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

doi:10.1016/j.xpro.2023.102509

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^*

^*Corresponding author for this work

Applied Sciences Department

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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.

Original language	English
Article number	102509
Journal	STAR Protocols
Volume	4
Issue number	3
Early online date	18 Aug 2023
DOIs	https://doi.org/10.1016/j.xpro.2023.102509
Publication status	Published - 15 Sept 2023

Keywords

Bioinformatics
Cancer
Molecular Biology
RNAseq
Sequence analysis
Sequencing

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1016/j.xpro.2023.102509Licence: CC BY

2914Final published version, 3.55 MBLicence: CC BY

Cite this

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

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.",

keywords = "Bioinformatics, Cancer, Molecular Biology, RNAseq, Sequence analysis, Sequencing",

author = "Hacking, {James P.R.} and Dean Thompson and Schwalbe, {Edward C.} and Clifford, {Steven C.} and Daniel Williamson",

note = "Funding information: This work was supported by Cancer Research UK (C8464/A13457 and C8464/A23391), the Tom Graham Trust/CCLG, LoveOliver, Star for Harris and the INSTINCT network, co-funded by The Brain Tumour Charity, Great Ormond Street Children{\textquoteright}s Charity, and Children with Cancer UK (grant no. 16/193).",

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AU - Schwalbe, Edward C.

AU - Clifford, Steven C.

AU - Williamson, Daniel

N1 - Funding information: This work was supported by Cancer Research UK (C8464/A13457 and C8464/A23391), the Tom Graham Trust/CCLG, LoveOliver, Star for Harris and the INSTINCT network, co-funded by The Brain Tumour Charity, Great Ormond Street Children’s Charity, and Children with Cancer UK (grant no. 16/193).

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N2 - 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.

AB - 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.

KW - Bioinformatics

KW - Cancer

KW - Molecular Biology

KW - RNAseq

KW - Sequence analysis

KW - Sequencing

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ER -

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

Abstract

Keywords

UN SDGs

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