Automating FASTQ to Clinical Report with Geneyx Analysis

Published: 04 August 2022

Eli Sward Ph.D.


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.

Geneyx Analysis is a complete clinical workflow solution. Within the application, users can upload fastq or VCF files from local or cloud infrastructures, perform the sequencing and interpretation, and render a customizable clinical report all in one solution. Geneyx Analysis eliminates the need to outsource to third-party applications for the different workflows and provides a transparent interface for all users of the application. Together, Geneyx Analysis reduces bioinformatic complexities and allows clinicians and geneticists to do what they do best: enable affordable and accurate results for their patients.

As shown in the snapshot above, users have many options when starting from fastq. Users can run, for example, GATK or DRAGEN (and soon Sentieon), implement somatic or germline workflows, and select from gene panels, exomes, or genomes. All opportunities are provided to our users to ensure that their customized workflow can be integrated. The best part about uploading fastq files is that command line experience is not required. Excel or text files can be loaded with the required sample IDs, and once the file is uploaded the pipeline starts.

In summary, Geneyx believes that every patient deserves to be diagnosed and treated with the value of genomics and genetic knowledge. Part of this requires automation and, with this, we are striving for a world without undiagnosed diseases. Geneyx is continuing to see the adoption of the platform on a global scale, and we would be happy to show you how this platform is a leading application in the NGS field. Whether it is starting from fastq or VCF, Geneyx can support your needs.

If you would like a demonstration of the software, or to learn more about the application, please contact support@geneyx.com.   

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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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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

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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.

Geneyx Analysis Version 5.9 Release

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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