Geneyx Analysis Version 6.2 is officially live!
Geneyx Version 6.2 introduces a powerful set of enhancements to improve variant interpretation, structural variant review, case tracking, and secondary analysis integration. Key updates include direct IGV Desktop integration, genetic model governance, expanded SMART Filtering controls, including now ability to filter on CoLoRSdb.
Additional improvements are improved API capabilities, advanced transcript annotations for CNVs, external caller compatibility, and improved gene fusion analysis.
Configuration and Reporting Enhancements
a. Genetic Model Management and Reporting Assignment
Users can now:
- Rename, reorder, and create custom genetic models (SNV & CNV)
- Assign models to custom report sections (e.g., Carrier, PGx)
- Maintain full compatibility with filters, panels, maps, and protocols
A new interface in Settings allows complete visibility and control over models, improving governance and customization.
b. PMID Reference Integration
A new “References” field has been added to the Selected Variants popup (for both SNVs and CNVs), enabling users to manually insert PMIDs (PubMed IDs) to support variant interpretation. These are displayed in reports and in house variant views, with support for up to 15 PMIDs per variant.
SMART Filtering Updates:
a. CoLoRSdb AF Integration
Allele frequencies from CoLoRSdb can now be used to pre-filter long-read sequencing variants in SMART Filtering, reducing noise in LRS datasets.
b. ‘Always Annotate ClinVar LP/P Variants’ function
A new option in SMART Filtering allows users to ‘Always Annotate ClinVar LP/P Variants’. When selected, this ensures all LP/P ClinVar variants are retained, even if they exceed thresholds from CADD, SpliceAI, gnomAD, or CoLoRSdb. This protects clinically significant findings from unintentional exclusion.
Annotation Updates
a. ACMG SF v3.3 Update
The updated list of medically actionable genes from ACMG Secondary Findings v3.3 (https://www.gimjournal.org/article/S1098-3600(25)00101-7/fulltext) is now fully supported by Geneyx.
b. CADD Scoring for Indels
CADD annotation now supports small insertions and deletions (indels), expanding predictive scoring to a broader range of variants.
c. Gene Fusion and Structural Variant Enhancements
- New “Gene Fusion” Column: Displays gene pairs involved in fusions in the CNV/SV table.
- Junction & Spanning Read Counts: Two new columns report support for fusion events.
- Transcript and Exon Annotation: Transcript IDs and exon numbers are now listed for CNVs/SVs, aligning with SNV interpretation.
d. gnomAD V4 Gene Constraint Data
Geneyx now includes pLI values from gnomAD v4, displayed alongside v2.1.1 metrics.
e. Frameshift HGVS Annotation Updates
Frameshift variants now include full HGVS annotations (e.g., p.Leu1204ValfsTer153), improving clarity in reports and compliance with clinical standards.
f. Tumor Analysis Field Integration
Users can now import tumor-specific metrics – including MSI, TMB, Ploidy, Tumor Fraction, and Genomic Instability Score – via TSV files, for improved integration of external pipelines.
g. Updated Repeat Region BED from PacBio
The latest PacBio BED file for pathogenic STR/repeat regions is now included, improving color-coding in repeat loci.
Pipeline and Workflow Enhancements
a. New API for TSV File Retrieval
An API endpoint has been introduced to programmatically retrieve TSV files, enhancing integration with downstream tools and pipelines.
b. Support for External JSON Uploads
Users can now upload structured JSON files from external DRAGEN special callers. This ensures Geneyx supports outside secondary analysis pipelines while maintaining rich variant visualization.
c. Desktop IGV Integration
Geneyx now supports native integration with IGV Desktop. Users can open local BAM and methylation files directly from the variant view, ideal for environments without cloud storage access.
Filtering and Interpretation Enhancements
a. New Imprinted Gene Filter
A dedicated filter allows users to isolate or safeguard imprinted genes during inheritance-based analyses.
b. Display of Unmatched Clinical Phenotypes
Geneyx now includes a new “Unmatched Phenotypes” section in the Phenotype popup. This addition displays any phenotypic term provided by the user that was not matched by the phenotype algorithm.
c. New “Variants” Tab in Gene Popup
A new tab aggregates ClinVar classification summaries for the selected gene:
- Condition vs. Effect for SNVs and CNVs
- Pathogenicity vs. Effect Summary
d. Exon Number Column in Default SNV View
The Exon Number is now included by default in the SNV table, providing immediate visibility into variant impact.
e. OMIM Edit History in Gene Table
A new column displays the latest update date from OMIM, providing context for gene interpretation.
f. Gene Descriptions in Annotate Dialog
Curated gene summaries are now viewable during variant annotation, offering quick access to functional context.
User Interface and Experience Enhancements
a. Analysis-Level Notes
A collaborative notes feature allows team members to leave timestamped, user-tagged comments at the analysis level. This supports auditability and intra-team communication.
b. Assign Analyses from Dashboard
Users can now assign analyses directly from the dashboard, streamlining task management for large case volumes.
c. Turnaround Time (TAT) Display
A new column on the Dashboard shows the number of days an analysis has been pending relative to the defined protocol TAT.
Administrative and Audit Features
Analysis Locking Upon Case Closure
Closed analyses are now locked into “View Only” mode. Variants cannot be modified unless re-opened by an admin, ensuring traceability and report integrity.
