Improving Case Diagnosis with Geneyx Analysis

Published: 4 August 2022

Eli Sward Ph.D.


Geneyx Analysis is becoming adopted globally as a flexible innovative solution for rare disease interpretation and has been shown to dramatically improve diagnostic yields. One of the many features that contribute to this capability is utilizing a novel phenotype-dependent algorithm, which finds relevant associations between gene and phenotype ontologies. This feature is utilized by researchers and clinical geneticists to identify candidate variants and investigate literature for novel biomedical findings.

The power of this algorithm is literature. Specifically, databases containing publications are scanned to find associations between the gene of interest and the phenotype of the patient. The more literature identified the stronger the correlation and phenotype score. Staying up to date on literature can be a very tedious process, yet Geneyx Analysis does this through an automated process to ensure the most recent literature is being displayed to our users.  This in turn alleviates the manual complexities of searching for relevant publications and staying up to date on additional annotation sources.   From a user perspective, the phenotyping algorithm in Geneyx Analysis provides comprehensive information on the variant, gene, and disease in question. Diseases related to the gene and relevant publications will be displayed to allow the user to understand what findings support the association. Similar information is displayed on the gene and variant levels. This interface offers a comprehensive and consolidated view for easy browsing and highlights the key search terms extracted from the publications

Coupled with the ability to deep dive into the literature is a calculated and prioritized gene list. When applied to the filtering protocol, the candidate variant is likely to be listed in the top 5 rows of the protocol. Geneyx analysis also supports a multitude of other annotation sources that can confirm the findings. Additionally, if an interpretation is made on the variant or gene level, it will improve the score for that variant and gene the next time it is encountered. This enables an AI-based feature with the Geneyx Analysis application and automates the process of variant classification.

In summary, Geneyx Analysis is an end-to-end solution for next-generation sequencing (NGS) data. Deployment can be cloud-based or on-premises, and users can start from fastq or VCF and generate fully customizable clinical reports. Geneyx Analysis has many innovative features, but one discussed herein was the phenotype-dependent algorithm. Implementation of this feature has been shown to significantly improve diagnostic yields for many of our customers and we would be happy to show you how it could improve your case diagnostics. If you are interested in learning more about this feature or how Geneyx could be integrated into your specific workflow, please contact support@geneyx.com.

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Geneyx Analysis is becoming adopted globally as a flexible and innovative solution for rare disease interpretation and has been shown to dramatically improve diagnostic yields. One of the many features that contribute to this capability is the utilization of a novel phenotype-dependent algorithm, which finds relevant associations between gene and phenotype ontologies. This feature is utilized by researchers and clinical geneticists to identify candidate variants and investigate literature for novel biomedical findings.

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We are proud to present fascinating findings in poster #eP105 at the coming ACMG 2022

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Geneyx Analysis Version 5.10 Release

The Variant Browser now supports the lookup of copy number and structural variants (CNV/SV). With this feature, users can query events based on relevant annotations, including events that overlap given gene(s), as well as events that overlap enhancers that impact specific genes. Pharmacogenomics (PGx) testing is now available for beta testers. This feature is optimized when starting from fastq and works with exome and whole genome data. The report contains interpretations for 13 CPIC Level A and B genes, with gene summaries, drug metabolism, interpretations, and recommendations. The user also has functionality to define the SNP array and select which genes to report on. Please contact us if interested.

Whole exome and genome sequencing in mendelian disorders: a diagnostic and health economic analysis.

What is better as an initial test WES or WGS? A recent paper in the European Journal of Human Genetics put this notion to the test. They found that out of 91 patients across 64 families with undiagnosed Mendelian disorders, in New South Wales, Australia, 13 of the 38 unresolved families (34%) were diagnosed when using WGS instead of WES. Previous WES analyses failed to resolve these cases due to previously unknown gene-disease association (23%), insufficient sequencing coverage (31%), the variant prioritization pipeline (15%), and the bioinformatics pipeline (23%), or CNV detection (8%). Comparing the diagnostic yield over these 64 families revealed a 9% increase in diagnostic yield by using WGS at the outset rather than contemporary WES analysis. As scientific knowledge accumulates both the analysis capabilities improve, hence periodical re-analysis of old unresolved cases might provide a genetical resolution.

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With more than 300 accounts and close to 200,000 cases analyzed, Geneyx Analysis is continuing to receive global adoption in clinical and academic settings. One differentiating feature that advances this adoption is our patient-centric vision. Our vision at Geneyx is to improve diagnostic rates and turnaround times. To do so requires implementing new and innovative features, and since the last release of Geneyx v5.8, there have been many exciting updates that are worth noting.

Improving Case Diagnosis with Geneyx Analysis

Geneyx Analysis is becoming adopted globally as a flexible and innovative solution for rare disease interpretation and has been shown to dramatically improve diagnostic yields. One of the many features that contribute to this capability is the utilization of a novel phenotype-dependent algorithm, which finds relevant associations between gene and phenotype ontologies. This feature is utilized by researchers and clinical geneticists to identify candidate variants and investigate literature for novel biomedical findings.

Automating FASTQ to Clinical Report with Geneyx Analysis

In the field of next-generation sequencing, one essential feature is automation. Automation can enable increased scalability and faster turnaround times with improved diagnoses. If applied correctly, this not only benefits the clinical environment but also the field of precision medicine. And although many companies advertise this, Geneyx Analysis actually delivers it.

We are proud to present fascinating findings in poster #eP105 at the coming ACMG 2022

Prof Revital Kariv, M.D, and her team diagnose and treat #coloncancer patients at the Tel Aviv Sourasky Medical Center. In recent research, utilizing the Geneyx Genomex Ltd. analysis platform, collaborating with Dvir Dahary, and Tel Aviv University, they identified novel mutations responsible for colon cancer predisposition.
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