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...

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Bibliographic Details
Published in:PloS one 2012-07, Vol.7 (7), p.e40092-e40092
Main Authors: Sinicropi, Dominick, Qu, Kunbin, Collin, Francois, Crager, Michael, Liu, Mei-Lan, Pelham, Robert J, Pho, Mylan, Dei Rossi, Andrew, Jeong, Jennie, Scott, Aaron, Ambannavar, Ranjana, Zheng, Christina, Mena, Raul, Esteban, Jose, Stephans, James, Morlan, John, Baker, Joffre
Format: Article
Language:English
Subjects:
Archives & records
Base Sequence
Bioindicators
Bioinformatics
Biology
Biomarkers
Biomarkers, Tumor - genetics
Breast cancer
Breast Neoplasms - genetics
Cancer
Cancer recurrence
Cancer therapies
Chemotherapy
Deoxyribonucleic acid
Diagnostic systems
DNA
DNA microarrays
DNA, Intergenic - genetics
Exons
Female
Formaldehyde
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Genes
Genomes
Health aspects
Health risks
Humans
Introns - genetics
Medicine
Multiplexing
Neoplasm Recurrence, Local - genetics
Paraffin
Paraffin Embedding
Patients
Polymerase chain reaction
Proportional Hazards Models
Ribonucleic acid
Risk
Risk Factors
RNA
RNA sequencing
RNA, Messenger - genetics
RNA, Messenger - metabolism
RNA, Neoplasm
Screens
Sequence Analysis, RNA
Statistical methods
Tissue Fixation
Tumors
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Summary: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
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0040092