one used to create the graph.
5494: In IGV, the SV variant track may show only one SV when multiple SVs are present in the same locus.
5599: Records from CIViC knowledge base for broad variant categories like “PTEN mutation” will match all variants for the given gene even when match is not appropriate, for example, it will match records for exon variants to intron variants.
6199: Data upload of analysis results generated by the DRAGEN WGS Somatic v4.2 pipeline fails when the pipeline was run on ICA starting with BAM files. A workaround is to download data locally first.
6200: Variant filtering based on SpliceAI score and gene name may return incorrect results due to use of different transcripts.
6231: Previewing Report template does not work on Safari browser.
6332, 6378: Fusion representation is impacted if one breakend is in chrM.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
6623: Oncogenicity prediction tool does not correctly calculate OP3 criterion for PI3CA p.Met1? variant.
7284: Some recruiting clinical trials could be omitted if their status changed from “suspended” to “recruiting”.
7336: When assertions from multiple knowledge sources are present on different transcripts of a variant, the default transcript may not be the transcript with the highest oncogenic classification.
7399: In extremely rare scenarios, if a large variant or splice variant overlaps with multiple variants in another case the seen count is incremented by more than 1.
7514a: OncoKB assertions that have “Colorectal cancer excluded” in disease name are displayed on Biomarker page, for example, a Level 1A record for BRAF V600E.
8403: Annotations including CGC, ClinGen, OMIM, 1000 genomes, and custom annotations are not displayed or filterable for SV deletions and CNVs over 10 Mb in size. It can cause these events to be omitted when filtering by annotations. Review of genome view and Circos plots are recommended to identify these larger events (seen as a large deletion arc in the SV track or abnormal coverage in the coverage and CNV track) and also by filtering for SVs and CNVs with length over 10 Mb.
8413: Column order change in the Variants tab is not remembered after changing column width.
2593 (local): Unable to create new user using “Add user“ action if the current logged Administrator user edits their profile from User list -> Edit action against their profile. Requires a re-login to resume new user creation.
2571 (local): Delete case action intermittently does not delete the complete Case data folder due to few non-Connected Insights NFS protocol’s hidden files.
2498, 2580 (local): Case processing fails with “Has issues“ status or may end up in “Processing“ status indefinitely if DRAGEN encounters an abrupt shutdown. In such cases, try deleting the case and reupload or contact Illumina Support team.
2570 (local): Intermittently Report PDF is missing “Assay Gene List“ title when a report is generated with the Default Report template version 2.
2490 (local): My Knowledge Base bulk upload assertions file fails with Nirvana validation error when the bulk upload is initiated along with multiple cases are in progress.
1608 (local): Admin console and Walkme menu do not open from the IGV viewer page.
1495 (local): After a system reboot, the CLI Uploader on the Configuration page shows as “Offline“ and necessitates manual restart of the service.
Product Limitations:
191: The software does not yet display records related to co-occurring variants.
895 and 1415: The software does not consider partial exclusion criteria while listing clinical trials, for example, the trial with the following criteria will be prioritized for all listed markers “Patients with known EGFR mutations (except exon 20 insertion), BRAF mutations (V600), MET Exon14 skipping or ALK or ROS1 translocations that can be treated with oral tyrosine kinase inhibitors are excluded”.
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Assertions created for variants uploaded with GRCh37 reference genome are not displayed for the same variants uploaded with the GRCh38 reference genome.
6099: Unable to create assertions for extremely large copy number variants or structural variants.
6614: Total depth and VAF are not calculated for RNA splice variants.
3729: DUX4 Rearrangement Caller in scope of DRAGEN Somatic Whole Genome v4.3 pipeline is not supported.
2535 (local): Software requires only Connected Insights packages present in the package source location when initiating a software or dependent package update.
2536 (local): Software displays “Software update failed” error for pre-installation checks failure when “Install All” is initiated.
v5.0.0
These Release Notes include new features, product limitations and known issues for Illumina Connected Insights v5.0.0.
New Features:
Illumina Connected Insights and Illumina Connected Insights – Research were consolidated into one product with the name “Illumina Connected Insights” (Research Use Only).
Ability to run different versions of Connected Insights in different workgroups, for example, v5.0.0 in one workgroup and version v5.1.0 in another workgroup.
New re-designed default report template with reorganized section, color accents, draft content in methodology and gene list sections.
Ability to view, search, filter, edit and archive assertions on My Knowledge Base page independent from specific cases.
Ability to create assertions as drafts, submit assertions for approval and approve assertions based on assigned user roles. A new role – Case Manager – Curator that can draft but not approve assertions was added.
Inclusion of PrimateAI-3D, a computational predictor for missense variant oncogenicity, as a stand-alone predictor and in scope of oncogenicity prediction feature.
Improved variant filtering logic on Biomarker details pages: if a user updates a filter for one variant, the updated filtering logic is applied for subsequently opened Biomarker Details pages within one case. A filter reset button was also added.
Ability to filter drugs on the Biomarker pages by the approval agency, for example, FDA, EMA, TGA, ANVISA, PMDA.
CNV plot in the Genome View in Visualize page can now display CNV events.
Visualization of exons, directionality and frame maintenance information for fusions on Biomarker Details pages.
Interactive CIRCOS plot.
Manual upload of secondary analysis data from Illumina Connected Analytics from Connected Insights interface.
Easier access to data upload error logs by searching analysis ID.
Access to audit logs from Connected Insights user interface.
Ability to assign case owners on the Cases page from the existing user list.
Compatibility with the following pipelines: DRAGEN Amplicon v4.3, DRAGEN Enrichment v4.3, DRAGEN RNA v4.3, DRAGEN Somatic Whole Genome v4.3, DRAGEN TruSight Oncology 500 ctDNA v2.6.0.
Defect Repairs:
2850, 5116, 5743: Fixed an issue causing a few assertions and clinical trials from CKB for Infant-type hemispheric glioma, oligodendroglioma IDH-mutant and 1p/19q-codeleted grade 2, and oligodendroglioma IDH-mutant, 1p/19q-codeleted grade 3 and several other cancer types to not be displayed in Biomarker pages.
3835: Fixed an issue causing filtering for variant type “Copy Number Neutral” returning no results even if CNV with CN=2 are present.
5074: Fixed an issue causing copy number gain false positive findings be displayed for non-PAR chrX regions.
7116: Fixed an issue causing incorrect processing of values with commas in the metadata file.
7216: Fixed an issue with OncoKB data not displayed on Biomarker pages if a case was created with v3.0 and processed with v4.0.
7241: Fixed an issue causing glioblastoma assertions to appear in the Other Diseases column on glioblastoma reports.
7284: Fixed an issue causing clinical trials that changed status from “suspended” to “recruiting” not to be displayed.
7329: Fixed an issue causing some CIViC level C assertions to not be displayed in the auto-generated draft report.
7418: Fixed an issue causing SBS2 Oncogenicity guideline criterion to be applied for both oncogenic and benign assertions.
7429: Fixed an issue causing RNA QC metrics for a merged case to not be displayed on the Overview page in certain scenarios.
7514b: Fixed an issue causing OncoKB assertions for colorectal cancer to not be displayed on the Biomarker page when filtered for “Malignant tumor of large intestine” or other related terms.
9976: Fixed an issue preventing the software from uploading and displaying CNV variants for TSO 500 non-HRD samples if a secondary analysis run includes TSO 500 samples with and without HRD and is ingested to Connected Insights using the data upload setting "DRAGEN TruSight Oncology 500 Analysis Software - 2.5.2 (with HRD)".
Known Issues:
940: Therapy packs (e.g., Orsythia 28 Day Pack) may fail validation when adding them to an assertion.
1298: Read order in the BAM track may change after zooming in the IGV viewer.
3409: CN calls produced by DRAGEN TruSight Oncology 500 v2.5.2+ Analysis Software with CN=2 or CN > 2 and annotated as
<DEL>are not displayed.3594: Command Line Interface logs may take long time to sync (up to 4 hours) and not reflect latest actions if exported before the sync is completed.
3660: The error notification for a failed Data Upload will be replaced with the successful upload of the subsequent run folder causing to lose the failure notification.
3723: The software will display two duplicating variants if they were called by two different pipelines, for example, a small variant caller and a structural variant caller.
3777: Users will not be able to upload NR transcripts into My Knowledge Base. JAX-CKB assertions will not be displayed for NR transcript variants.
3836: Biomarker page may not open and an error message “Variant not found in index” will be displayed when clicking on some events on the Genome View plot and the Variants page.
3934: Reopening an approved report does not trigger notification of assertion update even if there are updated assertions for the case.
3943: For DRAGEN RNA pipeline, RNA BAM track in IGV is not enabled by default for small variants and needs to be turned on manually.
5080: A case may move to “Has issues” status if its reprocessing is ongoing on one tab and a user tries to approve the report on another browser tab.
5133: User preferred transcripts for a gene may not be prioritized as expected if user incorrect gene-transcript pairs when uploading the file with user preferred transcripts.
5263: A valid case can be ingested with a status “Has issues” again if it was originally ingested with “Has issues” and there was a failure with report automation.
5491: Coverage graph may not display findings if they use a different transcript rather than the one used to create the graph.
5494: In IGV, the SV variant track may show only one SV when multiple SVs are present in the same locus.
5599: Records from CIViC knowledge base for broad variant categories like “PTEN mutation” will match all variants for the given gene even when match is not appropriate, for example, it will match records for exon variants to intron variants.
6199: Data upload of analysis results generated by the DRAGEN WGS Somatic v4.2 pipeline fails when the pipeline was run on ICA starting with BAM files. A workaround is to download data locally first.
6200: Variant filtering based on SpliceAI score and gene name may return incorrect results due to use of different transcripts.
6231: Previewing Report template does not work on Safari browser.
6332, 6378: Fusion representation is impacted if one breakend is in chrM.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
6623: Oncogenicity prediction tool does not correctly calculate OP3 criterion for PI3CA p.Met1? variant.
7284: Some recruiting clinical trials could be omitted if their status changed from “suspended” to “recruiting”.
7336: When assertions from multiple knowledge sources are present on different transcripts of a variant, the default transcript may not be the transcript with the highest oncogenic classification.
7399: In extremely rare scenarios, if a large variant or splice variant overlaps with multiple variants in another case the seen count is incremented by more than 1.
7514a: OncoKB assertions that have “Colorectal cancer excluded” in disease name are displayed on Biomarker page, for example, a Level 1A record for BRAF V600E.
8403: Annotations including CGC, ClinGen, OMIM, 1000 genomes, and custom annotations are not displayed or filterable for SV deletions and CNVs over 10 Mb in size. It can cause these events to be omitted when filtering by annotations. Review of genome view and Circos plots are recommended to identify these larger events (seen as a large deletion arc in the SV track or abnormal coverage in the coverage and CNV track) and also by filtering for SVs and CNVs with length over 10 Mb.
8413: Column order change in the Variants tab is not remembered after changing column width.
2593 (local): Unable to create new user using “Add user“ action if the current logged Administrator user edits their profile from User list -> Edit action against their profile. Requires a re-login to resume new user creation.
2571 (local): Delete case action intermittently does not delete the complete Case data folder due to few non-Connected Insights NFS protocol’s hidden files.
2498, 2580 (local): Case processing fails with “Has issues“ status or may end up in “Processing“ status indefinitely if DRAGEN encounters an abrupt shutdown. In such cases, try deleting the case and reupload or contact Illumina Support team.
2570 (local): Intermittently Report PDF is missing “Assay Gene List“ title when a report is generated with the Default Report template version 2.
2490 (local): My Knowledge Base bulk upload assertions file fails with Nirvana validation error when the bulk upload is initiated along with multiple cases are in progress.
1608 (local): Admin console and Walkme menu do not open from the IGV viewer page.
1495 (local): After a system reboot, the CLI Uploader on the Configuration page shows as “Offline“ and necessitates manual restart of the service.
Product Limitations:
191: The software does not yet display records related to co-occurring variants.
895 and 1415: The software does not consider partial exclusion criteria while listing clinical trials, for example, the trial with the following criteria will be prioritized for all listed markers “Patients with known EGFR mutations (except exon 20 insertion), BRAF mutations (V600), MET Exon14 skipping or ALK or ROS1 translocations that can be treated with oral tyrosine kinase inhibitors are excluded”.
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Assertions created for variants uploaded with GRCh37 reference genome are not displayed for the same variants uploaded with the GRCh38 reference genome.
6099: Unable to create assertions for extremely large copy number variants or structural variants.
6614: Total depth and VAF are not calculated for RNA splice variants.
3729: DUX4 Rearrangement Caller in scope of DRAGEN Somatic Whole Genome v4.3 pipeline is not supported.
2535 (local): Software requires only Connected Insights packages present in the package source location when initiating a software or dependent package update.
2536 (local): Software displays “Software update failed” error for pre-installation checks failure when “Install All” is initiated.
Revision History
Version
Description of Change
02
- Updated: Known issues related to Connected Insights - Local software tagged as (local) and 2 product limitation of Connected Insights - Local software
01
- Updated: Known issue 8403 on CNVs over 10 Mb in size. - Added new compatible pipelines. - Added a limitation related to DUX4 Rearrangement Caller
00
Initial Release
v4.0.1
These Release Notes include new features, product limitations and known issues for Illumina Connected Insights v4.0.1.
New Features
Compatibility with DRAGEN TruSight Oncology 500 ctDNA v2.5.0 analysis software.
Defect Repairs
7485: Issue causing display of additional erroneous records from OncoKB on the biomarker pages for copy number gain variants (additional records are correct but associated with different variant classes).
7494: Issue preventing data upload in certain cases due to Alt contigs in coverage files.
7517: Issue preventing display of certain assertions from OncoKB on biomarker pages.
9411: Issue impacting display of QC metrics on the Overview page and Lab QC page in certain cases generated with the previous software versions.
9412: Issue impacting variant display on the Variants page in certain cases generated with the version v2.0.0.
9487: Sorting on the Custom Case Data page.
Known Issues
940: Therapy packs (e.g., Orsythia 28 Day Pack) may fail validation when adding them to an assertion.
1298: Read order in the BAM track may change after zooming in the IGV viewer.
3409: CN calls produced by DRAGEN TruSight Oncology 500 v2.5.2+ Analysis Software with CN=2 or CN > 2 and annotated as
<DEL>are not displayed.3594: Command Line Interface logs may take long time to sync (up to 4 hours) and not reflect latest actions if exported before the sync is completed.
3723: The software will display two duplicating variants if they were called by two different pipelines, for example, a small variant caller and a structural variant caller.
3777: Users will not be able to upload NR transcripts into My Knowledge Base. JAX-CKB assertions will not be displayed for NR transcript variants.
3835: Filtering for variant type “Copy Number Neutral” returns no results even if CNV with CN=2 are present.
3836: Biomarker page may not open and an error message “Variant not found in index” will be displayed when clicking on some events on the Genome View plot and the Variants page.
3934: Reopening an approved report does not trigger notification of assertion update even if there are updated assertions for the case.
3943: For DRAGEN RNA pipeline, RNA BAM track in IGV is not enabled by default for small variants and needs to be turned on manually.
5074: Copy number gain false positive findings may be presented for non-PAR chrX regions.
5080: A case may move to “Has issues” status if its reprocessing is ongoing on one tab and a user tries to approve the report on another browser tab.
5133: User preferred transcripts for a gene may not be prioritized as expected if user provides incorrect gene-transcript pairs when uploading the file with user preferred transcripts.
5263: A valid case can be ingested with a status “Has issues” again if it was originally ingested with “Has issues” and there was a failure with report automation.
5491: Coverage graph may not display findings if they use a different transcript rather than the one used to create the graph.
5494: In IGV, the SV variant track may show only one SV when multiple SVs are present in the same locus.
5599: Records from CIViC knowledge base for broad variant categories like “PTEN mutation” will match all variants for the given gene even when match is not appropriate, for example, it will match records for exon variants to intron variants.
6199: Data upload of analysis results generated by the DRAGEN WGS Somatic v4.2 pipeline fails when the pipeline was run on ICA starting with BAM files. A workaround is to download data locally first.
6200: Variant filtering based on SpliceAI score and gene name may return incorrect results due to use of different transcripts.
6231: Previewing Report template does not work on Safari browser.
6332, 6378: Fusion representation is impacted if one breakend is in chrM.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
6623: Oncogenicity prediction tool does not correctly calculate OP3 criterion for PI3CA p.Met1? variant.
7241: Glioblastoma assertions on glioblastoma reports may appear in the other diseases column.
7284: Some recruiting clinical trials could be omitted if their status changed from “suspended” to “recruiting”.
7336: When assertions from multiple knowledge sources are present on different transcripts of a variant, the default transcript may not be the transcript with the highest oncogenic classification.
7399: In extremely rare scenarios, if a large variant or splice variant overlaps with multiple variants in another case the seen count is incremented by more than 1.
7429: RNA QC metrics for a merged case may not show on the Overview page in certain scenarios but are accessible from Lab QC.
7514a: OncoKB assertions that have “Colorectal cancer excluded” in disease name are displayed on Biomarker page, for example, a Level 1A record for BRAF V600E.
7514b: OncoKB assertions for colorectal cancer are not displayed on the Biomarker page when filtered for “Malignant tumor of large intestine” or other related terms. To display them, remove disease filter.
Product Limitations
191: The software does not yet display records related to co-occurring variants.
895 and 1415: The software does not consider partial exclusion criteria while listing clinical trials, for example, the trial with the following criteria will be prioritized for all listed markers “Patients with known EGFR mutations (except exon 20 insertion), BRAF mutations (V600), MET Exon14 skipping or ALK or ROS1 translocations that can be treated with oral tyrosine kinase inhibitors are excluded”.
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
2850, 5116, 5743: Few assertions and clinical trials from JAX-CKB for Infant-type hemispheric glioma, oligodendroglioma IDH-mutant and 1p/19q-codeleted grade 2, and oligodendroglioma IDH-mutant, 1p/19q-codeleted grade 3 and several other cancer types are not displayed in Biomarker pages.
3451: Assertions created for variants uploaded with GRCh37 reference genome are not displayed for the same variants uploaded with the GRCh38 reference genome.
6099: Unable to create assertions for extremely large copy number variants or structural variants.
6614: Total depth and VAF are not calculated for RNA splice variants.
9976: The software does not to upload and display CNV variants for TSO 500 non-HRD samples if a secondary analysis run includes TSO 500 samples with and without HRD and is ingested to Connected Insights using the data upload setting "DRAGEN TruSight Oncology 500 Analysis Software - 2.5.2 (with HRD)". Please run the secondary analysis separately for HRD and non-HRD samples until the improvement is implemented in v5.0.0. If you require additional assistance, please contact Illumina technical support or your local field support representative.
Revision History
Version
Description of Change
01
- Added a known issue SET-9976 on CNV upload for TSO 500
00
Initial Release
v4.0.0
These Release Notes include new features, product limitations and known issues for Illumina Connected Insights v4.0.0.
New Features
Integration of OncoKB™ by Memorial Sloan Kettering Cancer Center as an additional knowledge base
Automated oncogenicity prediction tool scoring variants to assign oncogenic, likely oncogenic, variant of unknown significance (VUS), likely benign and benign categories
Ability to create cases (one case or a batch of cases) by uploading Case Custom Metadata file ahead of uploading secondary analysis output data
Ability to include DNA and RNA samples into the same case using a Case Custom Metadata file if DNA and RNA secondary analysis outputs are coming from different pipelines, for example, DRAGEN TruSight Oncology 500 and DRAGEN RNA
Total depth (a sum of paired reads and split reads for reference and alternate alleles) and VAF (a proportion of supporting reads over total depth) are now calculated for RNA fusions and structural variants
RNA fusions and translocation structural variants are now each represented as a single record on the Overview and Variants page.
Visualize tab in the Biomarker page to display a genome browser showing position of the variant, location of protein domains, partner and breakpoint details in case of RNA fusions and structural variants, and other information
A plot with the number of lab’s samples including a particular variant in the Cancer Datasets section of the Biomarker page
A separate section listing Variants of Unknown Significance (VUS) in the report template
Audit logs accessible via API covering a comprehensive set of user actions
Ability to upload custom annotation. Specifically, for a list of variants users can upload categorical values, numerical values and frequencies and use them for display, sorting and filtering.
Ability to delete cases via user interface
Links to Mastermind by Genomenon and LitVar triggering smart variant search in the Biomarker page
Defect Repairs
4007: Fixed an issue of updates made to case information were not reflected in the report preview page unless the preview page is refreshed. The case information appears updated in the approved report.
4734: Fixed an issue related to CIViC evidence for frameshift variants.
5617: Fixed an issue of not recognizing a gene name if a space after the gene name is entered.
5618: Fixed an issue related to display of fusion breakpoints in key genes on the Overview page.
5976: Fixed an issue of how Report Automation feature was including in reports more and less specific assertions.
6022: Fixed an issue of displaying Gain-of-Function (GOF) and Loss-of-Function (LOF) consequence for a variant after archiving an assertion interpreting it as GOF or LOF and updating the case.
6068: Fixed an issue of erroneous display of the on/off status of the Report Automation feature in older versions of Test Definitions.
6126: Fixed an issue of displaying a wrong user on the Configuration page for Report Automation.
6194: Fixed an issue of Genome Coverage graphs on the Overview page not filtering the duplicate reads.
Known Issues
940: Therapy packs (e.g., Orsythia 28 Day Pack) may fail validation when adding them to an assertion.
1298: Read order in the BAM track may change after zooming in the IGV viewer.
3409: CN calls produced by DRAGEN TruSight Oncology 500 v2.5.2+ Analysis Software with CN=2 or CN > 2 and annotated as
<DEL>are not displayed.3594: Command Line Interface logs may take long time to sync (up to 4 hours) and not reflect latest actions if exported before the sync is completed.
3723: The software will display two duplicating variants if they were called by two different pipelines, for example, a small variant caller and a structural variant caller.
3777: Users will not be able to upload NR transcripts into My Knowledge Base. JAX-CKB assertions will not be displayed for NR transcript variants.
3835: Filtering for variant type “Copy Number Neutral” returns no results even if CNV with CN=2 are present.
3836: Biomarker page may not open and an error message “Variant not found in index” will be displayed when clicking on some events on the Genome View plot and the Variants page.
3934: Reopening an approved report does not trigger notification of assertion update even if there are updated assertions for the case.
3943: For DRAGEN RNA pipeline, RNA BAM track in IGV is not enabled by default for small variants and needs to be turned on manually.
5074: Copy number gain false positive findings may be presented for non-PAR chrX regions.
5080: A case may move to “Has issues” status if its reprocessing is ongoing on one tab and a user tries to approve the report on another browser tab.
5133: User preferred transcripts for a gene may not be prioritized as expected if user provides incorrect gene-transcript pairs when uploading the file with user preferred transcripts.
5263: A valid case can be ingested with a status “Has issues” again if it was originally ingested with “Has issues” and there was a failure with report automation.
5491: Coverage graph may not display findings if they use a different transcript rather than the one used to create the graph.
5494: In IGV, the SV variant track may show only one SV when multiple SVs are present in the same locus.
5599: Records from CIViC knowledge base for broad variant categories like “PTEN mutation” will match all variants for the given gene even when match is not appropriate, for example, it will match records for exon variants to intron variants.
6199: Data upload of analysis results generated by the DRAGEN WGS Somatic v4.2 pipeline fails when the pipeline was run on ICA starting with BAM files. A workaround is to download data locally first.
6200: Variant filtering based on SpliceAI score and gene name may return incorrect results due to use of different transcripts.
6231: Previewing Report template does not work on Safari browser.
6332, 6378: Fusion representation is impacted if one breakend is in chrM.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
6623: Oncogenicity prediction tool does not correctly calculate OP3 criterion for PI3CA p.Met1? variant.
7241: Glioblastoma assertions on glioblastoma reports may appear in the other diseases column.
7284: Some recruiting clinical trials could be omitted if their status changed from “suspended” to “recruiting”.
7336: When assertions from multiple knowledge sources are present on different transcripts of a variant, the default transcript may not be the transcript with the highest oncogenic classification.
7399: In extremely rare scenarios, if a large variant or splice variant overlaps with multiple variants in another case the seen count is incremented by more than 1.
7429: RNA QC metrics for a merged case may not show on the overview pagein certain scenarios, but are accessible from Lab QC.
Product Limitations
191: The software does not yet display records related to co-occurring variants.
895 and 1415: The software does not consider partial exclusion criteria while listing clinical trials, for example, the trial with the following criteria will be prioritized for all listed markers “Patients with known EGFR mutations (except exon 20 insertion), BRAF mutations (V600), MET Exon14 skipping or ALK or ROS1 translocations that can be treated with oral tyrosine kinase inhibitors are excluded”.
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
2850, 5116, 5743: Few assertions and clinical trials from JAX-CKB for Infant-type hemispheric glioma, oligodendroglioma IDH-mutant and 1p/19q-codeleted grade 2, and oligodendroglioma IDH-mutant, 1p/19q-codeleted grade 3 and several other cancer types are not displayed in Biomarker pages.
3451: Assertions created for variants uploaded with GRCh37 reference genome are not displayed for the same variants uploaded with the GRCh38 reference genome.
6099: Unable to create assertions for extremely large copy number variants or structural variants
6614: Total depth and VAF are not calculated for RNA splice variants
Revision History
Version
Description of Change
00
Initial Release
Last updated