Frequently Asked Questions

GenNext is a decentralized peer-to-peer (P2P) genomic data analysis platform. Due to the design and structure of GenNext, genomic data is not shared with anyone other than the computer where the analysis will be performed and the person performing the analysis.

GenNext is differentiated from other data analysis platforms on the market thanks to its unique architecture and network structure, providing an exceptional user experience.

Successful data analysis and reporting: The GenNext platform incorporates the latest literature in genetics/genomics, enabling successful analysis of next-generation sequencing data.

Privacy and security: With GenNext, data is not stored and saved in a centralized location, which means there is less risk of your data being compromised by malicious actors.

High-throughput and fast data transfer: Thanks to GenNext’s specially developed network structure, data is transferred directly between users. This significantly reduces the time and bandwidth required to transfer data to centralized servers or cloud platforms used in traditional big data analysis platforms.

Secure analysis of personal data and EU-GDPR compliance: In a decentralized P2P network, data is stored and analyzed locally on users’ devices. This provides greater privacy and security compared to traditional big data analytics platforms that depend on storing and processing data in a central location. In addition, this structure allows data to be analyzed in compliance with EU-GDPR (The European General Data Protection Regulation) and KVKK (Personal Data Protection Law-Turkiye).

Alignment with Web3.0 principles: Decentralized P2P networks are one of the underlying technologies of Web3.0, which can be defined as a decentralized and user-owned internet. GenNext’s network design, which enables decentralized P2P data transfer and analysis, is in line with the principles underlying Web3.0.

GenNextklinik is a genomic data analysis and reporting tool within the GenNext platform. With its rich analysis and annotation tools, advanced filtering and reporting options, and user-friendly interface, GenNextklinik offers a unique genomic data analysis experience.

Comprehensive analyses and streamlined diagnostic process: GenNextklinik aims to accurately detect and prioritize genomic variants thanks to its comprehensive workflow and rich annotation options developed by following the current literature and based on Best-Practice applications. This makes it a powerful aid in the diagnosis of genetic diseases. Using the pre-customized filtering options integrated into the platform, the clinically important variants among thousands are prioritized with GenNextklinik ,which helps accelerate the diagnostic process. In addition, thanks to the multi-sample analysis options, the genetic disease diagnosis process is supported by taking heredity into account with Duo and Trio analyzes.

Find actionable variants and treatment options in cancer: GenNextklinik uses a comprehensive somatic variant detection workflow and helps identify genetic alterations that can support the diagnostic-treatment process. Using up-to-date literature and databases, identified variants are reported and presented in terms of their diagnostic significance, pathogenicity and drug interactions that can help the therapeutic process.

Fast reporting: With GenNextklinik‘s automated report generation feature, you can report on the variants you select after analysis using report templates and print the report format instantly. You can also upload the report format you want to use to the platform and access variant reports in the format you specify in seconds.

To become a member of GenNext, you can click on the “Sign Up” button on our website, then fill in the required information, and submit a membership request. You can review the relevant document for the membership options suitable for you, which you will be asked to choose while creating your membership request: (MEMBERSHIP TYPES INFORMATION-DOCUMENT LINK)

After your GenNext membership request is approved, you must make a payment to activate your membership. Payments are made by credit card for individual memberships. For details on corporate payments, you can contact our team (SEND MESSAGE BOX LINK-Help, Contact section)

Make sure that the information you entered during payment is correct. If you are sure that it is, you can contact your bank as you may be experiencing a bank-related problem. If the issue is still not resolved, please contact our team.

The user can access VCF files and analyses performed for a duration of one month from the end date of the membership. The user will be informed about the issue near the end of the specified period.

GenNextklinik has a user-friendly interface for uploading sequencing data. First log in to your account and go to the “Run” section. After selecting the “node/edge” available for analysis, you will be connected through the platform. After entering “Sample Name” and “Process Type” on the screen you are directed to, your file (which should be in a compatible format) is uploaded to the relevant field. The platform will guide you through the next steps after the upload is complete.

The analysis workflows used in GenNextklinik accept raw data (.fastq extension) and BAM (.bam extension) files that are already aligned to the reference genome as input. Depending on the type of data uploaded, the GenNextklinik detect the data type and starts processing the data from the appropriate step. The platform also accepts ready-to-annotate variant files (VCF, with .vcf extension) into the workflow. GenNextklinik detects the file type for each data uploaded to the platform by the user complies with industry standards, and then performs the necessary processing.

The reason for the warnings encountered while uploading data may be that the files you want to upload are incompatible (see GenNext:file upload document-LINK for details). After making sure that the files you want to upload are in the appropriate format, you can perform the upload. If you want to upload BAM files and VCF files, do not forget to check the box indicating the type of file in the relevant field on the upload screen. The platform is programmed to treat uploaded files as raw data if the box is not checked. If you still encounter problems, you can contact our support team.

On the GenNext platform, raw data and BAM files are stored for 3 months during the active membership period if GenNextCloud is used. Near the end of the three-month period, the user will be notified that access to their data via the GenNextklinik platform will end. There is no time limit for the storage of VCF files uploaded or generated with the GenNextklinik analysis workflow.

The GenNext platform has many analysis workflows for processing next-generation sequencing (NGS) raw data. Within the scope of DNA sequencing, it is possible to analyze germline clinical exome (CES), whole exome (WES), whole genome, and somatic targeted, whole exome, whole genome sequencing data. In addition, GenNext provides customized analysis flows for the processing of RNA sequencing data. GenNext, apart from any other platform currently available, also offers the option to analyze DNA and RNA sequencing data simultaneously.

GATK-best-practices workflow is followed in the analysis workflows used for data processing within the GenNextklinik platform. In this context, in the standard workflow where the raw data is uploaded to the platform for analysis, the process starts with the quality control of the data, and the variant file is obtained after the standard NGS data analysis steps (https://gatk.broadinstitute.org/hc/en-us/articles/360035894711-About-the-GATK-Best-Practices). Depending on the format of the uploaded file, GenNextklinik starts the analysis workflow at the appropriate step. In addition to the standard analysis workflow, GenNextklinik is flexible enough to add extra steps according to user demand. You can contact our team to discuss the details of customized analysis workflows, and you can find the details of the analysis tools and algorithms used within the platform in the relevant document (PIPELINEs, ANALYSIS DOCUMENT LINK).

The GenNextklinik platform uses a GPU-powered data processing infrastructure. Thanks to this infrastructure, human WGS data with 30X coverage is processed in 15 minutes and 90 minutes on our fastest and slowest nodes, respectively.

The variation in the data processing and analysis speed of the GenNextklinik platform is one of the problems that GenNextCloud service users may encounter. GenNextCloud servers are GPU servers located in Türkiye and have an upload/download speed of 10 Gb. Therefore, since even a slight change in your connection speed may also affect your upload speed, you may observe that file upload and analysis processes take longer. In non-GenNextCloud services, connection problems are unlikely to occur as the compute engines are located at the user premises.

In addition to processing sequencing data with the GenNextklinik platform, variant analysis can also be performed from VCF files. In addition to a variety of variant analysis tools and approaches that you can customize for your case, GenNextklinik also offers GenNext-Best-Practice filtering options for the convenience of its users. Detailed information about GenNextklinik’s options for variant analysis and GenNext-Best-Practice can be found in the related document (GenNext-Variant Analysis document- LINK).

GenNextklinik offers filtering options for solo analysis as well as duo and trio case analyses. After the user assigns the data with Sample IDs of the individuals to be analyzed to the “Filter” field before the analysis, GenNextklinik lists the variants that meet the criteria, again, defined by the user. The user can also use GenNext-Best-Practice filtering options for these analyses (GenNext-Variant Analysis document- LINK).

GenNextklinik offers an export option for the variant list after analysis. You can export the variant list as a TSV file by simply clicking the “Export” button that you can access from the GenNext-Variant tab where you performed the analysis.

GenNext offers various filtering options to the user before variant analysis. In this section, the user can upload a pre-prepared gene list by themselves to the system or use the gene list creation option provided by GenNextklinik. In this context, when the user adds the phenotypic features of the case in the format of Human Phenotype Ontology (HPO) terms, it becomes possible to create a list of the genes that are associated with the phenotype according to the HPO system. The gene list is expanded for each term added. In variant analysis with the gene list, please be aware that only the variants located in the genes provided in the list will be displayed.

GenNextklinik uses multiple variant callers (HaplotypeCaller, DeepVariant, FreeBayes, BCFTools) within the analysis workflow and generates separate VCF files from each. It is up to the user to decide which variant callers to include in the workflow before the analysis. Unless the user makes a choice, GenNe GenNextklinik uses DeepVariant as the default variant caller (for more information on variant callers, see GenNext-Variant Analysis: GenNext-Variant Analysis document- LINK).

The GenNextklinik platform has the capacity to analyze multiple data simultaneously. In this context, when the user is uploading files, GenNextklinik offers the option to upload files in a “batch“. This allows the user to transfer multiple files to the platform in a single upload step. After the platform detects that multiple data files are uploaded, the user is also given the opportunity to perform a “joint-call” for the uploaded data. If “joint-call” is not selected, each data is transferred to the relevant analysis workflow and processed separately to create the VCF files. With the “joint-call” option selected, the uploaded data is combined into a single VCF file at the end of the analysis workflow. Since multiple file uploads require large data transfers, they can only be performed with GenNext Compute Engines (GCEs) (see relevant document LINK).

Within the GenNextklinik platform, the user is offered ten report draft options. The user can choose any of the drafts they deem appropriate for reporting. At the same time, the user can automate variant reporting by adding their own designed report format to the system. For the creation of user-specific report formats, please contact our team.

To get the variant result report, click on the “Report” button after selecting the relevant variant. The information entered by the user on the GenNextklinik platform (Sample ID, Analyst, Physician, etc.) is used to fill in the relevant fields in the report. The generated variant reports are listed in the “Reports” field on the left menu and can be downloaded in PDF format.