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Updated: Jul 19, 2025

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA
James P R Hacking1, Dean Thompson1, Edward C Schwalbe2
1Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University for Cancer, Newcastle University, Newcastle upon Tyne, UK.
Abstract:
Here, we present a protocol for deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray. We describe steps for utilizing NMF-defined group 3/group 4 metagenes to calculate a continuum score between 0 and 1 that can be projected onto new sample data analyzed via RNA-sequencing. We then detail procedures for reverse engineering a continuum score for samples analyzed via DNA methylation microarray using a random forest classifier.

