Monday, July 23, 2012

Whole-transcriptome RNA-Seq analysis from archival FFPE tumor samples

Many FFPE tissue blocks containing samples related to  known disease states are archived in a multitude of hospitals worldwide. The RNA available from these blocks is not only limited in quantity but also generally severely degraded. In this report, Sinicropi et. al., discuss methods for RNA-Seq  using RNA isolated from archival FFPE samples with low input levels of RNA, and compare the results to data previously generated by RT-PCR analysis.

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.

ResearchBlogging.orgSinicropi 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

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