The Latest Advancements in Genome Sequencing: Introducing Geneyx V5.12
Through invaluable customer feedback and internal ingenuity, we are pleased to announce the release of Geneyx V5.12. Many features, discussed below, enable greater flexibility and customizations, and aim to improve variant annotation and sample automation workflows. The descriptions below are brief, so we have also made individual videos for some of these topics, which can be found here below.
Geneyx Analysis v5.12 GenePanel App
Geneyx Analysis v5.12 LAF Update
Geneyx Analysis v5.12 Batch Upload to Protocol
Geneyx Analysis v5.12 Updates to CNV_SVGA
New Features:
Enhanced Variant Annotation and Automation Workflows with In-house Classifications and more
- In-house Classifications: If a user creates an interpretation for a variant or gene, Geneyx will now display the most recent classification (by pathogenicity) in the local allele frequency database. This classification can be applied as a filter and will enhance the understanding of variants and genes previously evaluated.
- Batch Upload to Protocol: The batch upload feature, which enables users to push large volumes of fastq samples to variant calling pipelines, now supports specification of a protocol. This will apply the output files directly into analyses and greatly improve sample automation workflows.
- VCF Variant Capture: VCF files containing pre-annotated or marked variants can be applied to the secondary pipeline to create a unique field in the output VCF file. These marked variants will enable the user to have a customized annotation in the variant interface. This is available on request.
Improvements to (WGS) whole genome sequencing
- Exclude AF Calculation: In the event where artifact or low quality samples are uploaded, there is now a feature to exclude the sample from the local allele frequency calculation. This will prevent inflation of local variant allele frequencies.
- UPD Notification: Uniparental disomy is automatically calculated for trio workflows, exome or greater, and now will provide notifications if significant results are identified. Significance thresholds have also improved for easier interpretation.
- Bulk HPO Import: When importing multiple HPO terms, the HPO input dialog now provides a “Select All” feature. This will pull and convert all HPO terms entered into the phenotypic prioritization algorithm.
- Updates to SpliceAI: Splice AI, used for evaluating cryptic splice sites, now supports precomputed scores for whole genomes. This will improve annotations for non-coding variants.
- CNV/SV Annotations: CNVs and SVs now have cytogenic representation and are now annotated with frequency databases according to the matching effect. CNV/SV frequency databases include DGV, DGV Gold, gnomAD SV, and gnomAD genomes.
- Layout Flexibility: At the protocol level, customizations now enable users to hide specific columns in the variant dashboard automatically. This will simplify the user view to only display relevant information according to preferred lab workflows.
- Dragen Variant Caller: The Dragen secondary pipeline has updated the reference genomes (hg19 and hg38) to improve alignment and variant calling. This will improve mapping accuracy in difficult-to-map regions.
Beyond these great new features and improvements, we are continuing efforts in analyzing long-read sequencing data, updating reportable genes for the pharmacogenomics workflow, and discussing implementation of polygenic risk scores.
If would like more information on these topics, please contact support@geneyx.com.
Additionally, members from the Geneyx team will be attending the ACMG conference from March 14th-18th, in Salt Lake City Utah.
If you are attending, please visit our Geneyx booth.
As always, we are grateful to our customers that continue to use Geneyx for their NGS analysis and interpretation. If there are any features that you would like to see in Geneyx Analysis, please contact support@geneyx.com with your suggestions.
