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This version was primarily focused on introducing new AI innovation, with the goal of streamlining workflows and further reducing time-per-case.
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.
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.
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.
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.
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%.
Learn more about the DRAGEN 4.0 release.
The Related Cases component in the variant page has been enriched with interpretation and classification data, in order to streamline use of lab curated data.
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.
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.
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
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
Users with permissions can upload new BED files for any reference, both for existing and new kits. Please follow the file format guide for BED files (link accessible only to Emedgene platform users).
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.
Support for Dragen 3.10 (support for Graph coming in 5.30)
Support for SV insertions called from Manta
Compound heterozygous filter supports SVs (in addition to CNV/SNV/indel)
Compound heterozygous feature for duos (single parent and proband)
Annotate cases with Emedgene Curate data
Enhancement | Update revel generation script, change revel file path
Emedgenizer for DRAGEN repeats with ExpansionHunter
Added STR annotation engine for 1K Genomes and gnomAD
Emedgenizer for DRAGEN SV caller
Retrieve and write variant interpretation from Emedgene Curate
Support for ICA2 storage
Files get corrupted, lines deleted, missing columns, that’s a fact of the bioinformatics life. We’ve added automatic file validation, so if there is an error with your file you will get a clear and detailed message right away, no support needed! We want to get your files running as soon as possible.
These are the most common error categories we see:
Extraction of data (reference, columns) has failed
Gzip file is invalid
Mismatch of data between samples or patient
File contains empty or unfinished lines
We view automation as a critical piece of the lab workflow and want to make it as easy as possible for our customers to automate accessioning via API.
That’s why our new and simplified API comes with Swagger. Swagger is a combination of live API documentation and testing sandbox that allows you to try out your API code before deploying, and identify errors and their origin immediately (and clearly!).
We now support SV Del/Dups called with the DRAGEN Manta SV caller. All the interpretation features available for CNVs are applied to SVs, including our time-saving automated ACMG-ClinGen classification.
We’ve updated our compound heterozygote algorithm and it now considers CNV deletions, CNV intra-genic duplications and SNVs. You can access the results through the filtering - whether ad hoc or presets.
We hope these features will help you solve more patient cases!
You can now import an existing curated variant interpretation into your case workflow, and populate it to a report with a single click if you are using our reporting system.
We’ll be gradually improving the panel interpretation workflow. For this version, we added a ‘Hide Gene List’ capability from both the API and UI.
Most labs work with hundreds of pre-defined gene lists, most often created via the API. Then, when creating a gene list on the fly for a specific test, it can be hard to find and apply it from the UI.
Hide gene list allows you to hide your pre-defined panels, so that the UI can be utilized for applying gene lists on the fly. Users with the relevant roles will have control of whether a gene list is hidden or exposed.
For those of you running from FASTQ, a genome trio now runs in under 7 hours. Don’t forget the output is a highly accurate AI Shortlist - with evidence! - that reduces time-to-preliminary-report to a few minutes in cases solvable with SNV/Indels.
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).
New pathogenicity filter
Allele frequency is now viewable in the proprietary STR visualization
Summary Table of Variant Types Supported by Test Type and Version
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 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.
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.
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.
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.
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 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.
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
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.
For labs using the Emedgene DRAGEN pipeline, QC metrics are now available for download.
Updated filters to support full ACMG 78 gene list.
This update follows the latest recommendation from ACMG for reporting secondary findings: https://www.acmg.net/PDFLibrary/Secondary-Findings-v3.1.pdf.
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.
You can now interpret STRs on Emedgene, including proprietary annotation and visualization.
STRs are available for customers starting from FASTQ. Calling is performed using ExpansionHunter, for which recent specificity/sensitivity data can be found in this Lancet Neurology publication. Annotation sources include gnomAD and a unique 1K genomes dataset.
This release also includes an easy way to visualize population data as well as the pathogenicity associated with the number of repeats for the variant you are viewing.
Support for SV deletions and duplications for customers starting from FASTQ is now available in all regions. Calling will be performed with the DRAGEN SV caller, and all the interpretation features available for CNVs are applied to SVs, including our time-saving automated ACMG-ClinGen classification.
Emedgene Curate now supports genes, enabling you to save and view gene interpretations and preferred transcripts.
You can now create private networks and share curated data between organizations in Emedgene Curate. This is in addition to the private networking feature available in Emedgene Analyze and enables sharing and transfer of curated data between trusted organizations.
Increased automated ACMG classification accuracy
In the analysis tools table, you can hover on disease to see all related diseases
View allele frequency full decimal number
Support for ICA2 storage
Feeling in control about your data is reassuring. With improved User Access Policy, at any given time, you can control whether the Illumina Support team has access to your organization.
Access is enabled by default, but can be disabled by the organization's Manager in Settings > Management > Illumina Support Access.
Do you offer genetic services to other health care providers? Consider delegating case creation to your customers. The new Ordering user role enables authorized third parties to create cases in your account with zero access to your data.
Annotation and automatic ACMG classification are not supported for CNV variants larger than 20Mbp [ACMG CNV Classification wizard].
Curate does not support CNVs greater than 10MBp or intergenic variants. [Curate]
Evidence page is not available for manually added variants. [Evidence page]
Switching between simple and advanced modes doesn't work for locally loaded BAMs [Visualization section]. Fix planned for 32.0*.*
After a gene list has been used as a basis for a preset, deleting it in Settings results in a 404 "Case not compatible" error [Gene lists]. Fix planned for 32.0.
Visualization is not supported for cases with VCF + CRAM files stored in Illumina Connected Analytics V1 or BaseSpace Sequence Hub, only for VCF + BAM.
Defining fields that are mandatory for case creation does not work from the UI [Settings]. Please contact support if you’d like to configure these fields for your account
If you navigate to the Lab tab first after entering a case, quality metrics will fail to display. Current workaround is to first load _Candidates tab_or Analysis tools tab. [Lab tab]. Fix planned for 32.0.
is a new way to store and manage your organization’s curated data. It forms a single repository for your expert manual curations, across human reference builds and test types. This knowledge management system clearly displays curated data where you need it, in analysis workflows.
If the variant has not been curated, you can export your variant and interpretation.
Most Emedgene users utilize two screens when viewing a variant, with one set to their preferred desktop viewer, whether Alamut or IGV. Emedgene automatically changes the desktop viewer as you move between variants.
The majority of our customers use APIs to add workflow automation and decrease manual labor through connectivity with LIMS, EHR and other health IT systems.
This version improves error tracing when API input doesn’t match expected data, for easier troubleshooting by our respective IT teams.
We’ve also added additional export capabilities using our API.
Automated ACMG/ClinGen CNV classification
The automatically scores sections 1, 2, 3, and partially - sections 4 and 5 of the , including the full PVS1 calculation needed for intragenic variants. It also summarizes all of the pertinent CNV data in an accessible table.
To view the automated classification, simply tag a variant.
Enhancements to Case Interpretation & Reporting
Now we’ve added three additional fields for case finalization notes - Interpretation Notes, Gene Interpretation and Recommendations. This data is saved per case. If you’re using our brand new customizable and editable reporting solution, the fields will automatically populate in the report.
View lab coverage data by gene list
Simply click the Add Gene List button and select any of your pre-loaded gene lists.
Okta Identity Management
With gnomAD no longer releasing GRCh37 versions, we expect increased lab transitions to GRCh38. We have incorporated the two most requested GRCh38 features in this release, thus offering you complete support for GRCh38:
A totally unified workflow for tests running on different in the same organization.
A solution for historical data. Curated and historical data are automatically lifted over on the fly and made available as you perform your analysis (in either reference).
The has a brand new design, but more importantly - a new feature set:
cases by Case Status,
refined case ,
effortless ,
and more!
You can now on the emedgene platform, using a streamlined workflow that makes it easy to focus your analysis on the clinically meaningful variants.
Our secondary analysis pipeline uses and leverages improved quality metrics to help reduce the number of variants for review,
We also support VCF files from , , and .
genes,
transcripts,
known disease-causing variants (MITOMAP).
Stay tuned for the curated data sharing between partner organizations!
you need to complement NGS with data from other genetic tests (long-read sequencing, optical mapping, CGH, SNP array, karyotyping/FISH, repeat-primed PCR, MLPA, Southern blot, etc);
you want to report a few adjacent variants as a single multi-nucleotide variant.
Supported variant types are SNV, CNV, UPD, ROH, and STR. SV is coming soon!
When analyzing a case, the , , and sections will clearly highlight that the variant already exists in emedgene Curate, and provide a link out. You can review curated data and determine whether to reuse it for this case.
Easily switch between and emedgene Curate, using the handy application icon on the left of your browser.
Version 2.26 adds more flexibility in setting own quality controls. In addition to allele bias and depth, we added the ability to , as well as a new (SNVs).
Now you can whether you’d like the desktop viewer to move between variants automatically or not. If you’re working (from home) on a single screen and not utilizing a desktop browser, you can disable the desktop viewer updates.
We have also expanded the list of ethnicities available during .
According to a small study we ran (), the tool is highly accurate and saves 75-90% of manual review time. Check out a detailed demo on our .
When on emedgene, you’ve always been able to specify whether the case was confidently solved or not and select the solving variant.
For finalized cases, you can view the Case Result, Interpretation Notes and Finalized Variants in a new Finalize tab in the righthand panel of the webpage. Alternatively, to see the variants that were selected while signing off the case, select Finalized in the dropdown onthe .
You’ve always been able to by gene. This version also allows you to search by any of your gene lists - streamlining quality review for gene lists applied on the fly.
The emedgene platform now utilizes the solution to control user access. This improves user management, enhances access and authentication security, and allows organizations to implement single sign-on for their users. Transitioning to Okta is a prerequisite for getting access to version 2.16.
You can focus on mtDNA variants by using the updated mtDNA filter in the . The filter can be added to your custom presets.
The and reflect basic mtDNA variant annotations including:
population annotations (gnomAD and ),
Missense Prediction scores ( and ),
The ACMG SNV Classification wizard is now . It utilizes only relevant ACMG criteria and automatically defines the resulting ACMG class based on the manually assigned criteria.
is a new section of the that highlights information on previous variant curation activity (i.e., assigning a and/or assigning Pathogenicity and/or adding Variant Interpretation notes).
You can now not present in the VCF or not called from FASTQ to your case. This is useful when:
We now support using DRAGEN. High precision and recall are achieved through a lab-optimized panel of normals (PON). Results vary per laboratory/sample preparation protocol, and validation is performed upon request.
The now includes a Test Subject VCF track presenting proband's variants stored in the VCF file.
Variant Type
WGS
WES
Panel
Emedgene DRAGEN
Bring your own DRAGEN
Platform Version
SNV
Yes
Yes
Yes
All
All
All
Indel
Yes
Yes
Yes
All
All
All
CNV
Yes
Yes
Yes
All Need PON - exome/panel
5.24+ Need PON - exome/panel
2.22+
mtDNA
Yes
Yes
Yes
All
5.26+
2.25+
SV del/dup
Yes
Yes
Yes
Yes
5.28+ Needs adjustment
2.28+
SV insertion
Yes
Yes
Yes
Yes
5.29+ Needs adjustment
2.29
STR
Yes
No
No
Yes
5.29+ Needs adjustment
2.28+
Two new CNV filters will help you focus on the genes that are most likely to be pathogenic:
LoF Genes will present all genes with a gnomAD pLI≥0.9;
Established HI/TS Genes filter will only return variants genes with an HI/TS score of 3.
Both are available under Gene Filters and can be added to your preset filters.
If you’d like to focus on high-quality CNVs, you can now set a minimum bin count of 1, 5, 10, 25, 50, 100 or 500 in CNV Bin Count filter. The filter appears under Quality Filters in Advanced mode.
Quality section for CNVs got updated! For each sample, you can now see copy number, CNV quality, size, and bin count.
The Variant page now features a clear Summary section that spotlights essential variant information - saving you precious clicks! If after the first glance you feel like diving deeper into the variant details - proceed to other Variant page sections below.
We redesigned Quality section: it has a slightly different style,
To change the sample in review for the particular variant, click on the corresponding icon in the family tree.
If you've read this far, here is a bonus insider tip! 🤫
Did you know that you can view the Evidence page for any tagged variant? We redesigned the See evidence button on the Evidence section to make it pop!
Piping hot Variant Type Filters at your command! Ready to filter variants by type (SNV, Indel, DEL, DUP). Additionally, variant type is shown in the variant table.
Administrators of your account now have total control over gene lists and can create and edit them in Settings.
The Finalized Case status locks the case to prevent further changes to interpretation notes, ACMG tags, variant tags, pathogenicity and case-level interpretations.
Starting from this version, access to finalizing a case requires a dedicated role, so the organization's manager can restrict access to a specific set of users.
Version 2.19 features improved CNV interpretation capabilities, most notably the ability to add a curated CNV database of chromosomal microarray results. We’ve also enhanced variant visualization, expanded Preset filter capabilities, and added the ability to reflex Case Type up to a broader testing option.
Add your curated CNV database
You can now upload your own curated CNV database, even using historical microarray data. The data can be accessed through a corresponding filter under the Analysis tools > Variant filters in Advanced mode and in the Clinical Significance section.
Filter by CNV length
We’ve added a CNV Length filter under the Quality filter to help you filter out small CNVs that are typically noise.
Improved visualization
We’ve added gene names to visualization tracks. You can also conveniently expand/collapse transcripts through a new control panel on the right. Stay tuned for more visualization tracks coming soon.
Reflex case type
You can expand to a broader genetic testing option if the results of more targeted testing are inconclusive. You may reflex from Custom Panel to Exome or Genome, or from Exome to Genome.
To do this, you should change the Case type in Edit case info flow, thereby rerunning the broader analysis.
Preset filters by test type
Everyone’s favorite feature, Preset filters, is getting an upgrade. You can now create different Preset filters for each of your test types. We hope this will streamline analysis and save you lots of time.
Enhanced reporting
Are you using our slick new customizable reporting module? We now support all test types AND all variant types. Let us know if you’d like a demo.
Support Help Center
Our live support knowledge base is finally here! If you’re looking for clarifications we’ve loaded answers to our most frequently asked questions, and we will continue to add articles on a weekly basis. You can also conveniently chat with the support team or send us a message.
Support and the new Help Center are accessible at all times via the question mark icon on the platform top bar.
