Report on emerging technologies for translational bioinformatics: A symposium on gene expression profiling for archival tissues

Waldron, Levi, Simpson, Peter, Parmigiani, Giovanni and Huttenhower, Curtis (2012) Report on emerging technologies for translational bioinformatics: A symposium on gene expression profiling for archival tissues. BMC Cancer, 12 124.1-124.4. doi:10.1186/1471-2407-12-124

Author Waldron, Levi
Simpson, Peter
Parmigiani, Giovanni
Huttenhower, Curtis
Title Report on emerging technologies for translational bioinformatics: A symposium on gene expression profiling for archival tissues
Journal name BMC Cancer   Check publisher's open access policy
ISSN 1471-2407
Publication date 2012-03
Sub-type Article (original research)
DOI 10.1186/1471-2407-12-124
Open Access Status DOI
Volume 12
Start page 124.1
End page 124.4
Total pages 4
Place of publication London, United Kingdom
Publisher BioMed Central
Collection year 2013
Language eng
Formatted abstract
Background: With over 20 million formalin-fixed, paraffin-embedded (FFPE) tissue samples archived each year in
the United States alone, archival tissues remain a vast and under-utilized resource in the genomic study of cancer.
Technologies have recently been introduced for whole-transcriptome amplification and microarray analysis of
degraded mRNA fragments from FFPE samples, and studies of these platforms have only recently begun to enter
the published literature.
Results: The Emerging Technologies for Translational Bioinformatics symposium on gene expression profiling for
archival tissues featured presentations of two large-scale FFPE expression profiling studies (each involving over
1,000 samples), overviews of several smaller studies, and representatives from three leading companies in the field
(Illumina, Affymetrix, and NuGEN). The meeting highlighted challenges in the analysis of expression data from
archival tissues and strategies being developed to overcome them. In particular, speakers reported higher rates of
clinical sample failure (from 10% to 70%) than are typical for fresh-frozen tissues, as well as more frequent probe
failure for individual samples. The symposium program is available at
Conclusions: Multiple solutions now exist for whole-genome expression profiling of FFPE tissues, including both
microarray- and sequencing-based platforms. Several studies have reported their successful application, but
substantial challenges and risks still exist. Symposium speakers presented novel methodology for analysis of FFPE
expression data and suggestions for improving data recovery and quality assessment in pre-analytical stages.
Research presentations emphasized the need for careful study design, including the use of pilot studies, replication,
and randomization of samples among batches, as well as careful attention to data quality control. Regardless of
any limitations in quantitave transcriptomics for FFPE tissues, they are often the only biospecimens available for
large patient populations with long-term history and clinical follow-up. Current challenges can be expected to
remain as RNA sequencing matures, and they will thus motivate ongoing research efforts into noise reduction and
identification of robust, translationally relevant biological signals in expression data from FFPE tissues.
Q-Index Code CX
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes A symposium held on August 5, 2011 at the Dana-Farber Cancer Institute ; Article number 124 ; 'Correspondence'

Document type: Journal Article
Sub-type: Article (original research)
Collections: UQ Centre for Clinical Research Publications
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Created: Tue, 05 Jun 2012, 03:32:26 EST by System User on behalf of UQ Centre for Clinical Research