Using microarray-based subtyping methods for breast cancer in the era of high-throughput RNA sequencing.

ABSTRACT: Breast cancer is a highly heterogeneous disease that can be classified into multiple subtypes based on the tumor transcriptome. Most of the subtyping schemes used in clinics today are derived from analyses of microarray data from thousands of different tumors together with clinical data for the patients from which the tumors were isolated. However, RNA sequencing (RNA-Seq) is gradually replacing microarrays as the preferred transcriptomics platform, and although transcript abundances measured by the two different technologies are largely compatible, subtyping methods developed for probe-based microarray data are incompatible with RNA-Seq as input data. Here, we present an RNA-Seq data processing pipeline, which relies on the mapping of sequencing reads to the probe set target sequences ins

SUBMITTER: Pedersen CB 

PROVIDER: S-EPMC6275246 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature