Frequently asked questions
Answers to the questions we are asked most often.
FAQs
Welcome to our Frequently Asked Questions (FAQs) section. Here, we have compiled answers to the most commonly asked questions about our methylation classifiers offered via the Epignostix platform. In addition, we provide a video tutorial where we guide you through the process of registering on our website, uploading your sample and downloading your report. If you cannot find the answer to your questions here, please contact our support team: support@epignostix.com
Please reach out to our licensing team at licensing@epignostix.com for on-premise versions of our classifiers
We will offer global access to cloud-based API services (AIaaS) for state-of-the-art diagnostics tools. If you are interested, please write an E-mail to info@epignostix.com.
In addition to epigenetic information (DNA methylation profiles), it is possible to extract genetic information (CNV profiles) from DNA methylation microarrays, without the need to run a separate genomic assay. Extracting copy number information from DNA methylation arrays is based on the assumption that the sum of the intensity values of the unmethylated and methylated signals are representative of the copy-number state of a given genomic location. We use the conumee 2.0 package for copy-number variation analysis and visualization.
To anonymize IDAT files further, we take these steps when you upload your files:
a) We will replace the Sentrix ID with a unique, random code. This ensures your data can’t be linked back.
b) We will replace some parts of the IDAT file with zeros. This further anonymizes your data while still allowing for accurate analysis.
Only these anonymized files are stored and used for further analysis. Your original data is never saved.
A UUID (Universal Unique Identifier) is a 128-bit value used to uniquely identify an object or entity on the internet. UUIDs can be generated to refer to almost anything, in the context of the Classifier analyses we use them to refer to the IDAT files. The original identifiers will not be used or stored by us.
It will take up to one hour to complete your analysis and generate your report. You will find the final report for each of your uploaded samples in the sample list.
The samples can be deleted after the analysis by the user in the sample list.
No specific order is required, but please make sure that the two IDAT files (.idat) belong to the same sample (one Grn and one Red File).
While recommended to do so, it is not required to specify the sex of the sample.
You don’t need to select a chip type. The classifier automatically detects it for you. Illumina Human Methylation 450k, Epic, Epicv2 chip types are supported.
Sample names must be completely anonymized and should not contain any patient-identifiable information.
You need to upload the unprocessed IDAT files of Illumina Human Methylation 450 BeadChip arrays or EPIC v1/v2 BeadChip arrays of your samples of interest. The quality and suitability of the tissue sample are essential for an accurate DNA methylation analysis. Therefore, they should have a tumor cell content exceeding 50%. Proper collection, handling and preservation of tissue specimens are critical to ensure reliable results.
The classifier app can run on the following browsers:
- Firefox (mobile & desktop)
- Chrome (mobile & desktop)
- Safari (mobile & desktop)
- Edge (mobile & desktop)
Please click on ‘Forgot my Password’ on the Sign in page to reset your password.
Length: Minimum of 8 characters if you use 4 complexities or 20 if you use two complexities following the BSI (Federal Cyber Security Authority of Germany) recommendations.
Complexity:
- At least one special character (!@#$%^&*(),.?””:;{}|<>_).
- At least one numeric digit (e.g., 0-9).
- At least one lowercase letter (a-z).
- At least one uppercase letter (A-Z).
Usernames are the institutional email address you provided in the registration process. Please use the exact email address that you used during registration. For example, while jane.doe@xyz.de and jane.doe@xyz-city.de might be the same mailbox, they are recognised as separate emails by our platform.
Please fill out the registration form. We will send you a link to verify your email address. After verification, your registration will be forwarded for approval to our team. It may take up to 5 days to get approval for your account. Please reach out to us at support@epignostix.com if you have not heard from us after 5 days of registration.
The classifier app is currently designated as Research Use Only (RUO). Access is limited to researchers affiliated with recognized research institutions and respective institutional emails. The user must be an active employee or affiliate of a recognized university, research institute, or hospital conducting research activities.
The CNS Tumor and Sarcoma Methylation Classifiers are now provided through our company Epignostix, but their underlying technology and functionality remain the same as those previously offered via the academic MNP website (molecular neuropathology.org). They continue to be free of charge and intended for research use only. As a company, we can now ensure more stable access to the classifiers and offer improved user support to enhance your experience.
The app.epignostix.com platform offers a user-friendly implementation of the Heidelberg Epignostix CNS Tumor Methylation Classifier and Sarcoma Methylation Classifier, which are freely accessible for academic research and scientific use. We invite research groups to contribute and validate our solutions, striving for continuous improvement in routine patient care and cancer research. We offer global access to cloud-based API services (AIaaS) for state-of-the-art diagnostics tools (Contact: info@epignostix.com)
More information is provided on our website.
