Geneyx Analysis: Version 5.14 Release

The Latest Advancements in Genome Sequencing: Introducing Geneyx Version 5.14

We are delighted to bring you the highly anticipated release of Geneyx version 5.14, packed with a range of exciting features designed to take your NGS data analysis to new heights. In this release, we have focused on streamlining workflows and providing powerful tools to enhance your analysis experience. Here we share with you some of the key highlights of this release, with particular emphasis on the features marked in bold, which are complemented by detailed video demonstrations for your convenience.

Geneyx Analysis Version 5.14 

Graphical In-House CNV Representation 

Geneyx AnalysisVersion 5.14

Gene Coverage Statistics 

Geneyx AnalysisVersion 5.14

 CNV Visualization 

Geneyx Analysis Version 5.14 

Gene Centric View

New Features:

New Features:

1. Gene Coverage Statistics: Starting from fastq files, you now have the option to calculate exon and gene coverage statistics at 10X and 20X for the specific genes you define. This powerful feature generates a comprehensive TSV file that provides invaluable insights into coverage metrics for gene panels, enabling you to make data-driven decisions with confidence.

2. Secondary Pipeline Sentieon: We are introducing Sentieon as a secondary pipeline option, recognized for its exceptional accuracy, speed, and scalability in the genomics community. Furthermore, we are delighted to announce a collaboration with our customers as Beta testers of this newly added feature. To explore this opportunity, please reach out to our support team.

3. Sample Quota Regulation: We understand the importance of maintaining accurate usage history and license information. With the new Rule Out feature, samples that have failed the secondary pipeline from the usage history can be excluded by administrators, ensuring full transparency and precise control over your data and licensing information.

4. Gene Centric View: To enhance your SNV genetic models, we have incorporated CNV/SV visibility within the analysis. The newly introduced column displays the total number of CNVs overlapping the given SNV position. Additionally, a dedicated column highlights CNV events predicted to be damaging, encompassing events that overlap exons and exhibit an allele frequency below 5%. To further simplify your analysis, you can now search for CNVs using the magnifying glass tool, providing efficient access to the desired information.

5. Patient and Clinical Record APIs: In our ongoing commitment to empower users, we have added the CreatePatient and AddClinicalRecord APIs to our GitHub directory. The CreatePatient API enables you to seamlessly upload patient/subject information before uploading a VCF sample. If you prefer to load patient data using a JSON file, we provide a convenient command line feature for streamlined data management. Furthermore, the CreateClinicalRecord API allows you to effortlessly add a clinical record to an existing patient, ensuring comprehensive record-keeping and enhanced collaboration.

6. Auto-Reporting for CNV/SVs: Building on the success of our automatic report generator, we are thrilled to extend its functionality to include CNV/SV analysis. Now, you can leverage the power of automation to generate TSV files based on your customized filtering criteria, saving valuable time and resources while ensuring consistent and reliable reporting.

7. VUS monitor: Keeping track of variant classification changes can be a daunting task. To simplify this process, we have implemented an auto-notification feature that alerts you whenever variants undergo classification changes according to ClinVar. This proactive notification provides comprehensive details, including a direct link to the analysis, enabling you to perform retrospective analyses with ease and precision.

Geneyx Analysis

Geneyx Analysis: An End-to-End WES & WGS Data Analysis & Interpretation Solution| Geneyx

In addition to these exciting new features, we have made significant improvements across the platform to enhance your overall user experience. Here are some notable improvements in Geneyx version5.14:

1. Graphical In-house CNV Representation: Analyzing CNVs and SVs becomes even more insightful with the introduction of a new feature. Now, you can visualize the event overlap of your sample of interest with other samples that share overlapping events. This graphical representation provides compelling supporting evidence to aid you in making informed decisions about including or excluding variants as candidate variants.

2. CNV Visualization: To improve the understanding of CNV events’ validity, we have enhanced the visualization of CNV events in the widely used Integrated Genomics Viewer (IGV). This feature is applicable when starting your analysis from fastq files in Geneyx, providing you with an intuitive and comprehensive view of CNV events for better interpretation.

3. New Filters: We understand the importance of customizable workflows to meet your specific analysis requirements. In Geneyx v5.14, we have added multiple new filters, expanding your options for tailoring your analysis pipeline. You can find comprehensive documentation on all the available filters enabling you to optimize your analysis according to your unique needs.

4. Always Show In-house LP/P Variants: We have introduced a valuable option in the filter chain that allows you to always display Likely Pathogenic (LP) and Pathogenic (P) variants based on In-house classifications. Enabling this option ensures that these variants are captured and presented to you, even if they fail to meet specific filtering criteria. This feature helps you uncover potentially clinically significant variants that might have been missed otherwise.

5. SMART Filtering: Defining target capture regions for an enrichment kit is now more powerful with the expanded capabilities of SMART filtering. In addition to existing features, you can now apply SMART filtering based on Splice-AI and Read Depth. By enabling SMART filtering, you can effectively pre-filter variants before their import into analyses, optimizing the efficiency and accuracy of your analysis pipeline.

6. ACMG Secondary Finding Genes: Geneyx v5.14 incorporates the latest guidelines from the American College of Medical Genetics and Genomics (ACMG) regarding secondary findings. In accordance with the recently published article titled “Secondary Findings from Clinical Genomic Sequencing: Prevalence, Patient Perspectives, Family Impact, and Healthcare Costs”, we have updated our platform to include the following genes as recommended secondary findings: CALM1CALM2, and CALM3.

7. We are pleased to inform you that all public annotation sources have been successfully updated to the latest version. This ensures that our data is current and reflects the most up-to-date information available.

These improvements in Geneyx v5.14 reflect our commitment to providing you with advanced tools and features that enhance your NGS data analysis capabilities. We hope you enjoy exploring and utilizing these new enhancements to their fullest potential.  

We would also like to express our gratitude for the fantastic turnout at the recent ESHG conference. It was a pleasure meeting you in person and learning how you are utilizing the Geneyx platform. We are excited to announce we will be exhibiting at ASHG (73rd Annual Meeting of the American Society of Human Genetics) from the 1-5 Novemeber. If you plan to attend any of these events, please let us know, and we will be delighted to meet with you.

Thank you for your continued support and valuable feedback that drives the evolution of Geneyx Analysis. We look forward to assisting you further in your genomic research endeavors.

 If you have any additional features or suggestions you would like to see implemented, please don’t hesitate to reach out to our dedicated support team.  

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