New Version 5.13 Updates to Whole Genome Sequencing Analysis

We are excited to announce the release of Geneyx Analysis v5.13. This release contains features aimed at improving customer workflows and paralleling advancements with new sequencing technologies. Below we cover some of the main highlights, but we have also made individual videos for some of these topics, which can be found here.

CNV_SV Improvements

Filters and Transcript Grouping

VCF Uploader Batch and Joint VCF Files

Genetics Analysis: New Features

APIs: New reporting APIs are now available to push and pull data from Geneyx and LIMS systems. All APIs and descriptions can be found here:

The new APIs include:  

  • CaseReports This API allows the user to extract all reports generated for a case. 
  • BatchCases This API allows the user to extract the cases generated from a batch workflow. 
  • BatchReportList This API allows the user to extract the reports generated from a Batch Upload of samples. 
  • AddClinicalRecord This API allows the user to add a clinical record to an existing patient.
  • Patient- This API allows the user to upload patient/subject information prior to a VCF sample being uploaded. 
  • CNV/SV Phasing: Phasing is now supported for CNV/SVs derived from long-read sequencing data. This will give insight into whether the CNV/SV event is observed on allele 1, allele 2, or both. 
  • “Gene-centric” Approach: The ability to search for a gene in an analysis using the magnifier feature has been improved to include findings related to CNV/SVs. This will allow users to easily investigate if a CNV is present in a given gene in the sample.  
  • Filter Logic Layout: The filter logic interface has been updated to enable faster logic identification with new querying capabilities. There are now also options to easily remove all column filters and reset to default filter settings. 
  • VCF Uploader: For uploading batch or joint (multiple sample in one) VCF files, there is a VCF uploader executable which can be found here: To run, requires having the API Key and ID specific to the account. For this information, please contact support@geneyx.com 

New Annotations:

ClinGen Dosage Sensitivity:ClinGen Dosage Sensitivity collects evidence supporting or refuting the haploinsufficiency and triplosensitivity of genes and genomic regions. This annotation source is now available when analyzing CNV/SV workflows.

OMIM for CNV/SV:OMIM phenotype information is now available for CNV/SV analysis. This new field will display OMIM information for all overlapping events observed in the database.

ClinVar Origin Annotation: The allele origin, being either germline or somatic, is now displayed when viewing the ClinVar hyperlink for SNVs of interest.

Recessive Het Tab: To accommodate for carrier screening workflows, or heterozygous variants with autosomal recessive mode of inheritance, a new Recessive Het tab has been developed that includes the ACMG classification using the autosomal recessive model. This can be applied at the protocol level by the user or upon request. 

Improvements: 

  • New Filters: New filter logic has been added, such as In-house Variant Classification, and In-house Gene Classification. This will allow users to filter using in-house interpretations. These filters, as well as others, can be found here: 
  • HGVS c. Nomenclature: Synonymous variant nomenclature has been updated according to the College of American Pathologists (CAP) guidelines. This can be seen in the HGVS annotation field in an analysis. Previously, synonymous variant representation was p.Ala528Ala and now it is p.Ala528=, for example.  
  • Canonical Transcript Representation: The canonical transcript is now selected according to Matched Annotation from the NCBI and EMBL-EBI (MANE). If a MANE transcript is not available, the canonical transcript will be selected based on shortest transcript ID. 
  • Severity Annotation: To improve accuracy, the Severity (SEV) algorithm now incorporates additional annotations including CADD and splice-site prediction scores. This will add further evidence for variant classification and candidate variant selection. 
  • GnomAD Hyperlinks: Hyperlinks for gnomAD exomes and gnomAD genomes have now been added to easily query the variants in the associated database. The hyperlinks will display when selecting the MaxAF value in the Frequency annotation column. 
  • CNV/SV Matching Genotype: For trio or associated sample CNV/SV workflows, the interface will now display events that directly match the proband. This will enable detection of de novo or transmitted events.   
  • CNV/SV QC Metrics: When analyzing CNV/SV, Geneyx now displays the Reference and Alternate alleles, if present, as well as read depth and variant allele frequency.  

Another announcement the Geneyx team is excited for is the implementation of a new secondary analysis pipeline called Sentieon, https://www.sentieon.com.  This solution enables genomic data processing with high computing efficiency, fast turn-around time, accuracy, and consistency. Sentieon will be offered as an alternative secondary pipeline in Geneyx in future releases. If you are interested in learning more about a Sentieon workflow in Geneyx, please contact support@geneyx.com 

We also are engaging in multiple conferences in the upcoming months. London calling by Oxford Nanopore (17th – 19th May) and ESHG (10th – 13th June, #booth). If you plan to attend one of these, we would be grateful to meet you in person. 

Lastly, we appreciate all the feedback from our customers. With your support we are continuing to be a leading diagnostic solution for NGS data analysis. If there are any features that you would like to see in upcoming releases of Geneyx Analysis, please contact support@geneyx.com with your suggestions.   

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