Geneyx Analysis: Our Most Significant Updates to Date
Geneyx Analysis 6.0: Low Pass Whole Genome
- ACMG Guidelines for CNV/SVs: The CNV/SV tab now supports the technical standards for reporting of constitutional copy number variants according to the joint consensus recommendations of ACMG and ClinGen, reference article here https://pubmed.ncbi.nlm.nih.gov/31690835. ACMG guidelines will be calculated automatically for all deletion and duplication events and there is an interface to modify criteria using internal evidence. The interface reflects a similar approach as the ClinGen CNV calculator with full transparency of activated or inactivated criteria, as well as audit trails for all actions implemented. This will drastically improve CNV interpretation times and aid in workflow automation.
- Somatic Databases: Clinical trials from clinicaltrials.gov are now accessible on the gene level as a hyperlink. This will enable users to perform quick searches for FDA trials that correlate to the gene.
- DRAGEN version selection: Users now have the option to select what version of DRAGEN is being utilized for the secondary pipeline. The baseline DRAGEN version will remain v4.0.5. This option will allow users to conform to their existing workflows whilst enabling the exploration of updated DRAGEN features. The optional DRAGEN version (4.2.4) enables several additional features, discussed below, including advanced callers and low pass whole genome options. For upgrading to the newest Dragen caller, please contact our support (support@geneyx.com). *Please be aware that over time DRAGEN v4.0.5 will be deprecated.
- DRAGEN v4.2.4: The comprehensive updates included in DRAGEN v4.2.4 can be found here. At a high level, this update includes improvements to small variant calling at high depths for WGS (>100X), High sensitivity mode results in increased sensitivity for reads with low MAPQ and low allele frequency (mosaic variants), Joint CNV/SV signal improves CNV detection for events ranging from 1-10kbp.
- Advanced DRAGEN Callers: When running whole genome workflows from the secondary pipeline, there are new sequence-graph realignment settings that run on the backend to improve calling for genes that have high identity paralogs. This includes genes such as: GBA, SMN1, HBA, LPA, RH, CYP2D6, CYP21A2, CYP2B6. For analyses that have whole genome workflows with at least 30X coverage, output metrics for these genes will be present in the Advanced Analysis link in the “Info” section of the analysis. All outputs are taken from Illumina and each output will reference the associated hyperlink.
- DRAGEN Low pass whole genome sequencing: Low-pass whole genome sequencing (low-pass WGS) is a genomic sequencing approach where the entire genome is sequenced at a relatively low depth, typically less than 5x coverage. Low pass whole genome sequencing is now supported in the secondary pipeline of Geneyx. To implement, the sequencing target will need to set to Whole Genome Low Pass.
- BIRD/OCEAN Pipeline: Results from DNA and RNA analyses are critical for advancing our understanding of genetics and molecular biology, leading to improved diagnostics, therapeutics, and insights into the fundamental biology of organisms. Geneyx has partnered with OCEAN Genomics to advance the DNA and RNA joint pipeline. This feature will be available upon request.
Microarray to VCF Converter: For customers that have microarray data, such as those from Affymetrix, Geneyx now provides a script to convert the file into a compatible VCF format. The script is available here, https://github.com/geneyx/geneyx.analysis.api/tree/main/apps/microarray. The converted files can then be loaded into the CNV/SV genetic model of Geneyx. Users can also select this as a sequencing target during data upload.
