V36.1 Update (October 16th, 2024)

• Fixed an issue with the DRAGEN targeted.json caller that resulted in missing variants in a case.

V35.3 Update (September 4th, 2024)

• Add New Case | Fixed an issue that caused Pending Sequencing workflows to fail in V35.

• Edit Case | Fixed a bug that prevented saving and running edited cases that were opened on versions <V35.

• Pipeline | Fixed an issue causing more frequent case failures in V35 due to incorrect infrastructure assignment to cases where BED selection for region of interest is larger than expected.

• Analysis Tools and Report/Export | V35.0 added support for large CNVs (over 20M bp). This caused ‘case incompatible’ errors for some CNV filters and in exporting/reporting. This hotfix fixes both issues.

• Curate | Batch upload – Fixed a bug that resulted in variants added to Curate via the batch uploader to only be available in the original reference, instead of in both with liftover-on-the-fly.

• User Access | Fixed a bug causing users belonging to several domains to lose their roles when switching between domains.

• Propagations of fixes from v34.6 and v34.7 including the ability to update an organization to gnomAD 4.1 non-UKB data for SNVs/indels.

V35.2 Update (July 24th, 2024)

• Edit Case | Fixed a bug preventing a rerun of cases when original files are no longer available on BSSH.

• Pipeline | Expanded RNA disease associated gene list in transcript selection logic. The genes added to the exception list are:

  • RNU7-1 RNA, small nuclear Aicardi-Goutieres syndrome 9

  • RNU4-2 RNA, U4 small nuclear 2

• Pipeline: Multiple fixes to improve pipeline robustness and reduce failure rates.

• Lab Tab | Fixed a bug resulting in no data loaded to the lab tab for new organizations.

• Analysis Tools | Filters | Fixed a bug for Variant Effect Filters, when moving from simple to advanced, not all variant effects were available for filtering, which also caused a variant count discrepancy.

• Analysis Tools | Preset Filters | Fixed a bug that always showed the description of removing polymorphic variants as ‘Display polymorphism: True’ although the behavior of the filter correctly removed the variants.

• Variant Page | Embedded IGV | Improved IGV performance by reducing API calls when moving between variants.

• Variant Page | Embedded IGV | Option to toggle embedded IGV off to improve performance for customers using external visualization tools.

• Export | Fixed a bug failing the export of parental data for some customers.

V35.1 Update (June 25th, 2024)

• Edit Case | Fixed an issue that could prevent reanalysis of cases that were created via API and were missing fields required in v35.

• Cases Page | Fixed a rarely occurring issue where cases can be displayed with the good quality green icon even though they contain an insufficient coverage warning.

• Analysis Tools | Filters | Fix an issue that caused frameshift indels to disappear from variant table when moving between simple and advanced mode in the quality filters.

• Curate | Batch upload enhancement that will ensure all characters uploaded to Curate are supported in Analyze.

• Curate | Curate now supports MNVs that are supported in Analyze, which are MNV indels only.

• Curate | Fixed an issue that prevented genes with no gene metrics to be uploaded to Curate.

• Propagations from V34.5.

Release highlights for both workbench 34.0 and pipeline 34.0:

• Analysis Tools have gotten an efficiency boost with multiselect variants, variants marked as viewed, and frequently requested new preset filters capabilities.

• Powerful new Organization Settings reduce your reliance on Illumina support, including Preset creation, management and validation and new Move to Trash status.

• New annotations are available - Illumina’s high performing PrimateAI-3D prediction score and an update to the newly published gnomAD v4.

• Lab Tab gets new case quality metrics, Peddy1 sample contamination, and view single gene coverage metrics.

• Workflow improvements – more visualizations for customers starting from VCF, visualize Curate data (SNV and SV), improved login flow and report/export enhancements.

Emedgene customers can select their preferred version out of any of the past 5 releases. Customers on 29.0 and below should select an upgrade path at this time.

Updates

Analysis Tools | Increase efficiency with new multiselect variants, viewed/unviewed variants and new preset filters on PrimateAI-3D, REVEL and more

i. Multiselect variants and bulk tag, assign pathogenicity and mark viewed

Increase the efficiency of your analysis by performing bulk actions on variants in the analysis tools. When hovering over any variant a checkbox will appear at the beginning of the row.

Actions available are:

• Tag or clear tag from all selected variants.

• Assign or clear pathogenicity from all selected variants.

• Mark selected variants as viewed/unviewed

These actions are only available for non-finalized cases.

More bulk actions will be included in future versions.

The multiselect feature requires an update to Workbench 34.0.

ii. New feature marks viewed/unviewed variants for increased analysis efficiency

Some variants may appear in multiple preset filters. In order to increase analysis efficiency, variants will appear in bold if they have not been viewed, and will appear in regular font weight if they have been viewed. This clear visual indication on whether a variant was viewed or not will help users avoid reviewed variants more than once.

Viewed/unviewed status is tracked by user. If multiple users are analyzing a case, their viewed/unviewed activity is tracked separately. This activity can be modified via the multiselect tool.

Variant color and weight indicate the following:

The viewed/unviewed feature requires an update to Workbench 34.0.

iii. New preset filter feature: Keep _AI Shortlist_** tagged variants in a preset filter even if tag is changed by user**

The majority of Emedgene users begin their workflow by reviewing the AI Shortlist tagged ‘Most Likely’ variants. Prior to 34.0, once a user has changed the tag, for example to ‘In Report’, the variant would no longer appear in the most likely preset filter.

In this version we have added the capability to filter on AI Shortlist tagged variants independently of user tags. These variants will remain in the preset filter even when user modifies their tag. This will facilitate reviews of a case by multiple analysts.

In order to revise your preset filters to this new capability, please contact your regional support team or reach out to techsupport@illumina.com.

The keep AI Shortlist tagged variants in filter feature requires an update to Workbench 34.0.

iv. New preset filter capability: Filter on PrimateAI-3D score

Presets can now be set to filter on both PrimateAI-3D scores and PrimateAI-3D predictions. Define a preset to show only variants with a PrimateAI-3D score value greater than a selected threshold and/or define a preset to display variants with a PrimateAI-3D prediction of either D (Damaging) or B (Benign).

This new capability can only be implemented through support teams and is not available from the user interface.

The PrimateAI-3D filter feature requires an update to both Workbench 34.0 and Pipeline 34.0.

v. New preset filter capability: Filter on REVEL score

Presets can now be set to filter on variants with a REVEL score value greater than a selected threshold.

This new capability can only be implemented through support teams and is not available from the user interface.

The REVEL filter feature requires an update to both Workbench 34.0 and Pipeline 34.0.

vi. New preset filter capability: Filter variants using values in the DRAGEN VCF filter field, for example QUAL=PASS

Presets can now be set to filter on DRAGEN VCF filter fields. These presets are exact match, text based. Multiple values can be selected, with an OR applied between them.

This new capability can only be implemented through support teams and is not available from the user interface.

The DRAGEN QUAL filter feature requires an update to both Workbench 34.0 and Pipeline 34.0.

vii. New preset filter capability: Filter variants where severity/main effect is unknown

Presets can now be set to filter on severity/main effect when those fields return an unknown value. This will help create filters for intergenic regions and speed analysis of genomes.

This new capability can only be implemented through support teams and is not available from the user interface.

The DRAGEN QUAL filter feature requires an update to Workbench 34.0.

Limitations

• Some new preset filter capabilities can only be configured by Illumina support teams and are not available from the UI yet. Future versions will make them configurable from the UI.

• The new Multiselect feature is only available for cases that have not been finalized.

• Multiselect is limited to 50 variants at a time.

• Multiselect activity record is for every variant individually, no aggregated activity.

• Mark viewed variants is limited to 5000 variants per user per case, and the API can send 50 at a time.

Organization Settings | Customize, manage & control your organization with these new features

This version introduces new features allowing customers to customize, manage and control their organization without requesting Illumina support. We focused on the most requested features and will progressively enhance the organization tab to cover all configurable organization settings.

i. Create and manage Presets and Preset Groups

Presets are combinations of Filters that serve to implement your interpretation Standard Operating Procedures (SOP) within the Emedgene software. Each Preset filter represents an analysis step, and there is full traceability on which presets have been reviewed by your various team members.

A Preset Group is a combination of Preset filters in a particular order that represents a case analysis workflow. Multiple Preset Groups can be created and used for the analysis of different case types. Preset Groups are designed to adhere to laboratory analysis standards while increasing analysis efficiency.

Up to 34.0, the Preset filters have been implemented to your requirements by Illumina support teams.

Starting in 34.0 you can save your own Presets, Preset Groups and also migrate existing Presets into the new self-managed feature.

As part of this new feature, an automatic and comprehensive schema validation covering over 120 fields and their associated unique values was added for Presets and Preset Groups to ensure validity across organizations.

As always, these new features require specific roles which you can distribute to select team members.

• Save Presets:

Saving Preset filters is simple.

1. Apply any filtration strategy using any of the available filters in either simple or advanced mode.

2. Click on the three-dot icon and select "Save as preset." Enter a unique name for the Preset (Note: Avoid using non-Latin symbols that don't follow the ISO-5589-1 standard).

3. Don’t forget to save!

• Preset and Preset Group management

A new Lab Workflow tab is now available in the the Organization Settings (click on your initials in the upper right to reach all settings).

In this tab you will be able to:

• Manage Presets

• Manage Preset Groups

• Set a default Preset Group for your organization

a. Manage Presets

This card enables you to perform the following actions on your Presets:

• Add New – will redirect you to the analysis tools to create a preset filter as described above.

• View Preset contents by pressing on the arrow to the left of the Preset name.

• Lock Preset – locked Presets cannot be edited or deleted.

• Delete Preset – Delete a Preset that is not locked and has not been used in a case analysis. Once a Preset has been used in an in-use Preset Group it cannot be deleted, in order to maintain access to the case.

b. Manage Preset Groups

This card contains the Preset Group and Legacy tabs.

Preset Group allows you to perform the following functions on your Preset Groups, which are defined combinations of Presets which will be reviewed in a particular order.

• View all existing Preset Groups for your organization.

• View the contents of each Preset Group in the table, revealing the list of presets it contains.

• Create and edit new Preset Groups:

• Select a name (Note: Avoid using non-Latin symbols that don't follow the ISO-5589-1 standard and ‘Default’ and ‘Presets’ are restricted names and cannot be used).

• Add and remove Presets from the Preset Group. A search functionality has been added for ease of use.

• Reorder a list of Presets within the Preset Group.

• Hide/unhide Preset Groups in the table for clear visibility on latest versions available for use. Note that hidden Preset Groups will not affect cases run with them, and when editing a case with a hidden Preset Group it will still be available.

c. Set a default Preset Group

A default Preset Group for your organization can be set and will be used for all cases without a selected Preset Group.

d. Migrating V1 Legacy Presets to V2 Preset Groups

We highly recommend performing the migration with the assistance of regional support teams.

At the time of your choice, you can elect to migrate your Preset Groups to the new Preset tool. The V1(legacy) tab will display a list of Preset Groups that are only available in the V1 schema and will require a migration activity to the new functionality.

To migrate:

1. Download the JSON file available for the Preset Group in the legacy tab.

2. Create a new Preset Group from file and upload the JSON file.

The migration tool will create all Presets contained within the V1 Preset Group, and also order them correctly in the V2 Preset Group.

The V2 Preset Groups have been migrated to a robust schema and the preset import will automatically run a schema validation on over 120 simple and complex fields along with associated values. This robust and automatic schema validation will ensure your Presets and Preset Groups function as expected after the transition.

If any errors are found during the automated validation of any single Preset, the migration will fail and no new Preset Group will be created. A clear error message regarding the Preset that was incorrectly formatted will be provided, at which point you can correct the error and re-upload. We recommend utilizing Illumina regional support teams to correct any such errors.

e. Using both V2 and V1 Preset Groups

If at any point in time you have both V1 and V2 Preset Groups available, you can select either when adding a new case.

When a legacy Preset Group was migrated to the new schema, only the V2 Preset Group will be presented.

f. Migrating Preset Groups from Staging to Production organizations

At any time, you can download a Preset Group from a staging organization, and create a new Preset Group from file in the Production organization.

Note that any Presets utilizing gene list IDs or tags will need to be modified in the production organization.

• An error message will appear on gene list IDs, providing the Preset Groups were migrated in the same region. If migrating from one cloud to another, please search and replace all gene list IDs.

• Please recreate tags in your Production organization before importing the Preset Group.

The Save/Manage/Migrate Presets and Preset Groups feature requires an update to Workbench 34.0.

ii. New ‘Move to Trash’ status replaces support archive request

Customers can now move cases ready for deletion to the new ‘Move to Trash’ status. This functionality replaces the request to archive cases via Illumina support teams.

Cases in ‘Move to Trash’ status are locked for editing, and only users with the correct roles can move them to another status.

Future versions will enable customers to automate deletion of cases in the ‘Move to Trash’ status according to selectable parameters.

Case Deletion is still a request via techsupport@illumina.com, please request that Illumina delete all cases in ‘Move to Trash’ status.

The Move to Trash feature requires an update to both Workbench 34.0.

iii. New organization settings configure default page, analysis table columns

The new organization settings require an update to both Workbench 34.0.

Limitations

• Some existing Preset functionality is only available via Illumina support teams – exclude benign, filtering on specific prediction scores and more. Please continue to work with your support team to implement these. Note that the newly introduced schema validation applies to all Preset functionality and any functionality added by support teams will undergo an automated validation.

• The additional functionality will be exposed to customers starting in mid-2024 versions.

• Complex Preset Groups (or/not conditions between filters) will be added in later 2024 versions. The most commonly requested exclusion of benign variants in Presets is possible today with the assistance of Illumina support teams.

New Annotations: PrimateAI-3D, gnomAD v4

i. Emedgene now includes the newly published Illumina PrimateAI-3D prediction score!

PrimateAI-3D is a deep-learning network trained on 4.5 million common genetic variants from 233 primate species. This state-of-the-art classifier accurately quantifies missense variant pathogenicity in humans, which improves discovery of genes affecting clinical phenotypes.

PrimateAI-3D demonstrated superior performance across 6 datasets in this Science publication:

PrimateAI-3D has been added to the In Silico prediction scores card on the Variant Page. It provides both a numerical score and also a prediction, which can receive the value D (damaging) or B (benign) per variant. The prediction is based on both the score and the gene, score range for damaging/benign is different per gene.

Emedgene users can also create presets based on either the score or the prediction, and also include either or both in their export.

Learn more about PrimateAI and view publications.

The PrimateAI-3D feature requires an update to both Workbench 34.0 and Pipeline 34.0.

II. gnomAD v4 is here!

gnomAD v4 was published on November 1st, 2023 and we’re excited to make it available in this release so quickly. It contains data from 807,162 total individuals and is nearly 5x larger than the combined v2/v3 releases, and more diverse. Both the exome callset (730,947 individuals) and the genome callset (76,215 individuals) were aligned to build GRCh38 of the human reference genome.

On Emedgene, this dataset replaces both the gnomAD Genome V3 and the gnomAD Exome v2 Liftover data.

gnomAD links have been updated in 32.0 and above.

The gnomAD v4 feature requires an update to both Workbench 34.0 and Pipeline 34.0.

Limitations:

• Note that since the gnomAD MID population has less than 1000 samples so it is not taken into account as a valid source.

Lab Tab | New case quality section, Peddy contamination, improved single gene coverage workflow

i. New Case Quality section in the Lab Tab

For all cases with a number of genes above a customer defined threshold, Emedgene performs an additional case quality check. Up to 34.0, results of this quality check were not made available to customers and any failure would cause the case to fail and trigger an Illumina support investigation. Starting with this version, cases will not fail, and the result of the case quality check will be provided to users, so they can determine whether to continue with the analysis.

The Case Quality section contains:

1. Gene list threshold: reflects the gene list threshold applied for the case quality check (default: 50).

2. A table displaying the results of the various validations performed:

• GnomAD Validation - Ensures that each chromosome contains a minimum of 1 variant annotated with GnomAD. Importantly, this validation applies only to chromosomes with at least 100 SNV variants within defined Kit or coding regions. Possible values are Succeed, Failed, Skipped.

• ClinVar Validation - Ensures that each chromosome contains a minimum of 1 variant annotated with ClinVar. Importantly, this validation applies only to chromosomes with at least 100 SNV variants within defined Kit or coding regions. Possible values are Succeed, Failed, Skipped.

• Auto Analysis Validation – Ensures that at least one variant was tagged by the Emedgene AI. This validation will not apply in cases with a gene list below the defined threshold. Possible values are Succeed, Failed, Skipped.

• Chromosome Validation – Ensures that each chromosome contains a minimum of 1 variant with high quality. Importantly, this validation applies only to chromosomes with at least 100 SNV variants within defined Kit or coding regions. Possible values are Succeed, Failed, Skipped.

• mtDNA Reference Validation – Ensures that the rCRS reference was used for mtDNA variants. If no mtDNA variants are present in the case the check will receive a Succeed value. Possible values are Succeed, Failed.

When one of the Case Quality checks fails, both the section and the Lab Tab will display an alert.

While the case quality check can identify issues with exome and genome cases, it can often be falsely triggered for small panel cases, and it is recommended to exclude it for these cases by setting an appropriate gene threshold. Panels carved out with BED files can also be excluded, please contact your regional support teams or techsupport@illumina.com to set up this exclusion.

The Case Quality feature requires an update to both Workbench 34.0 and Pipeline 34.0.

ii. Lab Tab | New Peddy contamination column

The Lab Tab will now display the results of the Peddy assessment of sample contamination (PMID: 28190455), which calculates a deviation using all the sample alt-alleles, providing a sample specific contamination estimation that can detect human and bacterial contamination.

A new column titled ‘Contamination’ will display the following values:

• Yes - IDR_BAF >=0.300

• Likely - 0.241<= IDR_BAF <0.300

• Unlikely - 0.200<= IDR_BAF <0.24

• No - IDR_BAF <0.200 but not 0

• N/A - IDR_BAF = 0.000 or no data is available for this sample (old case)

IDR_BAF is the inter-decile range (90th percentile - 10th percentile) of the b-allele frequency. Peddy analyzes a distribution of all sites of alts / (ref + alts) and then reports the difference between the 90th and the 10th percentile. Large values indicated likely sample contamination.

When hovering over the value a tool tip will also display the HET ratio (proportion of sites that were heterozygous) and the HET count (number of heterozygote calls in sampled sites).

The Peddy contamination feature requires an update to both Workbench 34.0 and Pipeline 34.0.

iii. Lab Tab | Workflow improvement – view single gene coverage metrics when analyzing a large panel

Users can now remove all genes in a large gene panel, to quickly search and view for a single gene.

The single gene coverage enhancement requires an update to Workbench 34.0.

General Workflow Improvements: Support BAF, ROH for customers starting from VCF, display Curated data in IGV, improved login and performance for ILMN clouds, new export/report capabilities

i. Support ingestion of additional visualization files for customers starting from VCF via the API and batch upload (but not via the UI). These visualizations were already supported for customers starting from FASTQ (32.0 and up).

• BigWig TNS (Tangent Normalized Signal) – The TNS track simplifies and increases reliability of CNV analysis and is available for customers running WGS. File supported: tn.bw.

• B-Allele Frequency BigWig – The track aids in CNV and LOH analysis and is available for WES and WGS samples. File supported: baf.bw.

• ROH BED file – The Regions of Homozygosity (ROH) plot is a visualization of homozygosity that may suggest the presence of uniparental isodisomy or partial isodisomy and is available for customers running WGS. File supported: roh.bed.

This feature requires an update to Workbench 34.0.

A summary of accepted DRAGEN 4.2 outputs in 34.0:

ii. Visualize Curate data! Visualize both SNV and SV Curated data within the IGV viewer

• Curate SNV and Curate SV tracks are available in addition to the ClinVar tracks that were already available

• Colors indicate variant pathogenicity:

  • Green = Benign/Likely Benign

  • Yellow = VUS

  • Red = Pathogenic/Likely Pathogenic

  • Black = Conflicting interpretation of pathogenicity

  • Grey = No assertion provided.

This feature requires an update to Workbench and Pipeline 34.0.

iii. Illumina cloud login improvements that will increase transparency on the selected domain and workgroup. This improves on current state where users are always logged into their previous workgroup regardless of the URL used.

• Logging in to any Emedgene URL on Illumina cloud will first direct you to select your domain, in case a user is active in multiple domains, and then to select a possible workgroup. Workgroups will be displayed if the Emedgene application is assigned, they are part of the domain, and the user logging in belongs to the workgroup.

• No need to remember a URL, you can login through app.emg.illumina.com and you will be directed to your domain and workgroup automatically.

• If no URL has been assigned to a workgroup, domain admins and workgroup owners can initiate a URL assignment workflow.

• Select the following parameters

  • The region your domain is in

  • A URL pattern from the list of available patterns

  • A platform version. If a URL is in use with a platform version, only that version will be available for the selected URL.

  • Both the URL pattern and the platform version can be changed from the Organization Settings later.

This feature requires an update to Workbench 34.0.

iv. Add New Case | Batch Upload now supports

• Commas within any cell

• Whitespace, semicolons & separated values will be ignored and information will be extracted regardless.

This feature requires an update to Workbench 34.0.

v. New frequently requested Export/Reporting fields have been added. Please contact your regional support team or techsupport@illumina.com if you’d like to modify your export/report.

• Case Level: List of genes with insufficient region based on coverage or BaseGT (for cases that have a gene list applied at case creation)

• Case Level: Sequencing lab information, sample quality metrics and pedigree metrics.

• Variant Level: SNV and CNV ACMG section.

This feature requires an update to Workbench 34.0.

vi. Analysis Tools | New export to csv capabilities

• Exports each missense prediction result as a separate columns: Polyphen2 HDIV, Polyphen2 HVAR, SIFT, MutationTaster, LRT, DANN, REVEL, PrimateAI-3D score, PrimateAI-3D Prediction.

• Export of Zygosity for Mother and Father as separate columns, in addition to Proband Zygosity and Other family members Zygosity.

• Exports disease inheritance mode (from Disease column).

• Exports "variant inheritance" – can have several values separated.

This feature requires an update to Workbench 34.0, but PrimateAI-3D and REVEL require a pipeline update.

Limitations

• CNV variants larger than 20 Mbp are not annotated with genes name and effect, these variants are shortlisted by default by the AI Shortlist, but ACMG automation is not applied to them.

• There is still a feature discrepancy for customers running DRAGEN through Emedgene (starting from FASTQ) or outside of Emedgene (starting from VCF).

• Export to excel is limited to 32KB in size, which may prevent exports with very large CNVs.

• API | No complex sorting via API is possible yet, only on a single column.

Fixed Issues

• Add New Case | Network | Default consent is ‘restricted’.

• Add New Case | Batch Upload | Fixed error where customers received a ‘Not Authenticated’ due to a timeout for large uploads.

• Add New Case | Fixed an issue for API/batch/UI users trying to create a case from BSSH with 15-20 sample files would timeout.

• Add New Case | Ordering portal users do not see Network Sharing fields, previously they could see but not edit them.

• Lab Tab, Sidecar | Pedigree | Fixed issue where in very large pedigrees some family members can’t be clicked to view quality.

• Candidates | Fixed a bug when clicking on See all candidates link, variant filters were inactivated.

• Candidates | Fixed issue where SV Insertions information was partially displayed.

• Variant Page | Visualization | Fixed an UI issue where IGV window was out of frame.

• Variant Page | ACMG SNV Score | Fixed but where incorrect score was showing for mtDNA variants, although classifier behaves as expected.

• Variant Page | Fixed issue where zygosity can’t be edited in the Sanger confirmation component.

• Cases Page | Fixed issue where contact support link for failed cases did not work.

• Report/Export | Fixed issue where variants tagged as ‘Most Likely’ order was not preserved when pushing to the report.

• Report/Export | Fixed issue in miniVCF header blocking subsequent analysis in other tools.

• Activity | Fixed issue where long names were not displayed properly.

• Pipeline | Multiple improvements to avoid pipeline failures due to unavailable files and resources.

• Infrastructure | Multiple improvements of resource allocations to increase robustness and performance.

Known Issues

• Add New Case | Batch Upload | Analysis Type field is not available with this version of Batch Upload, and it cannot be used to initiate the new Carrier workflow.

• Add New Case | Create a case from case creation summary does not work, please click on top Add New Case button from cases page.

• Add New Case | For customers starting from Joint gVCF, please make sure the proband is first in order to see the correct insufficient region calculation.

• Add New Case | Test type ‘Other Test’ is not supported on Illumina clouds yet.

• Add New Case | API | When sending due date please use UTC time, customer time zone is not taken into account with API, only through the UI.

• Reanalysis | If HPO terms were updated between analyses, the reanalysis will not automatically map previous HPO terms to new ones.

• Lab Tab | Reanalyzed cases will show up with duplicated insufficient gene regions.

• Lab Tab | STR repeats number for parents does not exist, proband values displayed.

• Lab Tab | Insufficient coverage export will not work via UI or API if an included gene does not have a start or end position in NCBI.

• Candidates | Gene name displayed on candidate page can be different than pipeline and variant Page.

• Candidates Page | Compound het SNV-CNV variants will not display the automated CNV classification. Workaround – view variants from analysis table.

• Evidence Graph | LitVar links will not work due to a change in the LitVar link structure.

• Variant Page | Clinical Significance | When a disease has both an OMIM and a CGD source, the CGD inheritance modes mistakenly override OMIM inheritance modes.

• Variant Page | Visualization | Chromosome ideogram visualization is missing for mtDNA variants in VCF case run on GRCh37.

• Variant Page | Visualization | Simple/Advanced selectors will not work for locally uploaded BAM files.

• Variant Page | Visualization | Zoom out of BigWig/TTS displays mean data.

• Variant Page | Visualization is not supported for users storing VCF and CRAM on ICA V1 and BSSH. Only VCF and BAM are supported.

• Variant Page | Manually Added Variants | Users without the role can add variants but not save them. Button should be disabled.

• Variant Page | Transcript selection in fusion genes may be blocked since only a transcript for a single gene can be selected.

• Analysis Tools | Preset Filters | Preset containing a gene list ID will display filtered data when an organization has configured a base gene list filter.

• Analysis Tools | ‘Last’ button on pagination does not work.

• Organization Settings | Set mandatory fields - does not work from the UI. Please contact support if you’d like to configure these fields for your account.

• Organization Settings | Gene Lists | Very large gene lists (>6700 genes) may return a false error message during creation, despite being successfully created.

• Network | GRCh37<-->GRCh38 Liftover not available for older components of Network infrastructure, as a result, [Variant Page | Clinical Significance | Networks Classified] may remain erroneously empty while [Variant page | Related cases section] shows relevant information. Same gap for manually classified variants.

• Network | Zygosity, even when set in extended sharing, may remain blank for older cases. Once you click on a case missing zygosity it will be saved for all future views.

• ILMN Clouds | Help Center | Some links may not work. Work around: Paste the title into the help center search.

• Curate | ILMN cloud users need to be logged in to the organization from which they are trying to access Curate.

• Curate | Discrepancy between Analyze and Curate HGVS parser may be experienced.

• API | Assign users to case fails with no error if faulty emails used.

• API | Creation of large gene lists may return an error (due to timeout) despite the creation of the gene list.

• API | Marking over 5000 variants as viewed will not result in an error message, although this is the database limitation for saving viewed variants.

• API | Swagger | Authorize function returns a 400 error.

• Webhooks | Not functioning for software case status changes.

• Activity | Editing interpretation paragraph yields an erroneous activity labeled reanalysis.

• Dashboard | Diagnostic Yield includes Uncertain as Resolved.

Version update needed for access to new features

References

1. Pedersen and Quinlan, Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy, The American Journal of Human Genetics (2017), http://dx.doi.org/10.1016/j.ajhg.2017.01.017

V33.3 hotfix released for the following issues:

• Analysis Tools | Preset filters | Fixed an issue introduced with v33.2 that caused some LOF preset filters to not return variants. Customers impacted by this issue were notified individually and resolution offered for potentially affected cases.

• Propagation of fixes included in . See release notes for detail.

V33.2 hotfix released for the following issues:

• Add New Case | NovaseqX added to selectable sequencers.

• Add New Case | Fixed a batch uploader issue where sex column was used correctly but also imported in additional data

• Pipeline | Fixed an issue where cases running with DRAGEN 4.2 on HG19 fail the pipeline

• Pipeline | Added support for multi-allelic CNVs when customers start from joint gVCF

• Pipeline | Added support for DRAGEN VCFs where hardware is unknown.

• Pipeline | Fixed a bug that caused discordant AI results between a first and second analysis due to model selection.

• Pipeline | Fixed an issue causing some reanalysis cases to fail due to insufficient backward compatibility with previous values. This fix will improve pipeline robustness.

• Cases Page | A search on this page will only search for EMG ID, sample names, or any string in the test data. This fix will improve performance.

• Analysis Tools | Fixed variant count issue for compound heterozygous filters caused by using a single source for what is essentially a two-step process. Only count displayed was incorrect.

• Analysis Tools | Fixed preset filter issue where presets were returning more results than expected due to ‘-‘ in the gene name in some preset filters. No data was missed.

• Variant Page | Fixed incorrect gnomAD link after the gnomAD v4 release.

• Organization Settings | Fixed an issue causing available URLs to become unviewable when changing the platform version from V34 to V33.

• Performance: Additional updates to increase performance through infrastructure modifications.

V33.1 hotfix released for the following issues:

• Add New Case | Fixed issue where new ethnicities added in v32 were not supported for reanalysis in subsequent versions.

• Batch Upload | Fixed issue for singleton cases uploaded with batch uploader that resulted in inability to edit cases after creation.

• Batch Upload | Fixed issue causing Not Authenticated error for customers with more than 100 BSSH projects.

• Batch Upload | Improved backward compatibility for Gender changed to Sex field.

• Pipeline | Improved error logging for DRAGEN for easier troubleshooting.

• Pipeline | Fixed issue where ingesting DRAGEN ExpansionHunter and SV caller VCFs from DRAGEN 4.2 failed cases due to unexpected header.

• Pipeline | SMN Caller | Fixed multiple issues causing case failures from FASTQ & BAM.

• Pipeline | SMN Caller | Fixed issue for GRCh37 & SMN caller where relatedness isn’t calculated due to Peddy failure.

• Pipeline | Enable flow where in a trio only the Proband has Ploidy outputs and parents don’t.

• Pipeline | Don’t fail cases where no samples are provided but ignore samples isn’t set.

• AI | Include full gene list in Phenomeld for virtual panels, irrespective of phenotypic match.

• Cases Page | Search from the cases page is now limited to case ID, sample name and test data fields to improve performance.

• Lab Page | Fixed issue of no coverage statistics for cases with missing samples. Coverage appropriately generated for the samples submitted with the case.

• Lab Page | Fixed missing average coverage affecting some pipelines.

• Analysis Tools | Manually Added Variants | Fixed an issue where STR manually added variants can’t be tagged or reported.

• Analysis Tools | Export | Resolved issue in export of some presets and filters due to incomplete customer facing role.

• Variant Page | Fixed issue where proband coverage copied to parents for customers starting from joint gVCF.

• Variant Page | Fixed all broken gnomAD links after the gnomAD v4 release.

• Variant Page | Updated Decipher link after link structure change.

• Curate | Fixed issue where selecting a disease associated with a gene for a variant appears to automatically apply it to all variants in that gene in the UI, while data is correctly applied in the backend.

• Curate | Enable customers to login to Curate when signed into a different organization on Analyze.

• Reanalysis | Fixed backward compatibility issue preventing variants in cases originally analyzed on and before V27.0 to be pushed into a report.

• Settings | Fixed issue where S3 credentials couldn’t be generated for long domain names. Character limit is eliminated.

• Settings | Fixed issue in kit BED validation for non-canonical chromosomes.

• Infrastructure: Multiple improvements of resource allocations to increase robustness and performance.

New Features (June 8th, 2023)

New AI Shortlist Features and Enhancements

On this version we continued focusing on new AI innovation, with the goal of streamlining workflows and further reducing time-per-case.

AI Shortlist now shortlists mtDNA variants

For customers analyzing mtDNA variants in Emedgene, the AI Shortlist will now shortlist SNV/CNV mtDNA variants (homoplasmy or heteroplasmy) that are likely to solve the case.

AI Shortlist now shortlists STR variants

For customers analyzing STR variants in Emedgene, the AI Shortlist will now shortlist STR variants with expansion size within the pathogenic range according to gnomAD STR and that are likely to solve the case, with evidence.

AI Shortlist now shortlists SV insertions

For customers analyzing SV insertions in Emedgene, the AI Shortlist will now shortlist SV insertions that are likely to solve the case, with evidence. Due to variant calling accuracy limitations, insertions, as well as other CNVs, are considered by the _AI Shortlist_in addition to the regular SNVs.

Shortlisting with evidence for Carrier Screening

Support for sequential (single parent) carrier status.

This new setting will prioritize variants for carrier status, rather than affected, in order to reduce time per case for expanded carrier screening applications.

• AI Shortlist can be configured on the organization level to consider only known P/LP variants or both known and high severity variants.

• Analysis type ‘carrier’ should be selected during case accessioning.

• Output of the _AI Shortlist_will be variants tagged as ‘carrier’ rather than the typical ‘most likely’ and ‘candidates’.

• A customer-generated gene list is required for the carrier analysis workflow.

Improved recall for AI Shortlist Focused Mode to 96%

Our AI Shortlist model can be run in two modes, including genes of unknown significance (GUS), labeled _Discovery Mode_or excluding GUS, labeled Focused Mode. In this version, we improved the recall for the _Focused Mode_to 96%, nearing the results of our Discovery Mode at 97%. The Focused Mode will display up to 7 SNVs, indels, mtDNA and STR variants, and up to an additional 3 CNV variants.

This new Focused Mode was validated on 3 datasets totaling 330 cases solved by SNV, indel, and CNV variants, and demonstrated 96% recall.

Performance Enhancement

AI Shortlist code was refactored to improve performance, scalability, and clean up errors. A bit-exact validation was performed on 3 datasets totaling 330 cases solved by SNV, indel, and CNV variants. A comparison of the precise ranking of most-likely and candidate variants was performed to ensure recall was not affected for cases solved by SNV, indels or CNV variants.

Full Featured Genome: New! Support for SMN, ROH, Ploidy & BAF visualization

Support for the DRAGEN SMN caller

• SMN1 copy number variants can be shortlisted by the AI Shortlist and interpreted just like other CNVs.

• SMN2 copy number can also be reviewed and interpreted as a prognostic biomarker of SMA clinical severity.

• Carrier status can be assessed by interpreting SMN1 copy number.

Support for the DRAGEN ROH (Regions of Homozygosity) caller

DRAGEN ROH detects and outputs the runs of homozygosity from whole genome calls on autosomal human chromosomes. Sex chromosomes are ignored. ROH output enables screening and prediction of consanguinity between the parents of the proband subject (see DRAGEN™ Bio-IT Platform documentation for more details about the algorithm).

In Emedgene, the ROH BED will be displayed in the IGV viewer. On hover, ROH score, # of Hom SNPs and # of Het SNPs in the region as well as Location (start to end positions) will be displayed.

Support for the DRAGEN Ploidy estimator

DRAGEN Ploidy estimator is used to assess if there are any copy number variants of complete chromosomes (Trisomy, Monosomy etc). ​ The results of the Ploidy estimator will be displayed on the lab tab. If ploidy estimation is marked as fail, the lab tab will have a warning in the page header. Results will be available to download from the sample quality section. (see DRAGEN™ Bio-IT Platform documentation for more details about the algorithm).

Support for B Allele Frequency visualization

The BAF bigwig file is available to view in the additional tracks, both in simple and advanced modes. It will be available for WES and WGS samples called with the Emedgene DRAGEN pipeline.

To avoid confusion, the TNF track, previously labeled as BigWig, is renamed TNF.

Research genome test type

A new Research Genome test type enables full analysis of a genome with no BED intersect. Most of the newly available variants will receive limited or no annotations. The Research Genome significantly increases time per case and performance and is only recommended for research labs with a need to interpret non-coding variants. The Emedgene Whole Genome test type covers 5Kbp upstream/downstream gene and known variants from the non-coding regions, all of which will be annotated.

Support for Illumina Complete Long Reads Interpretation

Support for the recommended Illumina Complete Long Reads interpretation flow.

• Ingests the combined long-read/short-read callers for both SVs and SNVs, along with the long read BAM.

• Short read callers supported by Emedgene from VCF can be added as well (CNV read-depth, STR (starting from DRAGEN 4.2)).

• Once ingested, ICLR variants will be shortlisted by the AI Shortlist and automated ACMG classification will be applied where relevant.

• All ICLR calling will be performed via the BSSH application and Emedgene will ingest VCFs and BAM via the existing BSSH integration.

Limitations

• Emedgene does not yet support the interpretation of complex SV variants such as inversions and translocations.

• ICLR cases must start from VCF, Emedgene doesn’t support case accessioning from both VCF and FASTQ.

Enhanced private sharing of curated data

Set sharing levels, opt-in/opt-out, improved interpretation workflow

• Private sharing of curated data between collaborating organizations in Analyze now include granular sharing permissions per network and opt-in/opt-out per case.

• Networks are managed from [Settings | Network]. Here the dedicated network manager can:

  • Create networks; Labs can belong to multiple networks.

  • Set data sharing policy for each of them.

  • Leave or delete networks.

Currently, to invite other organizations to their network(s), the network manager must reach out to tech support. (Network invitation flow will be enabled in a future version).

• Level of sharing of a particular case with a particular network of collaborators is defined by:

Sharing mode set for each data field for a particular network. There are 4 levels of sharing that can be applied to each data field: Mandatory – always shared by default; Not shared – never shared; Restricted – shared in cases with or without patient’s consent to Extended sharing; Extended – shared only in cases with patient’s consent to Extended sharing.

Sharing patterns are defined by the network manager in [Settings | Network]. Data fields that could be shared via Analyze Network include:

• Case subject consent for Extended data sharing.

• Review details of variants tagged by collaborators within organization network(s) in the [Variant page | Related cases section].

• View modes for [Variant page | Related cases section]: Simple (check/uncheck Network data from all collaborators) and Advanced (select collaborators).

• For each variant, extended sharing details are available at a click, as is the ability to contact a collaborator.

Analysis tools improvements: Exclude variants based on pathogenicity, view Presets & sort columns

Exclude variants based on pathogenicity

Exclude variants from your Preset filters based on their pathogenicity in ClinVar or Curate

View Presets

Added the ability to view the filters underlying each Preset. For variant analysts working on a preset filter, this will enable a quick refresher on the Preset composition, within the analysis flow.

Actions:

• Click on the name of the Preset to review the Preset variants.

• Click on the dropdown arrow to expand the Preset definition.

• Click on the checkbox to indicate that you have completed your review of this Preset.

Sort columns

Sort any column in the analysis table, with the exception of Phenomatch score (which will be available in v33) and Tags.

Primary and secondary sorting are enabled.

Search alternative allele

In the search bar, we now enable searching by a specific SNV/indel variant following the : >  format.

• Spaces are supported.

• This search will return an exact match.

Add New Case: Single click batch upload of cases

Case accessioning now enables batch upload of cases from the UI! This single click upload of a case manifest file, allows customers without API integrations to easily upload batches of 50 cases at once.

• Download the Batch Upload csv template, which is compatible with Sample Sheet v2, adding fields needed for tertiary analysis.

• Every field available in manual case creation and API, is included in the template: including Family Id, Case Type, Files Names, Visualization Files, Execute Now, BioSample Name, Relation, Gender, Phenotypes, Phenotypes Id, Boost Genes, Gene List Id, Kit Id, Selected Preset, Due Date, Label Id, Clinical Notes, Opt In, Storage Provider Id, Date Of Birth, Default Project including Additional Fields.

• Cases can be created with or without samples, just like in UI and API.

• Data from unknown columns will be saved in the 'additional data' fields.

• The uploaded file will be automatically validated. A CSV with reported issues can be downloaded, fixed and reuploaded.

• Once the full batch has been uploaded and no issues are identified, the cases will be created and analysis will begin.

• Up to 50 cases can be created at once.

Workbench | Workflow Improvements: IGV desktop integration, finalize case & more

Improved IGV desktop integration

The Emedgene variant page contains an IGV web viewer, which has limited functionality compared to IGV desktop. Some customers prefer to work in a dual screen set up, with IGV desktop open on a second screen.

Emedgene has an existing IGV desktop API integration for customers who start from VCF. In this version, the integration was expanded to customers who start from FASTQ or store files in an AWS S3 storage bucket.

By clicking the Load to IGV button, all available BAM/CRAM files will be loaded to the desktop IGV (only if the application is already running), and customers can further enhance and customize their viewer.

Case interpretation flow update

Users must select a case interpretation status (confidently solved, likely solved, uncertain, negative) before moving the case status to ‘Finalized’.

Interpretation notes, Gene interpretation and Recommendations are saved even if interpretation status is not selected.

Importantly, finalize case via API remains possible.

Add new case | Create existing gene lists

Increase flexibility to support customer workflows by enabling the creation of new gene lists that are identical to existing gene lists from API and UI. This will enable customers with a complex and large panel test menu to more accurately manage case creation.

Support for gene lists with up to 10,000 genes

Increase flexibility to support customer workflows by enabling the creation of large gene lists. Previous limitation was 900 genes.

Gene lists can be created via API and UI; Very large gene lists (>6700 genes) may return a false error message during creation, despite being successfully created.

New ACMG SNV Scoring!

• Each tag can be edited, and editing will modify the score.

Additional:

• API | New query returns a list of genes and NCBI IDs associated to the case phenotypes using the Phenomeld algorithm. This query will help laboratories meet compliance requirements.

• Variant Interpretation Paragraph - Now supports Catalan, Spanish, Portuguese, and Hebrew symbols.

New Settings

Manage your own S3 credentials

• Users can create up to two access keys.

• When creating a new key, there is only one opportunity to save/copy the access key and settings (warning appears).

• Users can deactivate keys.

• Following deactivation, users can delete keys.

• A help center article details the S3 buckets and how-to access.

• If assistance from Tech Support is needed, a new access key can be created and deleted after retrieval of the files needed for troubleshooting.

Gene Lists | View NCBI ID associated with a gene symbol; Download gene lists with NCBI IDs

The Emedgene pipeline and platform associates NCBI IDs to gene symbols, and preferentially utilizes NCBI IDs throughout the software to alleviate gene list changes due to gene symbol changes or user errors.

In the Management Page, users can view the NCBI IDs associated to the gene symbols within a list and download gene lists with NCBI IDs for review.

Limitations

• The accuracy of the AI Shortlist for the new variants (INS, mtDNA, STR, CNV/SV) depends on the variant calling accuracy. The user should be careful when interpreting these challenging-to-call variants.

• The new callers and visualizations – SMN, ROH, Ploidy, BAF - are only available for customers running WGS from FASTQ on Emedgene, with the exception of BAF, which is also available for customers running WES from FASTQ on Emedgene.

• To enable the SMN caller on your account please contact Support.

• Load to IGV will only work if IGV desktop is running.

• Load to IGV will upload all available case tracks to desktop upon every click, if a user accidentally clicks multiple times, the tracks will be uploaded multiple times.

• Emedgene Curate does not yet support CNV variants larger than 10M bp or intergenic variants

Fixed Issues

• The AI Shortlist typically ignores commonly occurring variants. There is an exception list of common variants known to cause disease. This list was expanded, and now includes:

• SV calling from WES | Updated DRAGEN SV command line for exomes, per DRAGEN recommendations.

• Disabled STR calling from WES | The DRAGEN ExpansionHunter method is only available for WGS.

• Update of the Emedgene UI to use the most updated version of the API, in alignment with the batch uploader and new Add New Case features.

• Error message time on screen was extended to 20 seconds following multiple customers requests.

• When customers tag a variant, evidence graph is created automatically along with variant summary and ACMG calculation. Previously, users had to enter evidence page in order to generate these features.

• Lab Tab | Insufficient regions – fixed a bug that sometimes displayed % > 100.

• Gene Lists | Fixed a bug where gene names with a hypen were split into two genes.

• Evidence Text | Fixed a bug with de novo on ChrX which generated a wrong inheritance in the interpretation text.

• Lab Tab | Fixed a bug where users couldn’t navigate directly to the Lab Tab.

• Illumina clouds | Fixed a bug where customers moving between several organizations were not redirected to the proper URL.

• Variant Page | Fixed a bug where large SNV indels were not displaying correctly in multiple page elements.

• Variant Page | Visualization | Fixed a bug where TNF bigwig tracks selected from advanced mode were misaligned to labels.

• Variant Page | Main effect field will always write ‘and’ instead of ‘&’ to avoid use of special characters unsupported by some reporting templates.

• Case Interpretation | Fixed bug in activity tracking that incorrectly mentioned reanalysis.

Known Issues

• CNV variants larger than 20 Mbp are not annotated with genes name and effect, these variants are shortlisted by default by the AI Shortlist, but ACMG automation is not applied to them. (Fix planned for v33).

• GRCh37<-->GRCh38 Liftover not available for older components of Network infrastructure, as a result, [Variant Page | Clinical Significance | Networks Classified] may remain erroneously empty while [Variant page | Related cases section] shows relevant information. Same gap for manually classified variants.

• Zygosity, even when set in extended sharing, may remain blank for older cases. Once you click on a case missing zygosity it will be saved for all future views.

• Sort by Phenomatch score is not available.

• Sort by Tags is not available.

• Analysis Type field is not available with this version of Batch Upload, and it cannot be used to initiate the new Carrier workflow.

• Analyze | Manually added variants | STRs -When manually adding an STR variant it cannot be tagged or reported.

• API | Creation of large gene lists may return an error (due to timeout) despite the creation of the gene list.

• ILMN Clouds | Help Center | Some links may not work. Work around: Paste the title into the help center search.

• Variant Page | Visualization | Chromosome visualization is missing for mtDNA variants in VCF case run on GRCh37.

• Variant Page | Visualization | Simple/Advanced mode for upload locally BAM does not work.

• Analysis Tools | Het count filters are not precise, include AC (total counts), display more data than expected.

• Analysis Tools | ‘Last’ button on pagination does not work.

• API | Assign users to case fails with no error if faulty emails used.

• Add New Case | Create a case from case creation summary does not work, please click on top Add New Case button from cases page.

• Lab Tab | % mapped reads is not populating data, can be viewed by downloading DRAGEN metrics. (Fix planned for V33)

• Candidates Page | Compound het SNV-CNV variants will not display the automated CNV classification. Workaround – view variants from analysis table.

• Candidates | When clicking on See all candidates link, variant filters are inactivated. Workaround: Reset filters to default.

• Organization Settings | Set mandatory fields - does not work from the UI. Please contact support if you’d like to configure these fields for your account.

• Gene Lists | Very large gene lists (>6700 genes) may return a false error message during creation, despite being successfully created.

Release highlights for both workbench 35.0 and pipeline 35.0:

• New AI capabilities: Sort by AI rank & Phenomeld score enhances use of AI models in analysis workflow.

• New gene list workflows: Apply multiple gene lists during and after case creation, with full traceability.

• Cases page gets two most frequently requested features to improve workload management: assign case to another user, & quality summary.

• CNV interpretation improvements: New visualization for target counts bigwig, sort by size, differentiate between variant callers for the application of noise DBs and more.

• New customer self-serve capabilities: Batch upload to Curate from the UI with validation, easy move/add of gene lists to organizations, new help center.

• Enhanced flexibility for lab implementations: Lab defined region of interest and QC per test type, more QC metrics with DRAGEN reports, custom BED annotations and filtering, efficient API queries.

• Expanding applications supported on Emedgene with a new haplotype variant and DRAGEN JSON ingestion support.

Emedgene customers can select their preferred version out of any of the past 5 releases. Customers on v30.0 and below should select an upgrade path at this time.

Updates

AI | Improved AI outputs for use in the interpretation workflow. AI rank and Phenomeld scores available and sortable in analysis tools.

Analysis Tools | Sort by AI rank

AI rank is now available in a sortable, exportable column in the analysis tools.

Emedgene does not provide the AI score as it can bias the analysis; whereas AI rank provides an unbiased method to utilize AI in the interpretation workflow.

• If two variants share an identical score they will have the same rank in the column.

• A reanalysis will update the AI rank values.

( i ) Requires workbench & pipeline update. Old cases can be rerun to retrieve the rank.

Analysis Tools | Sort by Phenomeld score

Phenomeld score is now available in a sortable, exportable column in the analysis tools, in addition to the available filter. Range is 0-2.

( i ) Requires workbench & pipeline update.

As a reminder, Phenomeld is a proprietary phenotypic match algorithm that estimates the concordance between patient phenotypes and an associated disease. It is an important component in our XAI model.

Phenomeld achieves an AUC of 0.94, and uses ensemble machine learning, which combines several phenotypic match models in order to improve model performance.

The Phenomeld model was validated with two data sets.

Utilizing an internal dataset of 314 well characterized cases, Phenomeld was compared to the open source phen2gene model, as well as to the previous Emedgene Phenomatch model, outperforming both.

A second validation used a set of 4648 ClinVar cases, and compared Phenomeld with phen2gene, where Phenomeld demonstrated improved results.

Apply multiple gene lists at and after case creation

This version improves support for labs that regularly apply multiple gene lists per case.

Add New Case | Apply multiple gene list or add genes to a gene list at case creation, from the UI

When applying a gene list at case creation, you can now create a new gene list comprised of multiple gene lists, or add genes to an existing gene list. The new ‘merged’ gene list will carry the same behavior as any other gene list on the platform.

Choose create a new gene list during add new case. Then, search for a single or multiple gene lists, or add genes to an existing gene list:

( i ) Requires a workbench update.

Analysis Tools | Dynamic gene list and search application to preset filters, with full traceability.

Customers can now dynamically couple a gene list, multiple gene lists, or any other search with their preset filters, and review the restricted subset of preset filters with full traceability. This enhancement addresses the need for users to track the reviewing of different gene lists in their case.

To increase flexibility of analysis, this feature is enabled using the search bar, which is now located above the preset filters.

Simply search for a gene list, multiple gene lists or any other supported search function.

By clicking on the 3 vertical dots, you can save your search as a custom preset filter. If you do not save a custom preset filter, you can still perform the restricted analysis, however it will not be saved, and you will not be able to populate it to a report.

You can then review the case according to any of your saved custom preset filters.

Custom preset filters are saved per case, have a full activity trail and can be automatically populated to a report.

( i ) Requires a workbench update.

Cases Page | Assign case to other user & quality summary for improved workload management.

The cases page is getting two of the most requested updates in this version.

Assign cases to users for improved workload management.

Lab directors can now assign cases to users, streamlining workload management within the lab. Previously only users could subscribe to a case.

( i ) Requires a workbench update.

Cases page now displays the case quality summary.

The case quality summary has been added as a column in the cases page. This quick view of case quality will improve workload allocation within the lab. The column is sortable and can also be filtered on.

Hovering on the quality icon will provide a quick summary of findings, indicating failure for case or sample quality, and also pedigree and gene coverage validation.

( i ) Requires a pipeline & workbench update.

CNV Interpretation Improvements | Added target counts BigWig, sort by CNV size & more.

This version adds multiple features aimed at improving CNV interpretation capabilities, an effort that will continue in subsequent versions.

• New visualization track = the target counts BigWig is now supported, in addition to the tangent normalized BigWig. This is a BigWig representation of the target counts bins. This new track is available from the UI, batch or API for customers starting from both FASTQ or VCF. ( i ) This feature requires both a pipeline and a workbench update.

• Analysis tools – new column for variant length (kb), can be sorted, exported and populated to the report. ( i ) This feature requires a workbench update.
• Analysis tools – New filtering capability by calling methodology. While this new feature applies to any variant caller used by customers, it can be used to create filters for CNVs called by the DRAGEN read-depth caller separately from the DRAGEN SV caller, so that customers can apply separate noise databases to each. The new filter appears under the Quality filters. Possible calling methodologies:

  • Small variant caller

  • CNV read-depth caller

  • Forced Genotyping

  • Star allele caller

  • STR repeat expansion caller

  • SV split-end caller

  • Targeted caller

  • Unknown

( i ) Requires a pipeline & workbench update.

• Annotation is now enabled for CNVs larger than 20M bp. ( i ) Requires pipeline & workbench update

• Visualization | Added the copy number value to CNV variants in the proband VCF track. ( i ) Requires pipeline & workbench update.

• Visualization | Improved performance for the embedded IGV enables quickly moving between variants when multiple new visualization tracks are selected. ( i ) Requires a workbench update.

Self-Serve: Batch upload to Curate with validation, easy move/create gene lists, new help center.

We continue to enable customers to control their Emedgene accounts, and to reduce their reliance on Illumina support teams.

Batch upload to Curate from the UI, with validation.

Customers can now batch add variants to Curate via the UI, utilizing a simple CSV template. Emedgene software will perform a validation on the upload to ensure compatibility and quality in customer Curate databases.

Simply switch to batch mode in the Add new pane in Curate to download an example CSV file and follow the link for more instructions. Note the size limitation for each upload is 5,000 variants. Multiple concurrent uploads are allowed.

After upload, a ‘toaster’ element will appear at the bottom left of Curate. While the toaster can be closed and the upload will continue, the report on the variants uploaded and any that might have failed or partially failed validation can only be accessed through the toaster.

( i ) This feature requires a workbench update.

Easy add/move gene lists in Management and Add New Case.

It’s easier than ever to create new gene lists in the Management page or Add New Case flow.

• When switching to batch mode, both gene symbols and NCBI IDs are accepted.

• When pasting a list of NCBI IDs or gene symbols from a CSV file, whether downloaded from an Emedgene staging organization or other, no further manipulation needed and the list is accepted as is.

( i ) This feature requires a workbench update.

We have a new help center!

Enhanced flexibility for lab implementations

This version adds multiple features that enhance flexibility to implement lab standard operating procedures.

• Define a region of interest and QC BED for any test type, previously only customization for test type ‘Custom Panel’ was enabled.

  • The region of interest BED, whether default or custom, determines the billing.

    • If the number of variants annotated is <55K, billing is for a panel.

    • If the number of variants annotated is 55K-300K billing is for an exome.

    • If the number of variants is greater than 300K billing is for a genome.

• If a reflex to a wider backbone is needed, the test can be edited and a different BED selected.

• QC BEDs can be uploaded separately.

The Region of Interest and QC BED files can be defined from the Add New Case flow in the UI batch upload, and API.

( i ) Requires a pipeline & workbench update.

• Many new QC metrics are now available in the Lab Tab through a DRAGEN report integration. If your DRAGEN report is available, a link will be added below the sample name. This feature is available for customers starting from FASTQ or VCF from API (See supported DRAGEN outputs below for details).

( i ) Requires a pipeline & workbench update.

• Efficient API queries are here! When fetching details of variant(s) and case(s) via the API, users can now define which values to return, rather than returning all values associated with the query. Each query will return default values, and in addition the fields requested.

( i ) Requires a workbench update.

• Support for custom BED annotations & filtering

Customers can now annotate their cases with a BED file, and filter on the variants based on the BED annotation. This feature requires support assistance for implementation.

( i ) Requires a pipeline & workbench update.

• Push genes of insufficient coverage to a report

Customers can push lists of genes with insufficient coverage at various thresholds (<=0x, <=5x, <=10x, <=20x; or % of BasesGt20x <=20%, <=50%, <=80%, <=90%) and details (transcript, exons affected, position etc) to a report.

( i ) Requires a workbench update

New haplotype support for DRAGEN star allele JSON.

This version expands the possible applications that can be interpreted and reported on in Emedgene to include haplotype driven applications.

This version expands the possible applications that can be interpreted and reported on in Emedgene to include haplotype driven applications.

• Ingest and annotate the DRAGEN star allele caller JSON file (*.targeted.json) including targeted caller CYP2D6 and CYP2B6 outputs as haplotype variants.

• New haplotype variant page displays haplotype, genes affected and quality parameters from DRAGEN.

• Haplotype variants can be interpreted and pushed into a report.

• Report pre-processing capabilities can be utilized to produce PGx reporting by integrating the customer’s own metabolizer status-drug database.

( i ) Requires a pipeline & workbench update.

Additional improvements to workflows and pipeline

• gnomAD PLI scores were added to export csv. ( i ) Requires a workbench update.

• ClinVar SV, ClinGen and MitoMap annotations were added to the monthly update automation infrastructure, and will be updated on a monthly basis going forward.

• DRAGEN pedigree pipeline, which improves accuracy of de novo calling for WGS, is now available for customers starting from FASTQ. ( i ) Requires pipeline & workbench update.

  • Only for ICA customers with input FASTQs in ICA, who are only running WGS in their organization.

  • This feature has always been available for customers who run their own DRAGEN pipeline.

  • From the customer perspective, no experience with ICA needed and this behaves just like the integrated Emedgene DRAGEN pipeline, fully and seamlessly executed for customers.

  • Billing for DRAGEN runs is on ICA with iCredits. On Emedgene, please purchase the Genome Equivalents VCF SKU.

• Customers starting from FASTQ will now run the DRAGEN 4.2 CNV-SV merged file by default. ( i ) Requires a pipeline update.

• This version supports ingestion of outputs from Illumina’s newly released Trusight Whole Genome IVD workflow. ( i ) Requires a pipeline & workbench update.

• This version supports ingestion of VCFs from Illumina’s CFTR IVD workflow. ( i ) Requires a pipeline and a workbench update.

• This version supports ingestion of small variant calling VCFs from the Illumina amplicon pipeline. ( i ) Requires a pipeline & workbench update.

• Supported DRAGEN 4.2 outputs in V35:

Limitations:

• Add New Case | Input file path cannot contain spaces or parenthesis.

• Add New Case | API | Applying multiple panels has a limit of 10,000 genes in total but no error message.

• Add New Case | For customers starting from Joint gVCF, please make sure the proband is first in order to see the correct insufficient region calculation.

• Pipeline | The DRAGEN pedigree pipeline for customers starting from FASTQ is only available for customers who have their FASTQ files stored on ICA, and only run WGS in their organization.

• Edit Case | Reanalysis | When applying a new gene list the original gene list is not displayed in activity.

• Lab Tab | Insufficient coverage export will not work via UI or API if an included gene does not have a start or end position in NCBI.

• AI Shortlist | Will not prioritize chr17:43124027 ACT>A in the BRCA gene which contains >600K links to publications, due to limitations on annotation file size. This limitation will be removed in upcoming patch releases V34.4 and V35.1.

• Analysis Tools | Multi-Select | Does not have an aggregated activity report.

• Analysis Tools | Manually Added Variants | Cannot be sorted on non-applicable column types e.g. AI rank.

• Analysis Tools | Manually Added Variants | STRs | Format is not aligned with format of STRs on the software, e.g. missing variant length.

• Variant Page | Population data | ‘af_max_any_pop’ utilizes rounding to 5 digits.

• Curate | When exporting a variant from Analyze to Curate, users may sometimes see an erroneous error message ‘None is not allowed for pathogenicity’. The actual error is an unsupported variant type.

• Curate | Transcript versions will not be identical in variants created in Curate vs variants created in Analyze. Future enhancement will align transcript selection logic.

• Curate | Discrepancy between Analyze and Curate HGVS parser may be experienced.

• Network | GRCh37<-->GRCh38 Liftover not available for older components of Network infrastructure, as a result, [Variant Page | Clinical Significance | Networks Classified] may remain erroneously empty while [Variant page | Related cases section] shows relevant information. Same gap for manually classified variants.

• Export to excel is limited to 32KB in size, which may prevent exports with very large CNVs.

• Webhooks | Cannot be trigger on internal software statuses such as ‘In Progress’ ‘Reanalysis’.

• Organization Settings | BED upload | Validation on the UI component does not check that all lines in the BED contain the same number of columns.

Fixed Issues:

• General | Users on Illumina clouds will now get a warning when they are logged out due to their IAM settings. The warning will prompt for a refresh, preventing loss of work on the Emedgene software. This issue was fixed in v34.2 patch and is re-documented with this release.

• General | When there is a mismatch of the number of variants in the VCF and the number of variants in the case, a prominent red warning banner appears on the software. Prior to V35 this banner was organization-wide, flashing up for all users even with unaffected cases. Starting with this version, the warning will be case specific.

• Candidate | Evidence Graph | Updated literature links to LitVar2.

• Variant Page | Fixed an issue where in some cases OMIM inheritance modes were incorrectly displaying CGD values.

• Analysis Tools | Fixed an issue that caused PLI filters relying on a ‘lof_intolerant_probability’ query to return partial results.

• Curate | Fixed an issue causing display of Related Cases component for the previously displayed variant.

Known Issues:

• gnomAD 4.1 fix will be supported in V34.5/V35.1. All gnomAD 4.0 links from the UI are directed to 4.1 data, as there is no way to link directly to 4.0 data. This creates a data<-->link discrepancy as Emedgene annotation data is still on gnomAD 4.0.

• Add New Case | Flow to run case as a singleton and add family members in a rerun is temporarily not working for cases starting from FASTQ. Targeted fix for V34.4 & V35.1.

• Add New Case | API | When sending due date please use UTC time, customer time zone is not taken into account with API, only through the UI.

• Edit Case | Reanalysis | If HPO terms were updated between analyses, the reanalysis will not automatically map previous HPO terms to new ones.

• Cases Page | Illumina Clouds | Users that have been removed from workgroups in IAM can still be added as participants to a case. They will not have access to the software, and there is no security/access risk.

• Candidates Page | Compound het SNV-CNV variants will not display the automated CNV classification. Workaround – view variants from analysis table.

• Lab Tab | Average coverage calculation in the UI can miscalculated and over 100% in rare cases. Targeted fix for V34.5 and V35.1.

• Lab Tab | UI issue makes it difficult to identify which sample is selected for viewing quality metrics. Fix planned for V34.5/V35.1.

• Analysis Tools | ‘Last’ button on pagination does not work.

• Variant Page | Rare lag in variant interpretation load time can cause text to be mistakenly overwritten.

• Variant Page | Visualization | Simple/Advanced selectors will not work for locally uploaded BAM files.

• Curate | Searching for a variant causes the related cases to disappear even when search is removed. Work around is to refresh.

• Curate | Orphanet links no longer work due to an Orphanet link structure update.

• Finalized Case | When user enters a variant in a case in finalized status, variant will be marked as viewed. Fix planned for V35.1.

• Activity | Editing interpretation paragraph yields an erroneous activity labeled reanalysis.

• API | Marking over 5000 variants as viewed will not result in an error message, although this is the database limitation for saving viewed variants.

• Dashboard | Diagnostic Yield includes Uncertain as Resolved.

V32.4 hotfix released for the following issues:

• Add New Case | Storage | Fixed a timeout issue retrieving BSSH projects for customers with very large numbers of projects.

• Pipeline | Fixed an issue that caused variants with GT = “.” to be displayed as Hemizygotes on the user interface.

• AI | Fixed a limitation of the AI with processing variants with large ClinVar annotations.

• Candidate Page | Fixed issue where displayed gene on candidate page differed from gene in evidence graph/analysis tools.

• Variant Page | Updated Orphanet links to new Orphanet structure.

• Variant Page | Fixed an issue where MitoTip prediction score quartiles were mislabeled, although the score appears correctly.

• Curate | Fixed an issue where related cases component could link to the wrong related case if payload data was missing.

• Reporting | Fixed an issue where reanalyzed cases between versions could sometimes result in issues tagging variants for reports.

• Performance: Additional updates to increase performance specifically for IGV component.

V32.3 hotfix released for the following issues:

• Add New Case | NovaseqX added to selectable sequencers.

• Cases Page | A search on this page will only search for EMG ID, sample names, or any string in the test data. This fix will improve performance.

• Analysis Tools | Fixed variant count issue for compound heterozygous filters caused by using a single source for what is essentially a two-step process. Only count displayed was incorrect.

• Variant Page | Fixed incorrect gnomAD link after the gnomAD v4 release.

• Performance: Additional updates to increase performance through infrastructure modifications.

• Pipeline | Fixed a bug that rarely caused discordant AI Shortlist results between a first and second analysis due to model selection.

• Pipeline | Fixed an issue causing some reanalysis cases to fail due to insufficient backward compatibility with previous zygosity values. This fix will improve pipeline robustness.

V32.2 hotfix released for the following issues:

• Performance: Additional updates to increase performance through infrastructure modifications.

V32.1 hotfix released for the following issues:

• Batch Upload | Fixed issue for singleton cases uploaded with batch uploader that resulted in inability to edit cases after creation.

• Batch Upload | Fixed issue causing Not Authenticated error for customers with more than 100 BSSH projects.

• Batch Upload | Improved backward compatibility for Gender changed to Sex field (in v33)

• Lab Page | Fixed issue of no coverage statistics for cases with missing samples. Coverage appropriately generated for the samples submitted with the case.

• Lab Page | Fixed missing average coverage affecting some pipelines.

• Analysis Tools | Manually Added Variants | Fixed a bug where manually added variants are sorted incorrectly causing them to ‘disappear’ from the UI.

• Analysis Tools | Export | Resolved issue in export of some Presets and Filters due to incomplete customer facing role.

• Variant Page | Updated Decipher link after link structure change.

• Curate | Fixed User Interface bug where selecting a disease associated with a gene for a variant, makes is appear like it is selected for all variants in that gene. Backend is behaving as expected, each variant is independent.

• Curate | Enable customers to login to Curate when signed into a different organization on Analyze.

• Reanalysis | Fixed backward compatibility issue preventing variants in cases originally analyzed on and before V27.0 to be pushed into a report.

• Settings | Fixed issue where S3 credentials couldn’t be generated for long domain names. Character limit is eliminated.

• Settings | Fixed issue in kit BED validation for chromosome validation.

• Infrastructure: Multiple improvements of resource allocations to increase robustness.

• Pipeline | Improved error logging for DRAGEN for easier troubleshooting.

• Pipeline | SMN Caller | Fixed multiple issues causing case failures from FASTQ & BAM.

• Pipeline | SMN Caller | Fixed issue for GRCh37 & SMN caller where relatedness isn’t calculated due to Peddy failure.

• Pipeline | Enable flow where in a trio only the Proband has Ploidy outputs and parents don’t.

• Pipeline | Don’t fail cases where no samples are provided but ignore samples isn’t set.

• AI Shortlist | Include full gene list in Phenomeld for virtual panels, irrespective of phenotypic match.

• Pipeline | Fixed issue where proband coverage copied to parents for customers starting from joint gVCF.

Release Highlights

2. - New self-serve features available to customers

Emedgene customers can select their preferred version out of any of the past 5 releases. Customers on v29.0 should select an upgrade path at this time.

The software release includes the following components, which can be selected independently:

• Platform 33

• Pipeline 33

Pipeline: Support for DRAGEN 4.2 Release

All supported DRAGEN callers can now be run with DRAGEN 4.2, for customers starting from FASTQ or VCF.

DRAGEN 4.2 includes enhanced multigenome (graph) reference and Machine Learning (ML) models that improve small variant calling accuracy. Emedgene supports the new graph and ML while maintaining backward compatibility for customers on previous DRAGEN versions.

Improved CNV calling accuracy achieved through joint CNV/SV detection is available for customers starting from VCF (FASTQ support coming in 34.0). In order to minimize duplication, SV variants that are not merged with CNVs are removed from the CNV_SV VCF, and are ingested separately via the SV VCF.

Supported DRAGEN 4.2 outputs in 33.0:

Limitations

• Discrepancies between DRAGEN callers supported from VCF and FASTQ, where some are only supported from FASTQ and some from VCF, will be addressed in Emedgene 34.0 (Q4 23).

• Not all DRAGEN 4.2 callers are supported.

• High sensitivity caller will be supported in 34.0.

• Additional targeted callers will be supported in mid-2024 with the release of DRAGEN 4.3.

Platform: Organization Settings. New self-serve features available to customers

In 33.0 we’ve added the following self-serve capabilities:

i. Select your own URLs from the available URLs in your domain

Customers on ILMN clouds can now select their preferred URLs. It takes 1-15 minutes for URL changes to go live.

ii. Select a platform version for your organization from officially released versions

This feature is available for both Emedgene and Illumina cloud customers. It takes 1-15 minutes for changes to go live.

Note:

1. This is available only on 33.0 and up. If you select a previous version the feature will disappear from your organization settings, and you will need to contact support to change platform versions.

iii. Set your own case identifier to display on the case and variant page

Emedgene by default displays the EMGXXXXXXXXX case identifier. Customers can now choose to display the proband ID instead. The proband ID has a visible 13-character limitation, and the remaining characters will be visible on hover.

Candidate page displaying a proband ID:

Variant page displaying a proband ID:

IV. Improved BED validation errors

When attaching a BED file to a kit in the Management tab, the system will generate clear and actionable error messages for any exceptions that may occur.

Limitations

• Proband ID field is limited to 13 characters.

• Changing a preferred URL or a platform version takes 1-15 minutes to go live.

Platform: Workflow enhancements

Support for ACMG Secondary Findings v3.2

For the XAI, when a user selects to receive secondary findings, we will apply the v3.2 gene list (requires pipeline 33).

Edit a case label after case creation from the UI

New export capabilities

• Export/report on the gene list associated with the case HPO terms. This gene list is produced with the Phenomeld phenotypic match algorithm. The capability was added in 32.0 but now customers can include the gene list in their report.

Limitations

• Analysis Tools | Sort by phenomatch score and tags is not yet available

• Curate | Some HGVS p-values not accepted yet, discrepancy between Curate and Analyze

Fixed issues

• ClinVar sanity check fails case if there are no known variants in ChrY with wrong message. Cases will still fail but with the correct error message.

• Variant Page | Fixed an issue where a manually added transcript would display twice.

• Analysis Table | Filters | Polymorphism Filters | Fixed an issue where a filter was mislabeled Het or Het Count instead of Allele Count. No variants were missed due to this mislabeling, as the Allele Count filter is more inclusive.

• Analysis Table | Preset Filters | Fixed bug where updated gene lists were resulting in a case incompatible error message.

• Analysis Table | Fixed an issue where manually added variants were sorted incorrectly causing them to ‘disappear’ from the UI.

• Add New Case, Lab Tab, Cases Sidecar | Gender changed to Sex.

• Add New Case | Fixed a bug where users couldn’t edit cases that failed due to bad inputs.

• Lab Tab | Fixed an issue where % mapped reads was always 0.

• Export/Report | Fixed an issue where synonymous variants were exported with ‘%3D’ instead of ‘=’.

• Notification | Fixed a bug where case delivery email notifications included organization parameters based on the user creating a case rather than the organization.

Known issues

• Organization Settings | Set mandatory fields - does not work from the UI. Please contact support if you’d like to configure these fields for your account.

• Gene Lists | Very large gene lists (>6700 genes) may return a false error message during creation, despite being successfully created.

• Visualization is not supported for users storing VCF and CRAM on ICA V1 and BSSH. Only VCF and BAM are supported.

• Variant Page | Visualization | Chromosome ideogram visualization is missing for mtDNA variants in VCF case run on GRCh37.

• Variant Page | Visualization | Simple/Advanced selectors will not work for locally uploaded BAM files.

• Variant Page | Visualization | Zoom out of BigWig/TTS displays mean data.

• Variant Page | ACMG SNV Score | Incorrect score for mtDNA variants, although classifier behaves as expected.

• Analysis Tools | Preset Filters | Preset containing a gene list ID will display filtered data when an organization has configured a base gene list filter.

• Analysis Tools | ‘Last’ button on pagination does not work.

• Candidates Page | Compound het SNV-CNV variants will not display the automated CNV classification. Workaround – view variants from analysis table.

• Candidates | When clicking on See all candidates link, variant filters are inactivated. Workaround: Reset filters to default.

• Candidates | SV Insertions information partially displayed. Work around: View from a preset filter.

• Network | GRCh37<-->GRCh38 Liftover not available for older components of Network infrastructure, as a result, [Variant Page | Clinical Significance | Networks Classified] may remain erroneously empty while [Variant page | Related cases section] shows relevant information. Same gap for manually classified variants.

• Network | Zygosity, even when set in extended sharing, may remain blank for older cases. Once you click on a case missing zygosity it will be saved for all future views.

• Manually Added Variants | STRs -When manually adding an STR variant it cannot be tagged or reported.

• Manually Added Variants | Users without the role can add variants but not save them. Button should be disabled.

• ILMN Clouds | Help Center | Some links may not work. Work around: Paste the title into the help center search.

• Add New Case | Batch Upload | Analysis Type field is not available with this version of Batch Upload, and it cannot be used to initiate the new Carrier workflow.

• Add New Case | Create a case from case creation summary does not work, please click on top Add New Case button from cases page.

• Reanalysis | If HPO terms were updated between analyses, the reanalysis will not automatically map previous HPO terms to new ones.

• Lab Tab | Reanalyzed cases will show up with duplicated insufficient gene regions. Fix planned for 34.0 .

• Lab Tab, Sidecar | Pedigree | In very large pedigrees some family members can’t be clicked to view quality.

• Lab Tab | STR repeats number for parents does not exist, proband values displayed.

• Curate | ILMN cloud users need to be logged in to the organization from which they are trying to access Curate.

• API | Assign users to case fails with no error if faulty emails used.

• API | Creation of large gene lists may return an error (due to timeout) despite the creation of the gene list.

• Report/Export | For variants tagged as ‘Most Likely’ order is not preserved when pushing to the report. Work around – use another tag, e.g. ‘In Report’.

• Activity | Editing interpretation paragraph yields an erroneous activity labeled reanalysis.

• Dashboard | Diagnostic Yield includes Uncertain as Resolved.

New Variant Types Supported

SV Insertions

Emedgene now supports calling and interpretation of SV insertions called by the DRAGEN Manta SV caller.

Calling:

The DRAGEN Manta SV caller detects simple insertion/deletion events , and detects both fully-assembled and partially-assembled (inferred) insertions. Minimum size of SV insertion is 50bp. Indels smaller than 50bp are called by the regular SNV caller and annotated as SNV.

Known caller limitations:

• The maximum fully-assembled insertion size should correspond to approximately twice the read-pair fragment size, but note that power to fully assemble the insertion should fall off to impractical levels before this size.

• Note that Manta does detect and report very large insertions when the breakend signature of such an event is found, even though the inserted sequence cannot be fully assembled.

• In the case of partial assembled insertions, the size of the variant displayed does not reflect its true size.

Note that for customers bringing their own DRAGEN pipeline into Emedgene, specific VCF headers in the SV file need to be added before sample ingestion. Contact support for more information.

Annotation:

SV insertions are annotated with gnomAD SV and ClinVar SV data, for population frequencies and known pathogenicity. Insertion annotation is performed on the basis of the insertion start position; the sequencing content is not considered.

Interpretation:

Variant page and analysis tools have been adapted to support SV insertions.

• Variant type will be clearly marked in the header

• New filters added for filtering SV insertions, quality filtering for both length and bin count can be applied (see remark above regarding the INS size).

STR Improvements

• New pathogenicity filter

• Allele frequency is now viewable in the proprietary STR visualization

Summary Table of Variant Types Supported by Test Type and Version

New Visualization Tracks

Curated Data Tracks

You can now add ClinVar and ClinVar SV tracks to the in-platform visualization. Pathogenicity corresponds to the ClinVar color scheme, with black denoting a conflict.

BigWig Track for CNV Visualization

BigWig visualization is now available for WGS cases, specifically the tangent normalized signal points view. This visualization helps interpret CNVs by clearly showing the bins and breakpoints.

For customers bringing their own DRAGEN output, a VCF and BigWig data can be shared via the API and batch upload tool.

These new tracks are available in both simple and advanced modes, allowing you to configure the visualization tab as needed.

Additional

A known mtDNA visualization discrepancy on GRCh37 was fixed in this version.

As always, we support synchronization with IGV desktop, and all settings in the platform can be mirrored to the IGV desktop environment which continuously displays the current selected variant data.

Emedgene Curate + CNVs

CNVs are now supported in Emedgene Curate! Including streamlined annotation and analysis flow integration, all the way through to auto-populating report template fields.

• Add a CNV variant directly to Emedgene Curate, or import during your case analysis;

• Search for a CNV by range, type or gene;

• Variant header, info card and gene’s related disease components have been adapted for CNVs;

• Select a disease for a curated CNV variant;

• Explore the related cases table - filter by % annotation overlap.

• In your Curate navigation, you will notice a new column denoting Variant Type. For labs with enabled private networks, the icon will denote pathogenicity by color, with a hover showing more details.

Additionally:

• Once you have curated a CNV variant, all future cases including in your private network if enabled, will be annotated with your data.

• Once a variant is reviewed, curated data can be imported and used to automatically populate a report template field.

Additional new features

Gene-related disease card update

The gene-related disease has always shown a numeric summary of phenotypic match, for patient phenotypes found in the disease out of all patient phenotypes.

This card now shows a numerical match between patient phenotypes and disease phenotypes. The full list of disease phenotypes is displayed, with the phenotypic match strength for each. A link to the full list of patient phenotypes will open the side car for an easy view and comparison.*

Edit interpretation summary

Edit the interpretation summary at the top of the page, in addition to the edit capability in the evidence tab.*

*Note that both of these new capabilities are only available for variants tagged by the AI Shortlist or users as most likely or candidates.

Variant page sidecar redesign

The variant page sidecar has been redesigned.

• Includes a default view:

  • Sample names of proband and family members.

  • Proband phenotypes, and family if available

• Allows you to configure your desktop IGV and Alamut connections, including the new Alamut API.

• The sidecar can be collapsed and expanded, and does not cover active window

Enhancement to Analysis Table

In the analysis tools, the known variant column colors had previously ignored VUS (variants of unknown significance) classifications if appearing in conjunction with P/LP or B/LB.

This has now been updated and if a variant has both P/LP and VUS classifications or B/LB and VUS classification, the appropriate mixed colors will appear.

If a variant has conflicting classifications it will appear in black.

Lab Page Enhancement

For labs using the Emedgene DRAGEN pipeline, QC metrics are now available for download.

ACMG 78

Updated filters to support full ACMG 78 gene list.

Expose input file errors

The majority of case pipeline failures are due to errors in customer input files. We now expose explicit and detailed input file errors on the cases page.

New AI Models

This version was primarily focused on introducing new AI innovation, with the goal of streamlining workflows and further reducing time-per-case.

Shortlist CNVs and Compound Heterozygous SNV-CNV Variants

Our AI Shortlist now compiles CNVs with evidence, along with compound heterozygous SNV-CNV variants. We expect this exciting new capability to drive significant time savings.

The model expands our core AI Shortlist model to CNV variants, and similarly considers dozens of features used by geneticists to interpret a case. The model was validated in a cohort of 51 singletons previously solved by a CNV variant. In 92% of cases (n=47 / 51) the solving variant was identified in a short list of 10 variants. In 6% (n=3), the solving variant was present in the candidate list. Only 2% (n=1), or a single case, was missed by the new AI Shortlist.

Due to the challenging quality nature of CNV variants, the conventional successful AI Shortlist model for SNV is not affected by newly added CNV results. CNV and compound heterozygous variants shortlisted variants are cumulative to SNV/indels, and the default short list for your organization will be extended by 5 variants on average.

The model supports deletions and duplications called both by the DRAGEN CNV read-depth caller and DRAGEN SV caller.

Improved Phenotypic Match Model

We have a new and improved phenotypic match model, Phenomeld. Phenotypic match algorithms estimate the concordance between patient phenotypes and an associated disease, and are a critical component in the AI Shortlist model.

Phenomeld, which achieves an AUC of 0.94, is used both as part of the AI Shortlist model, and as an independent filter in the analysis tools. The improvement was achieved with ensemble machine learning, which utilizes several phenotypic match models to improve model performance.

The Phenomeld model was validated against two data sets.

Internal Validation Set

A second validation used a set of 4648 ClinVar cases, and compared Phenomeld with phen2gene, where Phenomeld demonstrated improved results.

ClinVar Validation Set

For exploration of phenotypic match results outside of the AI Shortlist models, you can use the Phenomeld filter in the analysis tools.

Support for DRAGEN 4.0

This version supports DRAGEN 4.0 with ML and graph mapper, both for customers using the Emedgene DRAGEN pipeline and customers bringing their own DRAGEN.

DRAGEN 4.0 improves accuracy and reduces analysis time by ~26%.

Workflow Improvements

Related Cases Enrichment

The table now includes: solved/unsolved status, zygosity and affected and overlap % (for CNVs only).

When a case is selected, additional data is displayed: interpretation, phenotypes, proband ID, demographics, ACMG tags and case type.

Bulk Translation of Reports

Our reporting system now enables customers to upload custom data sets to reports. This enables customizable and flexible bulk translation and augmentation of reports with proprietary data.

Emedgene Curate Improvements

• Private Networks now support CNV variants, with selectable % overlap.

• Store gene interpretations and auto-populate to reports

• New gene metrics card for easier gene curation

Enhancements

• Lab Page | Gene Coverage - Region coverage statistics will now be calculated based on the case’s kit associated BED file. If none is defined, a default clinical exome BED will be used.

• Variant Page | ACMG - You can now write and store notes on ACMG tags for SNV variants (previously available only for CNV variants).

• Analysis Tools | Presets - New search bar in gene lists, for faster addition of gene lists to preset filters.

• In organization settings, you can now view and manage Enrichment Kits.

  • Standard users can view the BED file used for any kit

• PolyPhen2 is back! Illumina has acquired a license to include this data in tertiary analysis platforms.

• Gene Lists | When creating a gene list, the platform will save the NCBI ID for any gene in order to maintain compatibility with future gene symbol updates without the need for a lab gene list audit.

• Expanded ethnicity list to support an increasingly global and diverse customer base.

Release highlights for both workbench 36.0 and pipeline 36.0:

• Support for DRAGEN 4.3 for customers starting from VCF and FASTQ including expanded multi-genome mapping, improved high-sensitivity and mosaic calling algorithms, support for the new MRJD caller and higher targeted caller coverage.

• Significant run time decrease for a genome trio from 12 hours to 5 hours.

• New focused mode AI shortlist increases precision and recall, ranking solving variants higher and presenting a shorter ‘most likely’ list.

• New self-serve organization settings for more granular control over organization set-up.

Emedgene customers can select their preferred version out of any of the past 5 releases. Customers on v31.0 and below should select an upgrade path at this time.

Updates

Comprehensive DRAGEN 4.3 support

DRAGEN 4.3 offers significant improvements in accuracy, comprehensiveness and efficiency documented comprehensively in DRAGEN .

In these release notes we will focus on updates to the Emedgene workbench and pipeline that will result in a clear path to interpreting DRAGEN 4.3 outputs.

General compatibility with DRAGEN 4.3 variant callers

Emedgene enables customers to run DRAGEN in Emedgene, or in Bring Your Own DRAGEN (BYOD) workflows on DRAGEN server, BSSH or ICA pipelines.

The following table summarizes the supported DRAGEN 4.3 callers:

Improve mosaic calling and interpretation

New mosaic calling ML model results in 4x fewer FPs than DRAGEN 4.2 high sensitivity mode, and is both more accurate and faster than other mosaic callers.

In Emedgene, mosaic variants are now displayed with a ‘Potential Mosaic’ tag, and users can create preset filters with this tag.

When running DRAGEN through Emedgene, mosaic detection is activated by default with an AF filter threshold set to 0.2.

High sensitivity variant interpretation

High sensitivity mode is turned on by default in DRAGEN 4.3. In Emedgene, these variants are displayed with a ‘Homology Region’ tag, and users can create preset filters with this tag.

Interpret results from the new MRJD caller with the new connected variants component

The MRJD caller provides coverage for the following genes:

Variants will be displayed with ‘Ambiguous calling’ tag, and users will be able to filter for these variants using the Calling Methodology filter.

Since some of the variants output by the MRJD caller are ambiguously placed, and connected by a unique identifier called ‘JIDS’, Emedgene designed a new Connected Variants component to display the connected variants in one view.

When running DRAGEN through Emedgene, MRJD high sensitivity mode will be enabled by default.

New Connected Variants components

A new “Connected Variants” section has been added to the Variant Page providing geneticists with crucial insights into variant relationships within the same case. This feature aids in the accurate assessment of variant pathogenicity by displaying related variants and their connections.

The Connected Variants section displays 3 types of variant connections:

• MNVs – multi-nucleotide variants occurring within 2-nucleotides

• Ambiguously called variants by DRAGEN connected via the JIDS or Joined IDs.

• Compound Heterozygote variants (Only available for trio cases where both parental samples are provided).

Connected Variants will appear both in the summary tab and in a new component located between the Population Statistics and Related Cases vertical tabs. It is available for SNV/indel, SV, CNV, MtDNA, and STR variant types. Only the first 50 connected variants will be displayed.

The Connected Variants tab is available in both simple and advanced mode, where simple mode displays all connected variants, and advanced mode allows you to filter on either of the 3 available connected variant types.

Expanded targeted caller support

New Emedgene coverage for GBA, HBA & CYP21A2 was added with DRAGEN 4.3. Similar to the MRJD caller output, some targeted caller outputs are also ambiguously placed and connected via a JIDS identifier. The connected variants component supports the display of these variants. Variants will be displayed with ‘Ambiguous calling’ tag, and users will be able to filter for these variants using the Calling Methodology filter.

Quality metrics updates

In DRAGEN 4.3, Emedgene overall quality calculations are aligned with DRAGEN recommendations. See details in the table below.

In addition, new metrics are displayed in the variant page.

For CNVs called from exomes/panels (but not genomes), DRAGEN 4.3 has added a likelihood ratio score. The likelihood ratio is a Log10 likelihood ratio of ALT to REF.

For STRs, the ref and alt confidence interval is now displayed, and additional metrics will be added in V37.

Annotation pipeline speed improvements

This version greatly improved the case pipeline speed for a genome trio, and also reduced the high variability seen in genome trio processing times. Note that this pipeline is executed after DRAGEN secondary analysis.

New focused AI shortlisting model improves recall and precision

The Emedgene focused AI model for shortlisting variants likely to solve the case has been retrained to increase both precision and recall.

As a reminder, the AI model is available in two modes:

• Focused mode, which is trained to find a likely solving variant in known genes and will split the shortlist into known and unknown genes. This version of the focused mode will suggest very few genes of unknown significance.

• Discovery mode, which is trained to suggest a shortlist of likely solving variants in both known genes and genes of unknown significance.

AI mode is defined in the organization settings.

In this version, only the focused mode AI was updated.

Model Performance

The model was evaluated with a proprietary Illumina dataset of 1375 cases.

Rank of solving variant is significantly improved

• V36 focused mode: 97% of cases were solved by the top 3 variants

• V35 and under: 97% of cases were solved by the top 9 variants

Average number of variants shortlisted in a case is significantly reduced

• 45% of cases in the validation set had only 3 variants.

• An additional 15% had 4 variants.

• The median length of the short list is 4 variants.

Validation dataset characteristics

Self-Serve: New organization settings for granular and self-serve control.

These updates provide customers with the ability to view and edit information related to their organization directly, thus improving accessibility and reducing dependence on Illumina support. These new settings are available in Settings -> Organization Settings and require new roles per card. Any changes on this page are tracked with activities.

Information and POC Cards

The Information Card displays the cloud region, organization name, ID and URL, and environment version. There is no edit option in this card.

The POC, or Person of Contact card, displays the email of the primary point of contact regarding this Emedgene organization, and can be edited.

Pipeline Card

The Pipeline card enables users to select and manage pipelines for samples and cases, including the selection Human Reference and DRAGEN version settings.

A new toggle "Include Reference Homozygous & No Coverage calls" has been added. Enable this setting to include reference homozygous genotype and no coverage calls in cases.

AI Shortlist Card

This card allows user to select a preferred AI shortlist version:

• Focused mode, which is trained to find a likely solving variant in known genes and will split the shortlist into known and unknown genes. This version of the focused mode will suggest very few genes of unknown significance.

• Discovery mode, which is trained to suggest a shortlist of likely solving variants in both known genes and genes of unknown significance.

Limitations:

• Login | Emedgene does not support accents in User Names, despite support for these in IAM console. Users will not be able to login to the software.

• Add New Case | Input file path cannot contain spaces or parenthesis.

• Add New Case | API | Applying multiple panels has a limit of 10,000 genes in total but no error message.

• Add New Case | No validation that:

  • Sample IDs are unique

  • Input files are uncorrupted

• Add New Case | BSSH integration does not discard QC failed samples.

• Add New Case | For customers starting from Joint gVCF, please make sure the proband is first in order to see the correct insufficient region calculation.

• Add New Case | Selecting a disease should automatically suggest phenotypes, however, some diseases available for selection are from sources without phenotypes, and in that case, no phenotypes will be suggested.

• Add New Case | API/Batch/UI discrepancies:

  • Cannot add phenotypes for unaffected parent in batch upload.

  • Cannot use the same gVCF file for multiple samples from the UI.

  • Cannot upload JSON files in Batch upload.

• Pipeline | The DRAGEN pedigree pipeline for customers starting from FASTQ is only available for customers who have their FASTQ files stored on ICA, and only run WGS in their organization.

• Pipeline | Transcript selection prioritization limitations: sometimes prioritizing fusion genes over independent genes with the same severity.

• Edit Case | Reanalysis | When applying a new gene list, the original gene list is not displayed in activity.

• Cases Page | When sample pipeline (DRAGEN) fails, there is no clear error message.

• Lab Tab | Insufficient coverage export will not work via UI or API if an included gene does not have a start or end position in NCBI.

• Lab Tab | When sample gender is unknown, results of sex validation can be confusing as default gender in Emedgene is Female, so predicted Male will show up as failed.

• Analysis Tools | Search | When searching for positions range, search does not consider END for CNVs.

• Analysis Tools | Multi-Select | Does not have an aggregated activity report.

• Analysis Tools | Manually Added Variants | Cannot be sorted on non-applicable column types e.g. AI rank.

• Analysis Tools | Manually Added Variants | STRs | Format is not aligned with format of STRs on the software, e.g. missing variant length.

• Candidates, Variant Page | After editing the evidence graph, phenotypic match strength indications are missing from the sidecar and variant page.

• Variant Page | Evidence | ACMG automation will not be calculated for CNVs over 20MB.

• Curate | CNVs over 10MB are not supported. Fix planned in Q4 2024.

• Curate | When exporting a variant from Analyze to Curate, users may sometimes see an erroneous error message ‘None is not allowed for pathogenicity’. The actual error is an unsupported variant type.

• Curate | Transcript versions will not be identical in variants created in Curate vs variants created in Analyze. Future enhancement will align transcript selection logic.

• Curate | Discrepancy between Analyze and Curate HGVS parser may be experienced.

• Network | GRCh37<-->GRCh38 Liftover not available for older components of Network infrastructure, as a result, [Variant Page | Clinical Significance | Networks Classified] may remain erroneously empty while [Variant page | Related cases section] shows relevant information. Same gap for manually classified variants.

• Export | Export to excel is limited to 32KB per cell, which may prevent exports with very large CNVs.

• Reporting | PMIDs will only work if there is an author on link, no support for books.

• Webhooks | Cannot be trigger on internal software statuses such as ‘In Progress’ ‘Reanalysis’.

• Organization Settings | BED upload | Validation on the UI component does not check the following.

  • No validation at all for API uploads.

  • All lines in the BED must contain the same number of columns.

  • No duplicate lines.

  • No trailing whitespaces.

Fixed Issues:

• Add New Case | Blocked the ability to run a case from ICA where upload status is incomplete.

• Add New Case | Group FASTQ pairs by lane in Emedgene DRAGEN.

• Edit Case | Multiple fixes

  • Improved robustness of reanalysis for old cases.

  • Fixed issue where reanalysis of carrier analysis cases unselected this analysis type.

• Fixed issue where changing case status from finalized also automatically changed it from resolved to unresolved.

• Variant Page | Updated default annotation to gnomAD 4.1-non UKB data.

• Variant Page | Removed rounding of max AF% in order to accommodate very large gnomAD 4.1 data set.

• Report/Export | Fixed an issue with populating ACMG tags to the report.

• Management | Roles | Improved the addition of new user roles for new versions, so they are automatically available to assign.

• Pipeline robustness | Improved error messages for very large cases.

Known Issues:

• Add New Case | API | When sending due date please use UTC time, customer time zone is not taken into account with API, only through the UI.

• Add New Case | Storage | Issue loading BSSH VCFs from the UI, will be hotfixed with v35.4/v36.1. Please use batch upload to load files from BSSH.

• Edit Case | Reanalysis | If HPO terms were updated between analyses, the reanalysis will not automatically map previous HPO terms to new ones.

• DRAGEN 4.3 | When providing joint called DRAGEN 4.3 SV files, proband VCF filter field is copied to parents.

• DRAGEN 4.3 | For customers on DRAGEN 4.3 and on GRCh37, there is no DRAGEN ref validation on CYP21A2 variants from the targeted.vcf, may cause case to fail.

• Cases Page | Illumina Clouds | Users that have been removed from workgroups in IAM can still be added as participants to a case. They will not have access to the software, and there is no security/access risk.

• Cases Page | Reupload fails for JSON files.

• Candidates Page | Compound het SNV-CNV variants will not display the automated CNV classification. Workaround – view variants from analysis table.

• Lab Tab | When a gene is removed from the knowledge graph, no coverage will be shown, until gene is removed from gene list.

• Analysis Tools | Intermittent issues using variant type filters in combination with variant effects, will be resolved with a refresh.

• Analysis Tools | ‘Last’ button on pagination does not work.

• Variant Page | Summary | mtDNA variants displayed max AF from gnomAD does not utilize all sub populations, resulting in inaccuracy.

• Variant Page | Summary | When ACMG tags are updated by users, the summary component is erroneously not updated.

• Variant Page | Clinical Significance | DANN score showing as 0 on GRCh38 variants. DANN data is only available on GRCh37, and should not be visible for GRCh38 variants.

• Variant Page | Clinical Significance | For reanalyzed cases, network classified variants may appear as N/A for cases on GRCh38.

• Variant Page | Visualization | IGV component performs a mean calculation when zooming out, typically around 3Mbp. This will affect BAF and BigWig files visualization.

• Variant Page | Visualization | Intermittent appearance of "cannot read properties of undefined” error due to IGV component limitation.

• Variant Page | Visualization | Simple/Advanced selectors will not work for locally uploaded BAM files.

• Variant Page | Related Cases | For organizations on Illumina clouds, workgroup ID is shown instead of workgroup alias.

• Variant Page | Evidence | ACMG notes won’t save if tag was changed. As a workaround, please hit save after changing tag and before writing notes.

• Variant Page | Evidence | For finalized cases, ACMG notes are not visible.

• Variant Page | For chrY haploid males, showing HOM zygosity instead of HEMI.

• Versions Tab | After a reanalysis, some input files may not appear in versions tab.

• Report/Export | Cannot export regions of insufficient coverage to report.

• Curate | Searching for a variant causes the related cases to disappear even when search is removed. Work around is to refresh.

• Curate | Orphanet links no longer work due to an Orphanet link structure update.

• Activity | Editing interpretation paragraph yields an erroneous activity labeled reanalysis.

• API | Marking over 5000 variants as viewed will not result in an error message, although this is the database limitation for saving viewed variants.

• Dashboard | Diagnostic Yield includes Uncertain as Resolved.

• HistoricalDB for mtDNA variants | Mislabels Hom/Hemi counts, contact support to fix.

• Organization Settings | API Gene Lists | Does not support NCBI only export/import. This is supported from the UI.

• Organization Settings | Set mandatory fields - does not work from the UI. Please contact support if you’d like to configure these fields for your account.