通过 RNA 测序或 DNA 甲基化微阵列分析，为第 3 组和第 4 组髓母细胞瘤肿瘤样本生成连续评分。

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

机构信息

Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University for Cancer, Newcastle University, Newcastle upon Tyne, UK.

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.

出版信息

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

DOI:10.1016/j.xpro.2023.102509

PMID:37573504

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10448413/

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.

摘要

在这里，我们提出了一种通过 RNA-seq 或 DNA 甲基化微阵列分析的 3 类和 4 类髓母细胞瘤肿瘤样本进行连续评分的方案。我们描述了利用 NMF 定义的 3 类/4 类混合基因计算 0 到 1 之间连续评分的步骤，该评分可以投射到通过 RNA-seq 分析的新样本数据上。然后，我们详细介绍了使用随机森林分类器为通过 DNA 甲基化微阵列分析的样本反向工程连续评分的过程。