The authors used the MasterPure™ RNA Purification Kit to isolate total RNA from 136 FFPE primary breast cancer tumor specimens. The isolated RNA was used as input for the ScriptSeq™ mRNA-Seq Library Preparation Kit (now replaced by the ScriptSeq v2 Kit) for preparing whole-transcriptome libraries. Sequencing was performed on an Illumina HiSeq 2000 instrument. Analysis showed that the RNA-Seq data generated using 5- to 12-year-old FFPE tumor tissue compared very favorably with RT-PCR results published earlier, and enabled quantification of transcripts with accuracy and sensitivity sufficient for biomarker discovery. The study identified >1,300 transcripts associated with breast cancer risk; more than half of the RNAs identified as prognostic were noncoding. Thus, the study demonstrated the value of a whole-transcriptome approach, and the results obtained should prove valuable in future screens of biomarkers associated with breast cancer recurrence risk.
Sinicropi D et al. (2012). Whole Transcriptome RNA-Seq Analysis of Breast Cancer Recurrence Risk Using Formalin-Fixed Paraffin-Embedded Tumor Tissue. PloS one, 7 (7) PMID: 22808097