SeqOne Platform Preview Update - Fall26-RCFinal

Dear ,

We are excited to share our latest updates. The Fall26-RCFinal release introduces SeqOne PGx, our new pharmacogenomics module now open for early testing, alongside automatic VICC oncogenicity classification for somatic variants, a reworked Restricted Panels experience, and an automated LitFinder literature review. Somatic variant interpretation also gets a boost with a rebuilt RNA Fusion Viewer and reworked AMP tier handling.

Reminder: As announced earlier this year, these new features are currently available in Preview mode only. They will move to Main in our next release, coming within the next few weeks.

Please head over to our Knowledge Base intro article and FAQ for more details on how the Main/Preview system works and how to make the most of these early updates.

Any questions? We'd love to help.
Reach out to your dedicated SeqOne contact:

SeqOne Support

support@seqone.com

🔒 Restricted Panels, made simpler

We have reworked how restricted panels can be selected while creating analyses, and augmented them with the introduction of adjustments to the gene lists.

• Select applicable gene lists: Select all required gene lists for each analysis. Selecting and reviewing your choices is now easier.
  
  
• Adjust the gene list(s) selected: Add or remove genes to fit your analysis exactly, without creating a new gene list every time.
  
  
• Check the genes applied: View the full list of applied genes in one click to confirm it fits your requirements.
  
  
• Apply restrictions in bulk: Select several analyses to apply the same restrictions at once.

We've also made it easy to consult restricted panels directly from the analysis drawer.

• Restricted panel overview, at a glance: In the analysis drawer, any user can verify the gene list applied as restricted panels, along with any adjustments made to it.
  
  
• Edit the restricted panels: Users with permission can modify and adjust the restricted panels as needed, directly from the analysis drawer.

Last but not least, we've made it easier to capture which restrictions have been applied to your analysis in your clinical report.

• Pre-filling the form: If restricted panels have been applied to your analysis, the report form will automatically populate the "Evaluated genes" field with the complete gene list. Manual additions will appear in blue.
  
  
• Panel name: Use the toggle below the field to define whether the gene list name should be displayed in the report.

🚦 Analysis Status: know where your analysis stands in the workflow

A clarified list of statuses has been introduced, so you can identify at a glance which step of the workflow each analysis stands at.

Automated status changes: Status updates now happen automatically based on user actions, moving from "Ready to Interpret" to "Interpreting," and from any status to "Analysis completed."

💬 Comments filters

We're improving comments with filters, so you can focus your attention only where it's needed.

• Filter out resolved comments: Hide comments marked as resolved so you can focus on open threads.
  
  

• Select what you want to see: Use the filters to check comments associated with variants, or comments not associated with variants. Your call!

📋 Analysis list in projects

The list of analyses available within project folders has undergone a big redesign, so that all key information is available and clinicians can more easily scan the list to identify cases they need to work on.

• Assign your analyses: The assignment process is now one click away and can be done directly from the list of analyses. All users of the entity will also be visible directly, instead of having to type names to see them. You can also select several analyses to assign the same group of users at once.
  
  
• New features & information made their way into the list: Comments and protocols features, along with the last modification date, are now visible at a glance.
  
  
• Sort the list using (almost) any of the columns: Analysis name, assignee, protocols, comments, date. Your preferred sorting will be applied across projects.

🏷️ Create your custom metadata on analyses

The form to create custom metadata has been improved, to make it as easy as it gets to personalize the metadata you wish to add.

• Clean form: The required information to create metadata has been clarified & the form now appears in a popup.
  
  
• Delete custom metadata: You can now remove any metadata you have created.

📂 Classification drawer

From the Variant Viewer and Large Variant Viewer, display the classification drawer next to the details page of the variant, so that all useful information can be accessed while classifying.

• Classify: From the details page, simply hit “classify” to see the classification drawer appear.
  
  
• Keyboard shortcuts: To open and close the drawers

📍 Filter variants by genomic location

We introduced a Location filter in both the Variant Viewer and the Large Variant Viewer, so you can narrow short and large variants down to a chromosome, a specific genomic range, or (for large variants) a cytoband.

🧬 Genes filter, now alias-aware

We reworked the Genes filter in both viewers. Every gene symbol you enter is now checked against HGNC to resolve aliases and previous symbols, which is especially helpful when reviewing older analyses with outdated annotations.

• Matched: Your input symbol matches at least one variant in the analysis.
  
  
• Updated: Your input symbol doesn't match, but an alias or previous symbol does.
  
  
• No results: Neither your input symbol nor any alias or previous symbol matches any variant.
  
  
• Unrecognized: Your input isn't found in the gene database.

👪 Genotype filter & inheritance information

We introduced a genotype filter in the Large Variant Viewer, for both single-sample and family analyses.

• Custom transmission hypotheses: in a family context, select the possible genotypes for each member to build your own hypothesis.
  
  

• Built-in patterns for trios: in standard patient-father-mother trios, ready-to-use hypotheses cover common patterns such as de novo, recessive homozygous, or maternal/paternal inheritance.

• Inheritance in the genotype column: inheritance is now surfaced directly in the genotype column for every large variant.

💊 Introducing SeqOne PGx: pharmacogenomics in the platform

SeqOne PGx turns the capture-based data you already sequence into star-allele calls, metaboliser phenotypes, drug-level guidance, and a ready-to-share clinical report, the result of months of work, now open to early testers ahead of the official Fall26 launch.

• No new assay: PGx runs as a module of your GermVar analysis on capture-based data, targeted panels and WES alike (GRCh38), using a profile matched to your capture kit. Validated end-to-end with co-development partners on both panel and WES data.
  
  
• From star alleles to phenotypes: Star-allele calling, pharmacogene CNV detection, and diplotype resolution feed our phenotyper for the core pharmacogenes (CYP2D6, CYP2C19, CYP2C9, DPYD, TPMT, NUDT15, SLCO1B1), with the called variants and a genotype-quality indicator behind every result.
  
  
• HLA typing included: 2-field HLA-A/-B/-C typing flags the high-severity guideline markers: abacavir (B*57:01), carbamazepine (B*15:02, A*31:01), allopurinol (B*58:01), vancomycin (A*32:01), and dapsone (B*13:01).
  
  
• Guidance you can trace: Recommendations consolidated from CPIC, DPWG, FDA, PharmVar, and ClinPGx, browsable by gene or by drug, filterable by impact, source, and therapeutic area, and always traceable back to the call that drove them.
  
  
• A report, not an export: A modular PGx report builder (header, clinical summary, drug guidance grouped by indication, quality and methodology), previewed before generation and saved as a PDF straight into the analysis files.
  
  
• Coming next: Your own curated recommendations (PGx Knowledge Base), PharmGKB clinical evidence per variant-drug pair, manual genotype/phenotype override, and WGS support.

🗂️ Relevant genes and diseases in CNV reports

We've added a Relevant Genomic Content table to CNV findings in the clinical report, so you can report the specific genes or regions and the related diseases driving a CNV interpretation instead of a flat gene list.

• Pick the relevant gene(s): select from the CNV's affected genes; OMIM-morbid genes are shown first, sorted by relevance, with a toggle to see the rest.
  
  
• Attach disease and inheritance: choose one of the gene's associated diseases and the inheritance fills in automatically, or enter a custom disease and mode of inheritance.
  
  
• Recurrent regions supported: established regions such as 22q11.2 can be selected instead of a single gene, and are reported at the region level.
  

🔄 Large inversions, now visible in WES/panel data

We now surface large inversions (>10 kb) in GermVar and GermVar Family WES/panel analyses, a class of copy-neutral events that previously stayed invisible outside manual IGV review.

• Where to find them: surfaced in the CNV & SV tab and other events.
  
  
• Coverage depends on your capture: detection only works where the capture tiles the inversion's breakpoint. See the knowledge base for breakpoint-probe design guidance on known recurrent inversions like MSH2/Boland.

🔍 Mosaic variant detection, wherever you need it

We've made the mosaic variant caller configurable, so low-VAF variants are no longer silently dropped just because a gene happens to sit outside our default list.

• Bring your own regions: upload a custom bed file of coordinates for mosaic calling when creating a Germline project, or rely on our curated default gene list if you'd rather not.
  
  
• Nothing silently dropped: low-VAF variants in your chosen regions, custom or default, now come back as clean, reportable calls instead of disappearing with no flag.

💡 Distinguish "not covered" from "reference"

We now show coverage (depth) for every member in a GermVar Family case even when the variant wasn't called in their sample, so you can finally tell "not covered" apart from "covered, but reference."

• Works both ways: if a variant is called in the patient only, parental depth is shown; if called in a parent only, the patient's (and other members') depth is shown.
  
  

• A real zero means a real gap: if a family member genuinely has no coverage at that position, the cell shows 0, distinct from a position where the back-fill simply wasn't attempted.
  
  
• Everywhere it matters: covers SNVs, MNVs and indels, in both the Variant Viewer table and the Variant Drawer's coverage summary.

📈 More ways to bring CNV evidence into the Genome Browser

We've added two new ways to get CNV evidence for GermVar Tertiary into the Genome Browser. You can now bring additional visualisation data, so SeqOne offers a better interpretation UX when working with another secondary analysis provider.

• CNV tracks: Attach copy-ratio (tn track), BAF, target-count, and segment tracks at sample creation, and view them directly in the Genome Browser instead of switching to desktop IGV. These files are typically produced by Dragen and other callers.
  
  

• Bring your own CN track and ploidy files: Upload pre-computed CN track and ploidy files straight from the sample-creation form. They feed the Genome Browser and Ploidy modal the same way pipeline-generated ones do.

✍️ Autofill with DiagAI, now for germline CNVs

Autofill with DiagAI, previously available for short variants only, now drafts the interpretation comment for germline CNVs in the Large Variant Viewer, for you to review, edit, and validate.

• Where to find it: Open Classify on a CNV in the CNV & SV tab to reach the classification drawer, where the Autofill button sits in the comment field's toolbar.
  
  

• What the draft now includes: It contains the relevant annotation data like the ACMG class, the AChroPuce reference, zygosity (derived from copy number when genotype isn't called), the full inheritance and transmission mode. It also contains the interpretation, referring to the data when applicable.

📚 LitFinder: automated literature review on the variant page

Get smart literature suggestions prioritized based on the variant and case details through LitFinder, saving you time from manually searching publications and/or resources invested on private databases. You can trigger the suggestions in the Literature tab (renamed from Publications) on the variant page.

• What it shows: One card per relevant article, with journal, date, title, authors, a confidence score, and a relevance group, sourced from ClinVar, ClinGen, LitVar2, and PubTator3. Results are sorted by score or date, and PMIDs copy in one click.
  
  

• Scope: Available on GermVar and Germline worksets only. Other worksets just see the tab's new name.

🔬 VICC Oncogenicity Classification for Somatic Variants

We're introducing automatic VICC oncogenicity classification for somatic SNV/indel variants, giving you a structured, auditable verdict (Oncogenic, Likely Oncogenic, VUS, Likely Benign, or Benign) alongside your existing ACMG pathogenicity calls.

• Fully automated: The classification runs automatically in the pipeline for every somatic SNV/indel, no manual step needed for the criteria covered in this release. An AUTO ONCO column in the variant viewer carries the pipeline's call.
  
  

• Audit it in the Oncogenicity tab: A new Oncogenicity tab in the classification drawer opens on a summary, the class, the score, the criteria grouped by evidence type, and a ready-to-paste interpretation paragraph. Behind it sits the full matrix, one cell per criterion, with each tag's definition on hand.
  
  

• Three states, not two: A criterion is met, explicitly "Not met", or not evaluated. The tab keeps the three distinct, so you can tell a criterion that was ruled out from one that was never assessed.
  
  

• Accept or overrule: Approve a suggested tag from a quick action popover, apply tags in bulk, or open the edit modal to change a criterion. The class recomputes as you go. Validate to save the classification and add the variant to your Selection.
  
  

• Criteria implementation: This first version covers hotspot and known-oncogenic criteria, population frequency, computational predictions, synonymous variants, and null or loss-of-function variants. Criteria that depend on tumor type (OP2) aren't supported yet and will follow in a later release.
  
  

• A separate call, not a replacement: VICC oncogenicity is a distinct classification from ACMG pathogenicity. It doesn't change or override your existing ACMG results.

🧭 Oncogenicity, a classification of its own

Oncogenicity is now a classification axis alongside pathogenicity, in the Variant Viewer, the Large Variant Viewer and the RNA Fusions Viewer. Short variants, copy number variants and RNA fusions can all be classified the same way, in the same drawer.

• Set it anywhere: in a somatic analysis, the classification drawer carries an Oncogenicity section: Oncogenic, Likely Oncogenic, Uncertain Significance, Likely Benign, Benign. It combines freely with a pathogenicity class, a comment and tags.
  
  

• Both classes in one column: the classification column shows pathogenicity and oncogenicity together, so you read an alteration's full status without opening it.
  
  

• Into the report: variants classified Oncogenic or Likely Oncogenic are pre-selected for reporting, alongside Pathogenic and Likely Pathogenic, and the report sorts on both classes combined.
  
  

• It follows the variant: the oncogenicity class appears in the analysis classification history. VKB support to see classifications from other analyses is coming soon!

🎯 AMP tier and clinical evidence

AMP tier handling has been reworked in the Variant Viewer, the Large Variant Viewer and the RNA Fusions Viewer, so the tier reads the same wherever you meet it. Alongside it, the evidence behind a variant can now be pulled into its description instead of retyped, and the AMP tier shown in the viewers is specific to the selected cancer type at analysis launch.

• Filter by tier: narrow the variant list to the tiers you report on.
  
  

• Cancer-type aware evidence: evidence matching and AMP tiering now takes the patient's cancer type into account when it evaluates a match.
  
  

• Evidence into the variant description: each evidence carries an "Add to Variant Description" action. It appends the evidence text to what you already wrote, never replaces it, and adding the same evidence twice does not duplicate it.
  
  

• The heading is built for you: therapy, response, tier, indication and approval status for actionable evidences; evidence type, tier and indication for diagnostic and prognostic ones.

🧬 RNA Fusions: new tab, classification, and clinical evidence

A new RNA Fusions tab replaces the previous display, with a table-based view and a detailed side drawer for each fusion.

• Classify fusions: fusions can now be classified directly from the classification drawer, the same way short variants and CNVs are. VKB inclusion coming soon!
  
  
• Built-in clinical evidence: actionable, prognostic, and diagnostic information, along with matched clinical trials, is now available for each fusion, powered by Genomenon CKB.
  
  
• Add therapies and report them: therapies can be added to a fusion's description, and classified fusions can now be included in the clinical report.
  
  
• Add fusions to your Selection: classified fusions join the Selection, alongside short variants in RNA.
  
  
• Classification history: each fusion keeps its classification history, the same way variants do. VKB support to see classifications from other analyses is coming soon!

🔍 Interactive clonality review with Vidjil (preview)

The SomaHemato Clonality tab shows a static report. You can now take the same analysis into Vidjil and explore it interactively: clones, V(D)J detail and CDR3 sequences. Vidjil is an independent open-source platform developed by Inria, Université de Lille and CHU Lille (GNU GPL v3); SeqOne provides its viewer as a read-only convenience, and it is not part of the SeqOne Platform device.

You download the file, then load it into the viewer, which runs on SeqOne infrastructure and reads it in your browser. No clone or CDR3 sequence is sent to a public or third-party Vidjil server.

• Download the clonality file: a Download button on the Clonality tab gives you the analysis's Vidjil file, decompressed and named after the patient sample.
  
  
• Open Vidjil: a second button opens the Vidjil viewer in a new tab, with no SeqOne login to go through. Load the file you just downloaded into it and the interactive view appears.
  
  
• Same results, a different view: Vidjil displays the results your analysis already produced. It does not recompute anything, so the clones, counts and V(D)J assignments match your Clonality report exactly. The Clonality report remains the reference for clinical interpretation.
  
  
• Shown only where it applies: both buttons appear only on analyses that have a clonality artifact.

We’ve rolled out several refinements across our pipelines to enhance accuracy and improve your daily workspace efficiency.

Platform

• 🔧 Default Protocols at Project Level: It's now possible to set a default protocol at the project level. All new analyses created will inherit from it.
• 📝 Report Template Enhancements: The Summary & Recommendations field is now available in the clinical report template, and free text fields now support bullet points.
• 🇫🇮 Finnish Translations Updated: Finnish translations across the platform have been updated.
• 👤 Personal Info in My Account: You can now view your personal information in your account (first name, last name, and email address used in SeqOne).
• ⚠️ Clearer Error and Permission Messages: Key messages shown when errors occur or when users try to perform unauthorized actions have been clarified.
• 🧭 Chromosome Navigation and Genomic Context: Select a chromosome from a dropdown to jump straight to its full view. The search bar now shows the size of the current genomic interval and the active reference genome (e.g., GRCh38), and the redundant "Genome Browser" label has been removed.

• 🖱️ Smoother Scrolling: Scrolling is now smoother and more predictable, with scroll and zoom controls now separated.
• 📏 CNV/SV Event Sizing: Event sizes now display in the most relevant unit: bp below 1 kb, kb from 1 kb to below 1 Mb, and Mb from 1 Mb upward.
• 🎯 CNV/SV Event Highlighting: A light-grey background now marks the full width of the selected event across all tracks, updating correctly as you zoom.
• 🧫 Clearer ClinVar Pathogenicity Icons: ClinVar pathogenicity icons can now be expanded and read without ambiguity.
• 🧬 Gene Strand Orientation Fixed: Strand orientation now displays correctly in the Genes track.

Germline

• 🧬 Deep-intronic variants (WGS): known ClinVar Pathogenic, Likely Pathogenic or Conflicting variants located outside the RefSeq BED file are no longer dropped by the region filter.
• ⚧️ Zygosity: X-linked CNV & SV variants in male patients are now labeled Hemizygous instead of Homozygous, across the variant table, tooltips and reports.
• 🩺 Custom diseases: you can now select more than one mode of inheritance for a custom disease, including a new Semidominant option.
• 🔀 Transcript sorting: an info panel explains how transcripts are sorted, and a flag alerts you when a clinically relevant MANE transcript is hidden in the dropdown.
• 🧬 GnomAD FAF95 Frequency for Population Criteria: GnomAD's FAF95 frequency is now available in the Variant Viewer and used when scoring the ACMG population-based criteria (BA1, BS1, PM2).
• ✅ ACMG Scoring Framework Choice: The ACMG tab now lets you choose between the ClinGen point-based system and the original ACMG/AMP 2015 decision tree.
• 🎯 Gene-Specific ACMG Thresholds: The VCEP threshold resource has been corrected and fully re-validated, including the missing BRCA2 thresholds.
• 👪 Carrier Screening for Compound Heterozygotes: When a compound heterozygote pairs a short variant with a CNV, the CNV is now flagged in the DiagAI screening shortlist as well.
• 📚 Classification Tab Occurrences Rework: The Occurrences table has been reworked, and occurrences found in deleted analyses are now listed.
• ✍️ Autofill Wording Update (Short Variants): The model generating SNV interpretation comments has been updated, so the wording of generated comments has changed.

Somatic

• 📊 GeneCov: new coverage thresholds for SomaCGP and SomaHemato: The 400x and 800x coverage columns are now available for SomaHemato (which also displays its 200x column), in addition to SomaCGP.
• 🩸 IGHV clonality, 20% threshold explained: a tooltip in the clonality summary states what the 20% threshold does. It labels the summary, it never removes a clone from the list.
• 🩸 More reliable clonality results on MGI samples (SomaHemato): Fixed an issue that prevented MGI samples from producing a conclusive IGHV clonality result on SomaHemato, caused by read-header formatting and unconditional UMI trimming.
  

Several fixes have been rolled out to improve platform stability and performance.

Variant Viewer & Filters

• The Gene filter now accepts gene lists pasted from a spreadsheet concatenation formula.
• Variant, preset list, and project free/locked filters no longer fail to load for entities without custom preset filters.
• Long, unbreakable sample names no longer overflow the Active Sample banner in the HPO drawer.

Clinical Report

• Fixed font size and alignment issues on PDF and DOCX clinical reports that prevented proper reading.
• The result title and sub-title are no longer deleted when saving the report.
• Clinical reports no longer fail to display after creation.
• Report validation and analysis status updates are no longer blocked for users without the "Launch analyses" permission.
• Applying a report template now fills in category tabs you've already visited.

Variant Knowledge Base

• VKB-evaluated variants now appear correctly in the export immediately after validation.
• VKB export no longer fails for analyses created before 2022, regardless of archiving status.
• VKB export no longer returns a 502 error for some exports.
• Imported VKB evaluations now appear entity-wide after import.
• Fixed a VKB v2 issue where the evaluated transcript wasn't stored, causing dropped classifications and exports against the wrong transcript.

Germline

• Fixed an issue allowing analyses to run without a "patient" sample in Germline Family/WGS.
• The mosaic variant caller (TNscope) no longer reports variants outside the client BED file.
• Fixed a Mutect2 mitochondrial false negative on homoplasmic variants in GermVar Family analyses.
• Autofill no longer fails for certain variants linked to COSMIC.
• Autofill no longer switches languages mid-generation.
• The classification drawer no longer renders without its header or DiagAI Autofill on some entry points.
• HPO reprocessing status no longer gets stuck at "processing."
• Rejecting or cancelling an ACMG criterion change now restores the criterion to its original state instead of leaving it in the new column.
• Deleting a tag from the ACMG Selected Tags tab now works.
• ACMG CNV criteria 1A and 1B can no longer be selected together, as they are mutually exclusive.
• ACMG CNV sub-criterion modals now show a complete sentence as their title and default justification, so a fragment no longer leaks into the saved classification or report.

Somatic

• SomaRNA fusion merging no longer drops Arriba-called fusions with intronic or intergenic breakpoints.
• Evidences tab: opening it no longer shows an error snackbar.
• Cancer Frequency tab: no longer displayed on worksets that shouldn't show it.
• Variant drawer: nested tabs no longer stay visible and swallow clicks; all tabs fit on one line.
• MSI: the coverage threshold reported now matches what the pipeline applies (SomaMSI and MSI in SomaCGP).
• SomaHRD: single-index CGP analyses no longer fail at launch.
• SomaLBx: the genefuse-utils filter now emits gene database blocks in a stable order.

Settings & Platform

• Auto-save when updating entity details has been fixed.
• The message informing users attempting actions on a locked analysis now always displays at the right time.
• Users without assignment permission can no longer use inline assignment.

Our databases and resources have been updated to their latest versions to ensure you have access to the most current information for your analyses.

• ClinVar: 2026-06
• OMIM: 2026-06-15
• PanelApp Australia and England: 26-06-15

We value your input and encourage you to share your ideas and feedback to help us continually improve the SeqOne Platform: support@seqone.com.