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Frequently Asked Questions

FAQ

  • What is Geneyx Analysis?

     Geneyx Analysis is a powerful diagnostic analysis software specifically designed for genetic tests within health institutions. It serves as an automated solution for conducting secondary and tertiary analysis of variants identified in gene panels, exomes, and whole genomes, primarily generated through next-generation sequencing (NGS) assays.

    The primary objective of Geneyx Analysis is to facilitate the identification and classification of causal variants that have clinical significance. By leveraging advanced algorithms and annotation tools, the software assists healthcare professionals and researchers in making informed decisions related to targeted diagnoses and targeted therapy applications in both hereditary disorders and cancer.

    The software offers comprehensive features for variant analysis, including filtering, annotation, variant classification, and report generation. It streamlines the analysis process, providing a standardized and efficient workflow for variant interpretation.

  • How does Geneyx Analysis ensure data security and privacy?

    Geneyx Analysis employs stringent data security measures, including encryption, access controls, compliance with relevant privacy regulations, such as GDPR and HIPAA, as well as ISO certifications (ISO 13485:2016, ISO 27001:2013, ISO 27799:2016)This is an answer

  • How to upload a fastq file?

    This is an answerThe process of fastq upload is applicable to both local and remote fastq files. If your fastq files are stored on a cloud infrastructure, you will need to configure the Data Source in the Settings dialog before proceeding.

    Once the setup is complete, you can proceed with initiating the pipeline. Click on the Upload Single Sample icon in the Seq. Samples or through the Processing Tasks window. Follow the instructions provided in the interface to select and upload the fastq files. Make sure to provide accurate and relevant information, such as consent status, sequencing target, sample source, and any other required fields.

  • Does Geneyx Analysis provide annotation and interpretation of genomic variants?

    Geneyx Analysis provides robust annotation and interpretation tools to aid in understanding the functional implications, population frequency, and clinical significance of genomic variants. These features enable researchers, clinicians, and geneticists to gain deeper insights into the genetic variations identified through sequencing data. Here's a more detailed explanation of the annotation and interpretation capabilities of Geneyx Analysis:

     

    a) Variant annotation: Geneyx Analysis employs various databases, algorithms, and bioinformatics resources to annotate genomic variants. This process involves associating each variant with relevant information such as gene names, genomic coordinates, protein-level effects, predicted functional impact, and conservation scores. Annotation helps researchers understand the potential consequences of specific variants on gene function and overall genome biology.

    b) Functional impact prediction: The platform leverages computational algorithms and prediction models to estimate the functional impact of genetic variants. It provides insights into whether a variant might alter protein structure, affect protein function, or disrupt regulatory elements. These predictions can aid in prioritizing variants for further investigation and understanding their potential role in disease development or phenotypic expression.

    c) Population frequency data: Geneyx Analysis integrates population frequency databases, such as gnomAD (Genome Aggregation Database), 1K Genome, or specific ethnic-specific databases. By accessing these resources, the platform can provide information on the prevalence of a variant in different populations. This data is valuable in assessing the rarity or commonness of a variant and its potential relevance to specific genetic disorders or traits.This is an answer

  • What types of genetic variants can Geneyx Analysis detect?

    Geneyx Analysis can detect a wide range of genetic variants, spanning from single nucleotide variants to copy number variants/structural variants.

    Single-nucleotide variants (SNVs): Geneyx Analysis has the capability to detect SNVs, which are single-base changes in the DNA sequence. SNVs can include single-base substitutions. These variants can have significant implications for disease susceptibility, drug response, and other genetic traits.

    Copy number variations (CNVs): CNVs involve changes in the number of copies of a particular genomic segment. Geneyx Analysis is designed to detect CNVs, which can range from small duplications or deletions of a few hundred base pairs to large-scale amplifications or deletions spanning several kilobases. CNVs are associated with various genetic disorders and can contribute to phenotypic variability.

  • Can Geneyx Analysis handle multi-sample analysis?

    Yes, Geneyx Analysis supports multi-sample analysis, allowing for the comparison and identification of shared and unique variants across multiple samples or individuals.

    To link two or more individuals together, please follow these steps:

     

     

    a) Access the Geneyx Analysis Navigation Window and click on the proband’s analysis.

    b) In the Analysis Details window clicking on the Add icon will give the option to add a new or existing sample.

    c) A selection interface will allow you to choose a relation, affected status, and search for or select the second individual you wish to link.

    d) An existing sample can be added by clicking on the Search tab and entering Sample's ID

  • Can Geneyx Analysis generate customizable reports for genomic analysis results?

    Geneyx Analysis offers customizable reporting tools to enable users to generate comprehensive and tailored reports for their genomic analysis results. These reporting features provide a convenient way to summarize and present key findings from the analysis. Here's a more detailed description of the customizable reporting capabilities within Geneyx Analysis:

    a) Report templates: The platform typically offers a range of pre-defined report templates that serve as starting points for generating reports. These templates may cover various types of analyses or focus on specific clinical applications. Users can select the most suitable template and customize it according to their specific requirements.

    b) Variant calls and annotations: Geneyx Analysis allows users to include variant calls and associated annotations in the reports. The platform can generate a concise and organized summary of the detected variants, including their genomic coordinates, variant types, allele frequencies, predicted functional impacts, and additional relevant information. Users can select the specific annotations they want to include in the report, tailoring it to their analysis goals.

    c) Export options: Geneyx Analysis typically provides export options for generated reports. Users can export the reports in various formats, such as PDF, HTML, or Excel, depending on their preferred mode of sharing or further analysis. This allows for easy distribution of the reports to collaborators, colleagues, or clinicians involved in patient care.

  • Does Geneyx Analysis offer collaboration features for team-based projects?

    Geneyx Analysis provides collaboration features designed to support team-based projects and enhance collaboration among users. These features enable secure sharing of data, analysis workflows, and findings, fostering teamwork and facilitating efficient collaboration. Here's a more detailed description of the collaboration capabilities within Geneyx Analysis:

    a) Data sharing: Geneyx Analysis allows users to securely share genomic data with colleagues and collaborators. This includes the ability to upload and share datasets, such as VCF (Variant Call Format) files. By sharing data within the platform, team members can access and analyze the same dataset, promoting consistency and facilitating collaborative analysis.

    b) Workflow sharing: Geneyx Analysis often supports the sharing of analysis workflows or pipelines. Users can create and customize analysis workflows tailored to their project needs, and then share these workflows with team members. This allows for standardized and reproducible analyses across the team, ensuring consistency and streamlining the analysis process.

    c) Access controls and permissions: Collaboration features in Geneyx Analysis typically include access controls and permission settings. Users can define and manage access levels for different team members, granting them appropriate permissions for data access, analysis tools, or project-specific features. This ensures that only authorized individuals can view, edit, or interact with the shared data and analysis resources.

  • Is Geneyx Analysis compatible with third-party tools and pipelines?

    Yes, Geneyx Analysis is agnostic to sequencing technology and can perform exome, genome, and gene panels analyses.

  • Can Geneyx Analysis handle custom analysis pipelines and workflows?

    With Geneyx Analysis, users have the ability to design and implement custom analysis pipelines and workflows tailored to their specific needs. This flexibility empowers researchers, clinicians, and geneticists to conduct advanced analyses and gain deeper insights into genomic data.

    The platform offers a comprehensive suite of modular tools and features that can be combined and customized to create personalized analysis pipelines. These tools cover a wide range of applications, including variant calling, annotation, filtration, pathway analysis, and interpretation. Users can select the relevant tools for each step of the analysis, configuring them to meet their specific requirements.

    By allowing users to define their own data processing and analysis steps, Geneyx Analysis enables the integration of various algorithms, methodologies, and databases. This enables researchers to leverage the most up-to-date tools and resources available in the field of genomics.

  • Can Geneyx Analysis handle long-read sequencing data?

    Geneyx Analysis recognizes the importance and growing relevance of long-read sequencing data in genomics research and clinical applications. As a result, the platform is equipped to handle and analyze long-read sequencing data.

    Long-read sequencing technologies provide longer read lengths compared to traditional short-read sequencing methods. This enables the detection of complex genomic variations, such as structural variants, large insertions/deletions, and repeat expansions. By supporting long-read sequencing data, Geneyx Analysis enables researchers and clinicians to unlock the full potential of these technologies and extract valuable insights from the genomic data.

    When working with long-read sequencing data, Geneyx Analysis offers a range of tools and functionalities specifically designed to address the unique characteristics of long reads. These tools encompass various steps of the analysis pipeline, including data preprocessing, alignment, variant calling, and downstream analysis.

  • Which long read sequencing platforms are supported by Geneyx Analysis?

    Long read sequencing platforms play a crucial role in genomics research by providing high-quality sequencing data of longer DNA fragments. Geneyx Analysis, a comprehensive bioinformatics platform, is designed to support and analyze data generated by various long read sequencing technologies. In particular, Geneyx Analysis supports data from the Oxford Nanopore Technologies (ONT) platform and Pacific Biosciences (PacBio) platform, among others.

  • Can Geneyx Analysis determine variants’ phasing using long read sequencing data?

    Geneyx Analysis offers the capability to determine the phasing of both single nucleotide variants (SNVs) and copy number variants (CNVs) using long read sequencing data.

    SNVs, which are single base pair variations in the genome, play a significant role in understanding genetic variation and its impact on phenotypes and diseases. Geneyx Analysis employs specialized algorithms and methodologies to analyze long read sequencing data and accurately determine the phasing of SNVs. By identifying the parental origin of each allele at specific SNV positions, researchers can obtain a comprehensive view of the allelic combinations on each chromosome and better understand the inheritance patterns and potential disease associations.

    In addition to SNVs, Geneyx Analysis also addresses the phasing of CNVs, which are larger structural variations involving duplications, deletions, insertions, or complex rearrangements in the genome. CNVs can have significant implications for disease susceptibility and may contribute to genomic disorders. Analyzing the phasing of CNVs can provide insights into their origin and better elucidate their functional impact.

    The ability of Geneyx Analysis to determine the phasing of both SNVs and CNVs using long read sequencing data is crucial for accurately understanding the genetic architecture of an individual’s genome. By leveraging the advantages of long reads, such as spanning multiple variants and capturing complex genomic rearrangements, Geneyx Analysis enables researchers to discern the phase relationships of these variants and unravel the complexities of the genome at a higher resolution.

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