<5.4 Release Notes
v5.3.3
These release notes include new features, product limitations and known issues for Connected Insights v5.3.3.
New Features:
None
Defect Repairs:
13046: Fixed an issue where CNV deletions with a copy number of 2 were incorrectly tagged as CNV Neutral. This caused affected variants to lose biological classification and actionability annotations, potentially excluding reportable deletions from filtered views.
13060: Improved case list page load times.
Known Issues:
1298: Read order in the BAM track may change after zooming in the IGV viewer.
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.
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.
5133: User preferred transcripts for a gene may not be prioritized as expected if user uploads preferred transcripts file with incorrect gene-transcript pairs
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.
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.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
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.
10844: Data cannot be sent to IGV desktop when using Connected Insights on Safari.
10920: Merging a case containing tumor and normal samples with a case containing DRAGEN RNA splice variants may fail.
12040: Gene coverage threshold doesn't carry over after merging DNA and RNA cases.
12024: Some benign variants are not automatically marked as reviewed.
12023: Sample metrics filters (e.g., VAF, read depth) may error when applied to cases ingested in 4.0, 5.0, and 5.1.
12017: Some co-occurring assertions for oncogenic variants may display for copy number gains when they are not applicable.
12015: NCT06904066 (phase I) is not ingested as since clinical trials are not yet supported for HLA genotypes.
11927: Report automation may report clinical trials for Australia when EU is specified.
11905: Report automation does not report FDA resistance assertions when FDA is specified.
11904: Once a gene threshold has been specified, and the disease is changed for a case ingested in <5.3, only new disease-specific genes will have the specified threshold applied.
11900: When report automation is re-run on cases ingested in <5.3, assertions reported may be out-of-sync with assertions displayed.
11151: In the transcript modal for RNA fusions, some transcript pairs may be annotated as inframe when at least one of the other transcripts pairs are inframe.
10828: When merging a TN DNA case with an RNA case, the DNA BAM may not display in biomarker details.
10809: Some non-PASS CNVs are not plotted in the correct color in the whole genome and biomarker details visualization.
Product Limitations:
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Nucleotide-level 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.
10660: OncoKB PTD assertions are not yet supported.
Revision History
00
Initial Release
v5.3.2
These release notes include new features, product limitations and known issues for Connected Insights v5.3.2.
New Features:
None
Defect Repairs:
12416: Fixed an issue where archived assertions on a variant were not visually indicated in the results or variants pages, which could block report sign-off without a clear way to identify the affected variants.
12626: Resolved an intermittent connection timeout when communicating with Connected Analytics during sample ingestion.
12624, 12296: Fixed an issue where TMB and MSI biomarker values were missing for merged DNA+RNA analysis cases created via CSV placeholder upload.
12158: Resolved a performance issue where assertion updates on large cases could take several hours to complete.
13040: Improved performance of the report generation when there are a high number of low coverage regions.
12381: Pipeline overview section of Lab QC is now included in the report JSON
12982: Removed caching of error responses during Ontology service failures while fetching low coverage regions.
Known Issues:
1298: Read order in the BAM track may change after zooming in the IGV viewer.
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.
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.
5133: User preferred transcripts for a gene may not be prioritized as expected if user uploads preferred transcripts file with incorrect gene-transcript pairs
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.
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.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
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.
10844: Data cannot be sent to IGV desktop when using Connected Insights on Safari.
10920: Merging a case containing tumor and normal samples with a case containing DRAGEN RNA splice variants may fail.
12040: Gene coverage threshold doesn't carry over after merging DNA and RNA cases.
12024: Some benign variants are not automatically marked as reviewed.
12023: Sample metrics filters (e.g., VAF, read depth) may error when applied to cases ingested in 4.0, 5.0, and 5.1.
12017: Some co-occurring assertions for oncogenic variants may display for copy number gains when they are not applicable.
12015: NCT06904066 (phase I) is not ingested as since clinical trials are not yet supported for HLA genotypes.
11927: Report automation may report clinical trials for Australia when EU is specified.
11905: Report automation does not report FDA resistance assertions when FDA is specified.
11904: Once a gene threshold has been specified, and the disease is changed for a case ingested in <5.3, only new disease-specific genes will have the specified threshold applied.
11900: When report automation is re-run on cases ingested in <5.3, assertions reported may be out-of-sync with assertions displayed.
11151: In the transcript modal for RNA fusions, some transcript pairs may be annotated as inframe when at least one of the other transcripts pairs are inframe.
10828: When merging a TN DNA case with an RNA case, the DNA BAM may not display in biomarker details.
10809: Some non-PASS CNVs are not plotted in the correct color in the whole genome and biomarker details visualization.
Product Limitations:
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Nucleotide-level 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.
10660: OncoKB PTD assertions are not yet supported.
Revision History
00
Initial Release
v5.3.1
These release notes include new features, product limitations and known issues for Connected Insights v5.3.1.
New Features:
None
Defect Repairs:
12215: Fixed an issue where the deprecated Sample Metrics filter from earlier releases did not appear in the UI after upgrading a workgroup to v5.3, even though the filter logic was still functioning.
12180: Resolved a discrepancy between the oncogenicity prediction shown in the Variants page and the prediction displayed on the variant details screen.
12313: Fixed an issue where fewer variants were included in mutational signature analysis for GRCh37 cases.
12358: We have resolved ontology mapping and hierarchy issues that could cause certain assertions to be prioritized incorrectly. Please refer to the list of affected diseases below. Cases involving these diseases may require reprocessing to ensure results reflect the corrected prioritization.
Adenosquamous carcinoma of lung (SNOMEDCT: 1260042002)
Carcinosarcoma of lung (SNOMEDCT: 1255658004)
Endometrioid carcinoma of endometrium (SNOMEDCT: 1260086007)
Ewing sarcoma of bone of rib (SNOMEDCT: 1254781000)
Gastrointestinal stromal tumor (SNOMEDCT: 420120006)
Gastrointestinal stromal tumor (SNOMEDCT: 1187383001)
Hypoplastic myelodysplastic syndrome (SNOMEDCT: 1260270005)
Malignant colorectal neoplasm (SNOMEDCT: 1286877004)
Malignant neoplasm (SNOMEDCT: 1240414004)
Metastatic adenocarcinoma of lymph nodes of multiple sites (SNOMEDCT: 1197330006)
Metastatic adenoid cystic carcinoma (SNOMEDCT: 40581000146107)
Metastatic adenosquamous carcinoma (SNOMEDCT: 1264116009)
Metastatic carcinoma to breast (SNOMEDCT: 1264495000)
Metastatic carcinoma to stomach (SNOMEDCT: 1237525006)
Metastatic malignant neoplasm to colorectum (SNOMEDCT: 1286863002)
Mucinous adenocarcinoma of lung (SNOMEDCT: 1260057009)
Osteosarcoma (SNOMEDCT: 189878003)
Primary endometrioid carcinoma of ovary (SNOMEDCT: 1268349000)
Primary infiltrating ductal carcinoma of upper outer quadrant of right female breast (SNOMEDCT: 1259479001)
Primary serous papillary cystadenocarcinoma ovary (SNOMEDCT: 1259384008)
Primary undifferentiated carcinoma of ovary (SNOMEDCT: 1259386005)
Sarcoma (SNOMEDCT: 1187396000)
Transitional cell carcinoma of upper urinary tract (SNOMEDCT: 1208451008)
Undifferentiated carcinoma of endometrium (SNOMEDCT: 1255394008)
Undifferentiated pleomorphic sarcoma (SNOMEDCT: 1290732004)
12468: Resolved an issue causing OncoKB biological classification assertions to be missing for AR‑V7.
Known Issues:
1298: Read order in the BAM track may change after zooming in the IGV viewer.
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.
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.
5133: User preferred transcripts for a gene may not be prioritized as expected if user uploads preferred transcripts file with incorrect gene-transcript pairs
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.
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.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
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.
10844: Data cannot be sent to IGV desktop when using Connected Insights on Safari.
10920: Merging a case containing tumor and normal samples with a case containing DRAGEN RNA splice variants may fail.
12040: Gene coverage threshold doesn't carry over after merging DNA and RNA cases.
12024: Some benign variants are not automatically marked as reviewed.
12023: Sample metrics filters (e.g., VAF, read depth) may error when applied to cases ingested in 4.0, 5.0, and 5.1.
12017: Some co-occurring assertions for oncogenic variants may display for copy number gains when they are not applicable.
12015: NCT06904066 (phase I) is not ingested as since clinical trials are not yet supported for HLA genotypes.
11927: Report automation may report clinical trials for Australia when EU is specified.
11905: Report automation does not report FDA resistance assertions when FDA is specified.
11904: Once a gene threshold has been specified, and the disease is changed for a case ingested in <5.3, only new disease-specific genes will have the specified threshold applied.
11900: When report automation is re-run on cases ingested in <5.3, assertions reported may be out-of-sync with assertions displayed.
11151: In the transcript modal for RNA fusions, some transcript pairs may be annotated as inframe when at least one of the other transcripts pairs are inframe.
10828: When merging a TN DNA case with an RNA case, the DNA BAM may not display in biomarker details.
10809: Some non-PASS CNVs are not plotted in the correct color in the whole genome and biomarker details visualization.
Product Limitations:
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Nucleotide-level 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.
10660: OncoKB PTD assertions are not yet supported.
Revision History
00
Initial Release
01
Add fix of 12313 into scope.
02
Added 12358, 12468
v5.3.0
These release notes include new features, product limitations and known issues for Connected Insights v5.3.0.
New Features:
Compatibility
Create cases via UI / VCF upload
Latest TSO ctDNA versions
Latest DRAGEN Amplicon versions
IHC/FISH results (e.g., ERBB2 positive) via API
HLA typing results
Configuration
Configure gene coverage thresholds
Case Management
Case progress tracking
Streamlined overview page
Changed status "Report(s) Signed Off" to "Completed"
Variant Prioritization
Filter for inframe / frameshift fusions
Free text search across additional variant grid columns
Filter variants by VCF INFO values
Interpretation
Inframe / frameshift fusion annotation
Trial inclusion and exclusion matching
Age, sex, location trial matching
Co-occurring biomarker evidence
IHC/FISH evidence
HLA evidence
LOH evidence
Promoter evidence
Save assertion without adding to report
Oncogenicity prediction accuracy improvements
AML classification & risk stratification accuracy improvements
Reporting
Report low coverage regions
Expanded UI-based report customizations
Defect Repairs:
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.
7514: OncoKB assertion for BRAF V600E for all solid tumors excluding colorectal cancer is shown in colorectal cancer case.
9374: Variant count is incorrect for copy number neutral variants.
10960: Exon track may not display for Ensembl transcripts within variant details page.
11010: If the workgroup creator leaves the workgroup, there may be issues accessing necessary data.
11181: Variants with FILTER value "." are not returned when filtering for variants with FILTER PASS.
Known Issues:
1298: Read order in the BAM track may change after zooming in the IGV viewer.
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.
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.
5133: User preferred transcripts for a gene may not be prioritized as expected if user uploads preferred transcripts file with incorrect gene-transcript pairs
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.
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.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
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.
10844: Data cannot be sent to IGV desktop when using Connected Insights on Safari.
10920: Merging a case containing tumor and normal samples with a case containing DRAGEN RNA splice variants may fail.
12040: Gene coverage threshold doesn't carry over after merging DNA and RNA cases.
12024: Some benign variants are not automatically marked as reviewed.
12023: Sample metrics filters (e.g., VAF, read depth) may error when applied to cases ingested in 4.0, 5.0, and 5.1.
12017: Some co-occurring assertions for oncogenic variants may display for copy number gains when they are not applicable.
12015: NCT06904066 (phase I) is not ingested as since clinical trials are not yet supported for HLA genotypes.
11927: Report automation may report clinical trials for Australia when EU is specified.
11905: Report automation does not report FDA resistance assertions when FDA is specified.
11904: Once a gene threshold has been specified, and the disease is changed for a case ingested in <5.3, only new disease-specific genes will have the specified threshold applied.
11900: When report automation is re-run on cases ingested in <5.3, assertions reported may be out-of-sync with assertions displayed.
11151: In the transcript modal for RNA fusions, some transcript pairs may be annotated as inframe when at least one of the other transcripts pairs are inframe.
10828: When merging a TN DNA case with an RNA case, the DNA BAM may not display in biomarker details.
10809: Some non-PASS CNVs are not plotted in the correct color in the whole genome and biomarker details visualization.
Product Limitations:
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Nucleotide-level 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.
10660: OncoKB PTD assertions are not yet supported.
Revision History
00
Initial Release
v5.2.6
These release notes include new features, product limitations and known issues for Connected Insights v5.2.6.
New Features:
None
Defect Repairs:
13060: Improved case list page load times.
Known Issues:
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.
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.
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.
5133: User preferred transcripts for a gene may not be prioritized as expected if user uploads preferred transcripts file with incorrect gene-transcript pairs
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.
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.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
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.
7514: OncoKB assertion for BRAF V600E for all solid tumors excluding colorectal cancer is shown in colorectal cancer case.
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.
10844: Data cannot be sent to IGV desktop when using Connected Insights on Safari.
10920: Merging a case containing tumor and normal samples with a case containing DRAGEN RNA splice variants may fail.
10960: Exon track may not display for Ensembl transcripts within variant details page.
11010: If the workgroup creator leaves the workgroup, there may be issues accessing necessary data.
11181: Variants with FILTER value "." are not returned when filtering for variants with FILTER PASS.
Product Limitations:
191: The software does not yet display records related to co-occurring variants.
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Nucleotide-level 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.
Revision History
00
Initial Release
v5.2.5
These release notes include new features, product limitations and known issues for Connected Insights v5.2.5.
New Features:
None
Defect Repairs:
12416: Fixed an issue where archived assertions on a variant were not visually indicated in the results or variants pages, which could block report sign-off without a clear way to identify the affected variants.
12626: Resolved an intermittent connection timeout when communicating with Connected Analytics during sample ingestion.
12381: Pipeline overview section of Lab QC is now included in the report JSON
Known Issues:
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.
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.
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.
5133: User preferred transcripts for a gene may not be prioritized as expected if user uploads preferred transcripts file with incorrect gene-transcript pairs
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.
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.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
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.
7514: OncoKB assertion for BRAF V600E for all solid tumors excluding colorectal cancer is shown in colorectal cancer case.
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.
10844: Data cannot be sent to IGV desktop when using Connected Insights on Safari.
10920: Merging a case containing tumor and normal samples with a case containing DRAGEN RNA splice variants may fail.
10960: Exon track may not display for Ensembl transcripts within variant details page.
11010: If the workgroup creator leaves the workgroup, there may be issues accessing necessary data.
11181: Variants with FILTER value "." are not returned when filtering for variants with FILTER PASS.
Product Limitations:
191: The software does not yet display records related to co-occurring variants.
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Nucleotide-level 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.
Revision History
00
Initial Release
v5.2.4
These release notes include new features, product limitations and known issues for Connected Insights v5.2.4.
New Features:
None
Defect Repairs:
12180: Resolved a discrepancy between the oncogenicity score shown in the Variants page and the score displayed on the variant detail screen.
12313: Fixed an issue where fewer variants were included in mutational signature analysis for GRCh37 cases.
12358: We have resolved ontology mapping and hierarchy issues that could cause certain assertions to be prioritized incorrectly. Please refer to the list of affected diseases below. Cases involving these diseases may require reprocessing to ensure results reflect the corrected prioritization.
Adenosquamous carcinoma of lung (SNOMEDCT: 1260042002)
Carcinosarcoma of lung (SNOMEDCT: 1255658004)
Endometrioid carcinoma of endometrium (SNOMEDCT: 1260086007)
Ewing sarcoma of bone of rib (SNOMEDCT: 1254781000)
Gastrointestinal stromal tumor (SNOMEDCT: 420120006)
Gastrointestinal stromal tumor (SNOMEDCT: 1187383001)
Hypoplastic myelodysplastic syndrome (SNOMEDCT: 1260270005)
Malignant colorectal neoplasm (SNOMEDCT: 1286877004)
Malignant neoplasm (SNOMEDCT: 1240414004)
Metastatic adenocarcinoma of lymph nodes of multiple sites (SNOMEDCT: 1197330006)
Metastatic adenoid cystic carcinoma (SNOMEDCT: 40581000146107)
Metastatic adenosquamous carcinoma (SNOMEDCT: 1264116009)
Metastatic carcinoma to breast (SNOMEDCT: 1264495000)
Metastatic carcinoma to stomach (SNOMEDCT: 1237525006)
Metastatic malignant neoplasm to colorectum (SNOMEDCT: 1286863002)
Mucinous adenocarcinoma of lung (SNOMEDCT: 1260057009)
Osteosarcoma (SNOMEDCT: 189878003)
Primary endometrioid carcinoma of ovary (SNOMEDCT: 1268349000)
Primary infiltrating ductal carcinoma of upper outer quadrant of right female breast (SNOMEDCT: 1259479001)
Primary serous papillary cystadenocarcinoma ovary (SNOMEDCT: 1259384008)
Primary undifferentiated carcinoma of ovary (SNOMEDCT: 1259386005)
Sarcoma (SNOMEDCT: 1187396000)
Transitional cell carcinoma of upper urinary tract (SNOMEDCT: 1208451008)
Undifferentiated carcinoma of endometrium (SNOMEDCT: 1255394008)
Undifferentiated pleomorphic sarcoma (SNOMEDCT: 1290732004)
12468: Resolved an issue causing OncoKB biological classification assertions to be missing for AR‑V7.
Known Issues:
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.
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.
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.
5133: User preferred transcripts for a gene may not be prioritized as expected if user uploads preferred transcripts file with incorrect gene-transcript pairs
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.
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.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
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.
7514: OncoKB assertion for BRAF V600E for all solid tumors excluding colorectal cancer is shown in colorectal cancer case.
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.
10844: Data cannot be sent to IGV desktop when using Connected Insights on Safari.
10920: Merging a case containing tumor and normal samples with a case containing DRAGEN RNA splice variants may fail.
10960: Exon track may not display for Ensembl transcripts within variant details page.
11010: If the workgroup creator leaves the workgroup, there may be issues accessing necessary data.
11181: Variants with FILTER value "." are not returned when filtering for variants with FILTER PASS.
Product Limitations:
191: The software does not yet display records related to co-occurring variants.
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Nucleotide-level 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.
Revision History
00
Initial Release
01
Add fix of 12313 into scope.
02
Added 12358, 12468
v5.2.3
These release notes include new features, product limitations and known issues for Connected Insights v5.2.3.
New Features:
None
Defect Repairs:
We’ve made some important updates to improve your experience. Here’s what’s new:
QC metrics now display correctly for applicable DRAGEN TSO 500 cases.
Enhancements have been made to ensure more consistent and reliable case ingestion.
Users can once again create custom pipelines without interruption.
Known Issues:
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.
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.
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.
5133: User preferred transcripts for a gene may not be prioritized as expected if user uploads preferred transcripts file with incorrect gene-transcript pairs
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.
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.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
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.
7514: OncoKB assertion for BRAF V600E for all solid tumors excluding colorectal cancer is shown in colorectal cancer case.
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.
10844: Data cannot be sent to IGV desktop when using Connected Insights on Safari.
10920: Merging a case containing tumor and normal samples with a case containing DRAGEN RNA splice variants may fail.
10960: Exon track may not display for Ensembl transcripts within variant details page.
11010: If the workgroup creator leaves the workgroup, there may be issues accessing necessary data.
11181: Variants with FILTER value "." are not returned when filtering for variants with FILTER PASS.
Product Limitations:
191: The software does not yet display records related to co-occurring variants.
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Nucleotide-level 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.
Revision History
00
Initial Release
v5.2.2
These release notes include new features, product limitations and known issues for Connected Insights v5.2.2.
New Features:
Compatibility with DRAGEN 4.4.6 (Amplicon, Somatic Enrichment, RNA)
Compatibility with TSO 500 ctDNA 2.6.3
Defect Repairs:
We’ve enhanced the stability and reliability of case ingestion. The following issues have been resolved:
11014, 10962: Fixed an issue preventing access to reports for certain cases.
11074, 10997: Resolved a defect that blocked visualizations from loading for some cases.
11135: Addressed a memory exhaustion issue occurring during ingestion of specific cases.
Known Issues:
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.
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.
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.
5133: User preferred transcripts for a gene may not be prioritized as expected if user uploads preferred transcripts file with incorrect gene-transcript pairs
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.
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.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
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.
7514: OncoKB assertion for BRAF V600E for all solid tumors excluding colorectal cancer is shown in colorectal cancer case.
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.
10844: Data cannot be sent to IGV desktop when using Connected Insights on Safari.
10920: Merging a case containing tumor and normal samples with a case containing DRAGEN RNA splice variants may fail.
10960: Exon track may not display for Ensembl transcripts within variant details page.
11010: If the workgroup creator leaves the workgroup, there may be issues accessing necessary data.
11181: Variants with FILTER value "." are not returned when filtering for variants with FILTER PASS.
Product Limitations:
191: The software does not yet display records related to co-occurring variants.
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Nucleotide-level 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.
Revision History
00
Initial Release
v5.2.2 Local
These release notes include new features, product limitations and known issues for Connected Insights Local v5.2.2.
New Features:
Compatibility with DRAGEN TSO 500 ctDNA 2.6.3 and 2.6.4
Defect Repairs:
3883 (local): 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.3885 (local): Variants with FILTER value "." were not returned when filtering for variants with FILTER PASS.
3889 (local): Fixed an issue where the CNV variants were incorrectly ingested as Tandem Duplication from Local Run Manager TruSight Tumor 15 Analysis module v2.1.
3894 (local): Fixed an issue where the VAF was incorrectly calculated for varaints with REF supporting read as ".".
3897 (local): Fixed an issue where the Variant summary information was missing in the Report pdf.
3937 (local): Resolved a discrepancy between the Oncogenicity prediction shown in the Variants page and the prediction displayed on the variant details screen.
4004 (local): Oncogenicity prediction in variant grid is incorrect after case gone through "assertion update"
4008 (local): Fixed an issue where the Temporal logs are not cleaned up and fills up the /var/log storage.
4017 (local): Fixed an issue where CNV deletions with a copy number of 2 were incorrectly tagged as CNV Neutral. This caused affected variants to lose biological classification and actionability annotations, potentially excluding reportable deletions from filtered views.
Known Issues:
4021 (local): Illumina License manager is not auto updated when the ICI local Software is updated from v5.2.1 to 5.2.2. Requires manual update.
2571 (local): The 'Delete Case' action intermittently fails to remove the entire Case data folder due to hidden files associated with non-Connected Insights NFS storage protocols.
2580 (local): Case processing fails with “Has issues“ status or may get stuck in “Processing“ status indefinitely if DRAGEN encounters an abrupt shutdown. In such cases, try deleting the case and re-upload or contact Illumina Support team.
2490 (local): My Knowledge Base bulk upload assertions file fails with Nirvana validation error when the bulk upload is initiated along with multiple cases analysis in progress.
1608 (local): Admin console and Walkme menu do not open from the IGV viewer page.
3499 (local): Walkme Walkthroughs are not working.
3483 (local): Case custom data upload fails using the auto-uplod "Data Upload" daemon. Alternatively use the "+New Case" action on Case list page to upload the csv files containing the Case data.
3477 (local) Storage usage displayed on Administration console page does not consider all the folder used by Connected Insights. Alternately monitor the Storage usage from the DRAGEN Server terminal.
3464 (local): IGV desktop intermittently does not load the VCF/BAM tracks. Alternatively use the IGV web version to interpret variant visualization.
3514 (local): The software does not prevent subsequent software or data package updates from Administration console, when a case ingestion analysis is currently in progress. Perform updates when the application is idle and are not currently processing any case ingestion.
1495 (local): After a system reboot, the CLI Uploader on the Configuration page shows as “Offline“ and necessitates manual restart of the service. Refer Trouble shoot section for command to restart the Daemon service.
v5.2.1
These release notes include new features, product limitations and known issues for Connected Insights v5.2.1.
New Features:
Compatibility with DRAGEN TSO 500 Solid 2.6.2
Compatibility with DRAGEN 4.3.17
Defect Repairs:
10875: Re-analysis using previous BAM/CRAM files in ICA pipelines may fail due to incorrect file selection or sample name conflicts, especially when sample names overlap or default output prefixes are not overridden.
10942: When the case disease is meningioma, classifications for some assertions may not display in the user interface and report.
10943, 10953: Filtering variants by sample metrics
In version 5.2, we separated sample metrics filters and added more conditional operators for variant filtering. This may have caused some existing filters to appear differently. To avoid confusion, we’re reverting these filters to their original format. All existing filters will continue to function as expected - no action is required.
For new filters in version 5.2 and beyond, we recommend using the new filter conditions instead of the now-deprecated Sample Metrics section.
10945: Report may fail to load for hypermutated cases with 100+ reported variants.
11043: Improved data uploader (v6.0.6) to support larger batches of PiVAT-analyzed samples.
Known Issues:
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.
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.
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.
5133: User preferred transcripts for a gene may not be prioritized as expected if user uploads preferred transcripts file with incorrect gene-transcript pairs
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.
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.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
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.
7514: OncoKB assertion for BRAF V600E for all solid tumors excluding colorectal cancer is shown in colorectal cancer case.
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.
10844: Data cannot be sent to IGV desktop when using Connected Insights on Safari.
10920: Merging a case containing tumor and normal samples with a case containing DRAGEN RNA splice variants may fail.
10960: Exon track may not display for Ensembl transcripts within variant details page.
11010: If the workgroup creator leaves the workgroup, there may be issues accessing necessary data.
11181: Variants with FILTER value "." are not returned when filtering for variants with FILTER PASS.
Product Limitations:
191: The software does not yet display records related to co-occurring variants.
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Nucleotide-level 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.
Revision History
00
Initial Release
01
Updated to include 11043
02
Updated to include 11181
v5.2.1 Local
These release notes include new features, product limitations and known issues for Connected Insights v5.2.1 Local.
New Features:
Compatibility with Non-standard data inputs. Please contact Illumina for support.
Defect Repairs:
3724: Fixed an issue with service level communication loss after the periodic certificate renewal.
11135: Addressed a memory exhaustion issue occurring during ingestion of specific cases.
10914: Improved scrollbar usability in the Variant Grid.
3732: Improved Connected Insights installation reliability when server response is slow during TLS certificate signing.
3736: Non admin user unable to access "Edit Profile" page to edit their own profile.
3735: Connected Insights to retain IP address configuration on a server reboot.
3734: Fixed Knowledge base and Configuration package installation through the Browse and upload action.
3737: Resolved report preview loading issue and approve report failure when a large number of clinical trials are added by report automation.
3741: Mapping file used in converting the Pierian Dx disease to SNOMED CT Disease terminology is updated with latest contents.
Known Issues:
2571 (local): The 'Delete Case' action intermittently fails to remove the entire Case data folder due to hidden files associated with non-Connected Insights NFS storage protocols.
2580 (local): Case processing fails with “Has issues“ status or may get stuck in “Processing“ status indefinitely if DRAGEN encounters an abrupt shutdown. In such cases, try deleting the case and re-upload or contact Illumina Support team.
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.
3499 (local): Walkme Walkthroughs are not working.
3483 (local): Case custom data upload fails using the auto-uplod "Data Upload" daemon. Alternatively use the "+New Case" action on Case list page to upload the csv files containing the Case data.
3477 (local) Storage usage displayed on Administration console page does not consider all the folder used by Connected Insights. Alternately monitor the Storage usage from the DRAGEN Server terminal.
3464 (local): IGV desktop intermittently does not load the VCF/BAM tracks. Alternatively use the IGV web version to interpret variant visualization.
3514 (local): The software does not prevent subsequent software or data package updates from Administration console, when a case ingestion analysis is currently in progress. Perform updates when the application is idle and are not currently processing any case ingestion.
1495 (local): After a system reboot, the CLI Uploader on the Configuration page shows as “Offline“ and necessitates manual restart of the service. Refer Trouble shoot section for command to restart the Daemon service.
Product Limitations:
Mutational Signature is not supported on Local version.
00
Initial Release
v5.2.0
These release notes include new features, product limitations and known issues for Connected Insights v5.2.0.
New Features:
Compatibility with new inputs
Non-standard data inputs. Please contact Illumina for support.
Upload from Connected Analytics folder
TSO 500 ctDNA MSI sumJSD
DRAGEN 4.4
DRAGEN HRD score
Configuration
Set tumor-, normal-specific QC thresholds
Version configurations (e.g., filters)
Case Management
Centralized free-text case search
Variant Prioritization
Filter variants by knowledge base + oncogenicity prediction
Sort variants by gene alphabetically
Filter variants by tumor- and/or normal-specific metrics
Interpretation
Only oncogenic variants are linked to actionable unspecified gene mutation evidence
Evidence for subtypes are prioritized
Evidence for options for other diseases are prioritized
Classifications across knowledge bases are normalized in the UI
AR-V7, EGFR vIII, negative evidence
Visualization
Visualize filtered variants
Visualize variants in an ideogram
Visualize mutational signatures (e.g., UV exposure)
Visualize grouped reads
Visualize normal BAM
Reporting
Automated reporting based on approval authority (e.g., FDA, ESMO)
Automated trial reporting based on lab location
English-UK and Spanish translations
Defect Repairs:
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”.
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.
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.
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.
5599: Records from CIViC knowledge base for broad variant categories like “PTEN mutation” will match all variants for the given gene even when a match is not appropriate, for example, it will match records for exon variants to intron variants.
6231: Previewing Report template does not work on Safari browser.
6332, 6378: Fusion representation is impacted if one breakend is in chrM.
6623: Oncogenicity prediction tool does not correctly calculate OP3 criterion for PIK3CA p.Met1? variant.
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.
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.
2570 (local): Intermittently Report PDF is missing “Assay Gene List“ title when a report is generated with the Default Report template version 2.
Known Issues:
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.
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.
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.
5133: User preferred transcripts for a gene may not be prioritized as expected if user uploads preferred transcripts file with incorrect gene-transcript pairs
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.
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.
6584: COSMIC links for some variants lead to non-existing pages due to inconsistencies in content provided by COSMIC.
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.
7514: OncoKB assertion for BRAF V600E for all solid tumors excluding colorectal cancer is shown in colorectal cancer case.
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.
10844: Data cannot be sent to IGV desktop when using Connected Insights on Safari.
10875: Re-analysis using previous BAM/CRAM files in ICA pipelines may fail due to incorrect file selection or sample name conflicts, especially when sample names overlap or default output prefixes are not overridden.
10920: Merging a case containing tumor and normal samples with a case containing DRAGEN RNA splice variants may fail.
10942: When the case disease is meningioma, classifications for some assertions may not display in the user interface and report.
10943, 10953: After upgrading from version 5.1 to 5.2, filters using an 'exclude' condition on sample metrics (e.g., Allele Depth, Paired Reads, Split Reads, Supporting Reads, Total Depth, VAF) may not behave as expected. Additionally, the column order for these metrics may have shifted.
Workaround: Adjust the filter to remove any 'exclude' conditions for sample metrics, add >/>=/</<= conditions as needed, reorder columns as needed, save the revised filter with a new name, and update your test definition to reference the new filter.
10945: Report may fail to load for hypermutated cases with 100+ reported variants.
10960: Exon track may not display for Ensembl transcripts within variant details page.
11010: If the workgroup creator leaves the workgroup, there may be issues accessing necessary data.
2571 (local): The 'Delete Case' action intermittently fails to remove the entire Case data folder due to hidden files associated with non-Connected Insights NFS storage protocols.
2580 (local): Case processing fails with “Has issues“ status or may get stuck in “Processing“ status indefinitely if DRAGEN encounters an abrupt shutdown. In such cases, try deleting the case and re-upload or contact Illumina Support team.
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.
3499 (local): Walkme Walkthroughs are not working.
3483 (local): Case data upload fails using the auto-uplod "Data Upload" daemon. Alternatively use the "+New Case" action on Case list page to upload the csv files containing the Case data.
3477 (local) Storage usage displayed on Administration console page does not consider all the folder used by Connected Insights. Alternately monitor the Storage usage from the DRAGEN Server terminal.
3464 (local): IGV desktop intermittently does not load the VCF/BAM tracks. Alternatively use the IGV web version to interpret variant visualization.
3514 (local): The software does not prevent subsequent software or data package updates from Administration console, even if an case ingestion analysis is currently in progress. Perform updates when the application is idle and are not currently processing any case ingestion.
1495 (local): After a system reboot, the CLI Uploader on the Configuration page shows as “Offline“ and necessitates manual restart of the service. Refer Trouble shoot section for command to restart the Daemon service.
Product Limitations:
191: The software does not yet display records related to co-occurring variants.
2489: The software fails to ingest data from network drive when data uploader utility is initiated for data ingestion on Mac computer.
3451: Nucleotide-level 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.
Revision History
00
Initial Release
01
Added known issues 10942, 10943, 10953, 10945, 10960
v5.1.7
These release notes include new features, product limitations and known issues for Connected Insights v5.1.7.
New Features:
None
Defect Repairs:
13060: Improved case list page load times.
Known Issues:
1298: Read order in the BAM track may change after zooming in the IGV viewer.
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”.
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.
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 a 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.