Webtool to classify gliomas

What is GliomaBiolinks

Recently, we developed the R/Bioconductor TCGAbiolinks tool, which allows users to search, download and prepare cancer genomics data for integrative data analysis. In addition, our tool uses machine learning, trained on published pan-glioma data, and classify glioma into seven prognostic epigenomic subtypes (G-CIMP-low, G-CIMP-high, Codels, Classic-like, Mesenchymal-like, LGm6-GBM, and PA-like). Despite the popularity of our tool among computational scientists the use of this package requires advanced knowledge of R thus excluding those with limited bioinformatic resources. To improve the accessibility of our classifier, we developed a webtool called ‘​GliomaBiolinks’. The webtool calculates:
Find Meaning in Biological Data Black_White

  1. the epigenomic subtype
  2. copy number alterations
  3. the risk of progression from G-CIMP-high to G-CIMP-low
  4. MGMT promoter status

Upon generating DNA methylation data from glioma tumor tissue the user simply uploads raw IDAT files and subsequently receives an emailed report containing the aforementioned data (see below for details).

We encourage researchers to test out the prediction model using their data. We developed a site to aid and facilitate the neuro-oncology research colleagues, however we stress that this portal is to be used for research and not for clinical diagnosis. We also encourage users to submit tumor tissue DNA methylation derived from EPIC or 450K data.

To get started​​​

  • Visit ​https://glioma.lab.foundation and acknowledge that this tool is to be used for research only.
  • New users will be asked to register:
    • Username
    • affiliation
    • email
    • password (passwords must be longer than 8 characters, have upper and lower case letters, and at least 1 digit.)
  • Existing users will login, enter username and password.

Once logged in, user will enter the home tab where user can manage their user account info and view data on samples previously uploaded and analyzed. Users can download their previous reports.
Upload Files

To use GliomaBiolinks tool will require 4 steps by the user:

Visit the UPLOAD tab

  1. Fill out the form about the metadata associated with the sample. The sample Identifier is required, the rest is optional but suggested.
  2. Click the Browse button to view current filesystem to upload the idat file. Both the red and green idat files are required.
  3. * Optional to check the box about the use of the uploaded data.
    * Required to check the box stating that the user understand that GliomaBiolinks is a research tool and should not be used as an official diagnosis.
  4. Click Submit.

A message will appear indicating the samples have been successfully uploaded and 1 hour or less, your results will be emailed to you. You can return to the home page to download the report.​

GliomaBiolinks REPORT

The report will be emailed to your email on file. You can revisit GliomaBiolinks and retrieve a copy of the report. The report will include the following information:

  • Sample Summary which includes the meta data you entered when uploading the samples
  • Analysis Summary is the results of your data
    • Table includes the categorical and numeric score
      • Diagnostic Subtype
      • Predictive
    • 3D Principal Component Analysis (PCA). Your sample is highlighted in solid Black. This is compared to TCGA PanGlioma data
    • Copy Number Variance estimated by DNA methylation
  • Citations are included for reference.