NGS Data - secondary and tertiary analysis

Accelerate patient diagnosis with Geneyx Analysis AI-based platform

WES and WGS data analysis & Interpretation software

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.

 Contact our team to see how Geneyx Analysis can solve your undiagnosed cases.

Customizable Workflows and Integrations

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.

Workflow and Reports
Processing Task Screenshot

NGS Pipeline Management & Genetic Data Storage

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.

Variant Analysis

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.

Variant Analysis
New Qeury

Variant Browser

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.

Rapid Phenotype-Driven Interpretation

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.


Advanced ACMG/ClinGen Variant Classification

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. 

Comprehensive and Customizable Reports

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.

New Reports
Geneyx-QA Account

Account Dashboard

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

Long-Read Sequencing Analysis

Geneyx provides bioinformatics analysis services to help researchers interpret the data generated by long-read sequencing technologies. This includes services such as genome assembly, variant calling, and structural variant analysis.

Geneyx’s platform offers several advantages for researchers using long-read sequencing technologies. For example, the platform can handle large datasets with ease and provide rapid
turnaround times for analysis. Additionally, the platform offers a user-friendly interface and advanced visualization tools that make it easy for researchers to explore and interpret their

Read on: All you need to know on LongRead Sequencing Data Analysis From A-Z.

Integrating DNA and RNA Sequencing

Geneyx Analysis integrates RNA sequencing data with DNA sequencing information, providing a comprehensive view of genetic insights that were previously challenging to achieve with separate analyses. This integration is designed to significantly enhance the accuracy of detecting structural variants, including gene fusions and complex genomic rearrangements, while also providing thorough genomic insights.

Unlock Insights with Automated UPD Analysis

Geneyx Analysis’s Uniparental Disomy (UPD) Analysis feature not only provides automated alerts for positive findings in trios (exomes/genomes) but also delivers essential UPD scores. These values, combined with notifications detailing chromosome number, significance (p-value), and inheritance categories, are pivotal for understanding and diagnosing genetic disorders. UPD analysis holds particular significance in identifying conditions associated with genomic imprinting patterns, aiding in the clinical diagnosis of disorders like Prader-Willi syndrome and Angelman syndrome, which are linked to specific UPD patterns. Users can delve deeper into these insights with a simple click on the “Details” icon, facilitating informed decision-making in clinical settings.

Automated star allele analysis

Geneyx Integrated PGx Workflow

Geneyx offers an advanced pharmacogenomics (PGx) workflow, unraveling the genetic nuances influencing drug metabolism. Our curated data, covering 13 CPIC level A/B genes for 68 commonly prescribed drugs, ensures precise insights. Sourced from CPIC, FDA, and PharmGKB, our user-friendly PGx reports facilitate informed decision-making, including automated star allele calculation. Customizable reports and electronic signatures ensure compliance. By leveraging key databases and unique genetic profiles, Geneyx empowers clinicians and diagnosticians with potent tools for personalized medicine, optimized drug selection, risk reduction, and efficient healthcare delivery, leading to improved treatment outcomes and patient safety.

Input files: WGS, exome sequencing, microarrays

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Geneyx Analysis Version 5.12 Release


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