Laboratories can select from a range of NGS-based assay products to sequence either the entire human genome or a targeted set of genes (gene panels), exomes, or genomes. This sequencing process generates raw variant calls for each patient. Geneyx Analysis seamlessly handles these raw variant calls and offers the following key features:

• Reading and processing input in standard VCF files, which contain both small variants (detectable using short-read NGS data) and CNVs (detected through coverage profile analysis of NGS data).
• Annotating imported data with comprehensive information from numerous public and licensed databases, enhancing the understanding of variant characteristics.
• When a user selects Custom Coverage, it will provide the option for Gene List or Gene Panel coverage. Gene List allows the user to enter a list of genes, whereas the Gene Panel requires a panel to be integrated into the account. The outputs will provide coverage for the genes at 10 and 20X.
  
• Evaluating the quality of samples and variants through a robust set of metrics, derived statistics, and intuitive visualizations.
• Utilizing advanced algorithms to conduct in silico analyses, providing valuable insights into the impact of variants on the patient’s genes and their respective functions.
• Adhering to industry-standard guidelines for scoring and classifying germline variants and CNVs, employing guided workflows and auto-scoring algorithms.
• Reviewing relevant clinical evidence and literature to assess whether a variant meets the criteria for reporting and further analysis.
• Creating customizable clinical reports that include all selected variants, along with patient and sample-level data, facilitating effective communication of findings.
• Storing variants from previously sequenced samples in a secure warehouse, enabling the computation of cohort-level statistics and per-variant frequencies for future analyses and research.

Although Geneyx Analysis comprises several modules catering to diverse market needs, it is developed, deployed, and distributed as a unified software solution, ensuring a seamless and comprehensive user experience.