Welcome to our Frequently Asked Questions (FAQs) section. Here, we have compiled answers to the most commonly asked questions about the Research Use Only (RUO) Tumor Methylation Classifiers that we offer via the Epignostix website. 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
What services does app.epignostix.com offer?
A user-friendly platform of the Heidelberg Epignostix CNS Tumor Methylation Classifier and Sarcoma Methylation Classifier, which is 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.
What has changed with the Heidelberg methylation classifiers now being offered by Epignostix?
The CNS Tumor Classifier and Sarcoma Classifier 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. 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.
Registration
Who can get access to the classifier app?
The classifier app is currently designated as Research Use Only (RUO). Access is limited to researchers affiliated with recognized research institutions. The user must be an active employee or affiliate of a recognized university, research institute, or hospital conducting research activities.
How can I get access to the classifier app?
Please fill out the registration form.
What are the username requirements?
Usernames are typically the institutional email address you provided in the registration process.
What are the password requirements?
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).
What should I do if I forget my login details?
If you forget your username, please send an email to support@epignostix.com. Include the following information in your email: Your full name, your institution and any additional details that may help verify your account. If you forget your password, please use the forgot password button and you will receive an E-Mail to reset your password.
What are the Browser requirements?
The classifier app can run on the following browsers:
- Firefox (mobile & desktop)
- Chrome (mobile & desktop)
- Safari (mobile & desktop)
- Edge (mobile & desktop)
What does the classifier version number mean? How is it different from previous versions?
Older versions of the Classifiers included fewer methylation classes and tumor subtypes and were trained on a smaller tumor reference sample cohort. The Classifiers have undergone continuous refinement and validation, and its latest version is widely used in clinical practice and research settings around the world.
Upload sample
What are the prerequisites for my sample?
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.
What are the requirements for naming my sample?
Sample names must be completely anonymized and should not contain any patient-identifiable information.
What are the prerequisites for my sample?
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.
What should I choose if I don’t know the chip (methylation array) type of my samples?
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.
Do I need to specify the gender of my sample?
There is no need to specify the gender of your sample.
Do I need to upload the IDAT files in a specific order?
No specific order required, but please make sure that the two IDAT files (.idat) belong to the same sample (one Grn and one Red File).
How long does the analysis take to complete, and when will I receive the Classifier report?
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.
Can I delete my sample files after classifier analysis?
The samples can be deleted after the analysis by the user in the sample list.
What is a UUID?
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.
How does the anonymization process of the IDAT files work?
To anonymize the 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.
How are the tumor copy number variation (CNV) profiles generated for the Classifier report?
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.
I want my own tumor classifier to be hosted by Heidelberg Epignostix. Whom should I contact?
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.