Data from: Whole transcriptome RNA-Seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue

RNA biomarkers discovered by RT-PCR-based gene expression profiling of
archival formalin-fixed paraffin-embedded (FFPE) tissue form the basis for
widely used clinical diagnostic tests; however, RT-PCR is practically
constrained in the number of transcripts that can be interrogated. We have
developed and optimized RNA-Seq library chemistry as well as
bioinformatics and biostatistical methods for whole transcriptome
profiling from FFPE tissue. The chemistry accommodates low RNA inputs and
sample multiplexing. These methods both enable rediscovery of RNA
biomarkers for disease recurrence risk that were previously identified by
RT-PCR analysis of a cohort of 136 patients, and also identify a high
percentage of recurrence risk markers that were previously discovered
using DNA microarrays in a separate cohort of patients, evidence that this
RNA-Seq technology has sufficient precision and sensitivity for biomarker
discovery. More than two thousand RNAs are strongly associated with breast
cancer recurrence risk in the 136 patient cohort (FDR < 10%). Many
of these are intronic RNAs for which corresponding exons are not also
associated with disease recurrence. A number of the RNAs associated with
recurrence risk belong to novel RNA networks. It will be important to test
the validity of these novel associations in whole transcriptome RNA-Seq
screens of other breast cancer cohorts.