Using singscore to predict mutation status in acute myeloid leukemia from transcriptomic signatures [version 3]
Journal Title
F1000Research
Publication Type
Journal Article
Abstract
Advances in RNA sequencing (RNA-seq) technologies that measure the transcriptome of biological samples have revolutionised our ability to understand transcriptional regulatory programs that underpin diseases such as cancer. We recently published singscore - a single sample, rank-based gene set scoring method which quantifies how concordant the transcriptional profile of individual samples are relative to specific gene sets of interest. Here we demonstrate the application of singscore to investigate transcriptional profiles associated with specific mutations or genetic lesions in acute myeloid leukemia. Using matched genomic and transcriptomic data available through the TCGA we show that scoring of appropriate signatures can distinguish samples with corresponding mutations, reflecting the ability of these mutations to drive aberrant transcriptional programs involved in leukemogenesis. We believe the singscore method is particularly useful for studying heterogeneity within a specific subsets of cancers, and as demonstrated, we show the ability of singscore to identify where alternative mutations appear to drive similar transcriptional programs.
Publisher
F1000
WEHI Research Division(s)
Bioinformatics
PubMed ID
31723419
Open Access at Publisher's Site
https://doi.org/10.12688/f1000research.19236.2
NHMRC Grants
NHMRC/1128609
Rights Notice
Refer to copyright notice on published article.


Creation Date: 2019-11-20 02:45:16
Last Modified: 2019-11-21 09:40:42
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