Geneyx Analysis is an end-to-end solution for next-generation sequencing (NGS) data that can scale the process of FASTQ to clinical reports for hospital and commercial labs. This advanced platform integrates machine learning and AI-based features to identify novel biomedical insights, while also improving diagnostic yields and turnaround times. By providing a fully transparent and intuitive solution, Geneyx Analysis enables clinicians and researchers to have complete control over data analysis and alleviates the complexities of regulating in-house bioinformatics pipelines. Protocols can be fully customized to accommodate gene panels, exomes, and genomes, and our comprehensive annotation engine supports the analysis of all genetic variants including structural and copy number variations as well as regulatory elements. Together, Geneyx Analysis automates the diagnostic process from sequencer to report, while creating a comprehensive resource for novel variant discovery.
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Geneyx Analysis provides customizable protocols which enable labs to standardize genetic tests and analysis workflows for whole genome sequencing, exome sequencing, and gene panels. Protocols can include combinations of simple or complex filters on any set of annotation entities, can define gene lists or genomic regions, and can be locked down on the user and annotation level. Protocols can also be optimized to automatically render reports and include any user interpretations for given variants. Default protocols are provided and include germline, somatic, and health screening. This allows all users to quickly become proficient in the system and provide a template to optimize.
Geneyx Analysis stores all sample data in user accounts following HIPA and GDPR guidelines. At any point, samples can be queried and reanalyzed with the most up-to-date annotation sources. Geneyx Analysis also creates an in-house database that includes annotations and interpretations previously entered by the analyst. This assists in applying accumulated in-house knowledge to new cases. Labs may also participate in Inter-Lab sharing, which permits viewing of variant allele frequency within all cases in accounts sharing data with their lab.
Geneyx Analysis also offers account management capabilities that can be used to set permissions for individual users within a group. This allows full control of all processes and steps performed by individual users, which helps reduce mistakes made by other departments. In conjunction, every process performed in the application is stored and can be reviewed, offering a comprehensive audit trail for labs.
Geneyx Analysis offers an intuitive, streamlined variant browsing interface with an interactive table. Each row represents a single genomic position with a variation, and each column is populated with the relevant details gathered during the annotation process. Columns can be expanded to view additional information and clicking on a hyperlink will open a new tab associated with the annotation source. All annotations in the variant dashboard can be applied to the filter, and variants can be sorted according to any column.
Geneyx Analysis offers the capability to rapidly filter across all variants present in an account in all samples. This feature allows users to see if a variant has been observed previously, as well as associated information, such as classifications, phenotypes, and observed samples. The logic can be based on any annotation source and the remaining variants can be exported into multiple formats. This tool provides an easy way to perform retrospective analysis within an account.
Geneyx Analysis integrates a novel algorithm that scans over 150 biomedical databases to identify strong phenotypic associations. This algorithm gives users the flexibility of entering phenotypes using HPO and/or free search terms. Variants are rapidly prioritized and displayed to users to quickly identify candidate variants associated with the phenotype. Geneyx Analysis outputs a phenotypic evidence score that can be filtered on, but also includes the ability to deep-dive into relevant literature to find novel disease associations.
Geneyx Analysis integrates an annotation engine that provides automated and up-to-date annotations, ensuring the most relevant version of annotations is being used. This leverages both standard ACMG-recommended databases, as well as all publicly available annotation sources. Geneyx Analysis automates 18/28 ACMG criteria to reduce workflow complexities and ensure best practices are being followed. ACMG classifications automatically include case-level information such as inheritance models and relevant findings in associated samples, and if additional information or expertise is available, users can incorporate their data, modify criteria, and store changes for all downstream cases.
A comprehensive and flexible reporting system enables information automatically from selected annotation sources, key findings, and user summaries to be incorporated. The comprehensive clinical reports can be customized according to the organization’s logo and formatting requirements to incorporate static and dynamic information. The reports are also offered in multiple languages, preventing the need to translate generic information.
The usage dashboard provides detailed and colorful reports on workflows performed within the Geneyx Analysis account. This includes information such as VCF samples imported by sequencing target, distribution of samples processed using secondary pipelines, and total number of analyses created based on protocols. The dashboard is also longitudinal, giving insight into peak seasons of analyses performed within the software. This feature is a great tool for management purposes
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