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. 2023 Sep 15;4(3):102509.
doi: 10.1016/j.xpro.2023.102509. Epub 2023 Aug 11.

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

James P R Hacking  1 , Dean Thompson  1 , Edward C Schwalbe  2 , Steven C Clifford  1 , Daniel Williamson  3
Affiliations

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

James P R Hacking et al. STAR Protoc. .

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.

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Conflict of interest statement

Declaration of interests The authors declare no competing interests.

Figures

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Graphical abstract
Figure 1
Figure 1
Step-by-step breakdown of project.NMF() function
Figure 2
Figure 2
An example of the plots generated and exported to PDF (A) Cumulative frequency plot showing where your samples lie upon the continuum. (B) Survival curve with no risk factors accounted for. (C) Survival curve taking into account patient’s age. (D) Table of raw group 3–4 scores.
None
See this image and copyright information in PMC

References

    1. Williamson D., Schwalbe E.C., Hicks D., Aldinger K.A., Lindsey J.C., Crosier S., Richardson S., Goddard J., Hill R.M., Castle J., et al. Medulloblastoma group 3 and 4 tumors comprise a clinically and biologically significant expression continuum reflecting human cerebellar development. Cell Rep. 2022;40 - PMC - PubMed
    1. Tamayo P., Scanfeld D., Ebert B.L., Gillette M.A., Roberts C.W.M., Mesirov J.P. Metagene projection for cross-platform, cross-species characterization of global transcriptional states. Proc. Natl. Acad. Sci. USA. 2007;104:5959–5964. - PMC - PubMed
    1. Schwalbe E.C., Lindsey J.C., Nakjang S., Crosier S., Smith A.J., Hicks D., Rafiee G., Hill R.M., Iliasova A., Stone T., et al. Novel molecular subgroups for clinical classification and outcome prediction in childhood medulloblastoma: a cohort study. Lancet Oncol. 2017;18:958–971. - PMC - PubMed
    1. Venables W.N., Ripley B.D. Springer; 2002. Modern Applied Statistics with S. ISBN 0-387-95457-0.
    1. Gaujoux R., Seoighe C. A flexible R package for nonnegative matrix factorization. BMC Bioinf. 2010;11:367. - PMC - PubMed

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