Whole transcriptome RNA-seq analysis of breast cancer recurrence risk using formalin-fixed paraffin-embedded tumor tissue

Dominick Sinicropi, Kunbin Qu, Francois Collin, Michael Crager, Mei Lan Liu, Robert J. Pelham, Mylan Pho, Andrewi de Rossi, Jennie Jeong, Aaron Scott, Ranjana Ambannavar, Christina Zheng, Raul Mena, Jose Esteban, James Stephans, John Morlan, Joffre Baker

Research output: Contribution to journalArticlepeer-review

59 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article numbere40092
JournalPloS one
Volume7
Issue number7
DOIs
StatePublished - Jul 13 2012
Externally publishedYes

ASJC Scopus subject areas

  • General

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