Previously available under the MolecularNeuropathology.org website, our sarcoma methylation classifier is now available on our portal. It currently supports both Illumina Human Methylation EPIC v1 and EPIC v2 BeadChip arrays, as well as the older 450k platform.

METHOD 

Our sarcoma classifier is trained on a well-annotated reference set of 1,077 samples covering 62 classes of sarcomas. Similar to our CNS tumor classifier, we employ a random forest algorithm, providing a confidence level for each class determination. This ensemble method merges several independent component classifiers to enhance overall prediction accuracy. 

Our classifier algorithm rapidly compares each new case with thousands from our reference cohort, outputting a classification score reflecting resemblance to a particular tumor class. Each class yields a confidence score between 0 and 1. For a positive identification of a tumor type, the methylation class score must surpass a 0.9 threshold. For more information, read our approach published in Nature Communications in 2021 here.

DATA 

The classifier operates on DNA methylation data. The cancer methylome combines somatically acquired DNA methylation alterations and attributes indicative of the cell of origin. Proven to be highly robust and reproducible, DNA methylation profiling can even be successful with small or low-quality samples. This technique has been employed to meaningfully classify sarcomas which may have homogenous histology. 

USE 

To leverage our methylation profiling classifier, simply upload unprocessed IDAT-files of your samples from either Illumina Human Methylation 450K BeadChip or EPIC v1/v2 BeadChip arrays. Your data will automatically be classified with our classifier resulting in a predicted class. You will also receive a copy number profile and the MGMT promoter methylation status prediction. A detailed report of your methylation profiling will be available in the portal. You can also download it as a PDF file. 

GET STARTED

The classifier is available at https://app.epignostix.com as the ‘Sarcoma Methylation Classifier’. You will need to register as a new user here. Once your registration is approved, you can login to the portal using your email credentials. For step-by-step instructions on how to use our portal, please check our instructions video. If you have any questions, please check our FAQs or reach out to us through our Contact Form.