Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray

James P.R. Hacking; Dean Thompson; Edward C. Schwalbe; Steven C. Clifford; Daniel Williamson

STAR Protocols (Sep 2023)

Deriving a continuum score for group 3 and 4 medulloblastoma tumor samples analyzed via RNA-sequencing or DNA methylation microarray

James P.R. Hacking,
Dean Thompson,
Edward C. Schwalbe,
Steven C. Clifford,
Daniel Williamson

Affiliations

James P.R. Hacking: Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University for Cancer, Newcastle University, Newcastle upon Tyne, UK
Dean Thompson: Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University for Cancer, Newcastle University, Newcastle upon Tyne, UK
Edward C. Schwalbe: Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University for Cancer, Newcastle University, Newcastle upon Tyne, UK; Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
Steven C. Clifford: Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University for Cancer, Newcastle University, Newcastle upon Tyne, UK
Daniel Williamson: Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University for Cancer, Newcastle University, Newcastle upon Tyne, UK; Corresponding author

Journal volume & issue: Vol. 4, no. 3
p. 102509

Abstract

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Summary: 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. : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.

Published in STAR Protocols

ISSN: 2666-1667 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science: Science (General)
Website: https://star-protocols.cell.com/

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Abstract

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