Integrated Analysis of Gene Expression, CpG Island Methylation, and Gene Copy Number in Breast Cancer Cells by Deep Sequencing
Published by PLoS ONE
In a recent PLoS ONE publication by Sun et al., the authors used deep sequencing technology to profile the transcriptome, gene copy number, and CpG island methylation status simultaneously in eight commonly used breast cell lines (7 cancerous and one non-tumorigenic) to develop a model for how these genomic features are integrated in estrogen receptor positive (ER+) and negative breast cancer. This project constituted “one of the most comprehensive genomic portraits of a collection of tumor cell lines reported to date”. The nCounter Analysis System was selected to validate RNA-seq data for 236 cancer-related genes and “very high correlations were observed between mRNA-seq and NanoString data for each of the 7 cancer cell lines (Pearson correlation coefficients ranging from 0.84 to 0.9).” For the 25 genes in that set scored as differentially expressed in the RNA-seq data, the Pearson coefficients between RNA-seq and nCounter data were 0.97 demonstrating the utility of using NanoString’s digital probe-based technology for NGS validation.