Use of Formalin-Fixed Paraffin-Embedded Samples for Gene Expression Studies in Breast Cancer Patients
Open Access
- 6 April 2015
- journal article
- Published by Public Library of Science (PLoS) in PLOS ONE
- Vol. 10 (4), e0123194
- https://doi.org/10.1371/journal.pone.0123194
Abstract
To obtain gene expression profiles from samples collected in clinical trials, we conducted a pilot study to assess feasibility and estimate sample attrition rates when profiling formalin-fixed, paraffin-embedded specimens. Ten matched fresh-frozen and fixed breast cancer samples were profiled using the Illumina HT-12 and Ref-8 chips, respectively. The profiles obtained with Ref 8, were neither technically nor biologically reliable since they failed to yield the expected separation between estrogen receptor positive and negative samples. With the use of Affymetrix HG-U133 2.0 Plus chips on fixed samples and a quantitative polymerase chain reaction -based sample pre-assessment step, results were satisfactory in terms of biological reliability, despite the low number of present calls (M = 21%±5). Compared with the Illumina DASL WG platform, Affymetrix data showed a wider interquartile range (1.32 vs 0.57, P<2.2 E-16,) and larger fold changes. The Affymetrix chips were used to run a pilot study on 60 fixed breast cancers. By including in the workflow the sample pre-assessment steps, 96% of the samples predicted to give good results (44/46), were in fact rated as satisfactory from the point of view of technical and biological meaningfulness. Our gene expression profiles showed strong agreement with immunohistochemistry data, were able to reproduce breast cancer molecular subtypes, and allowed the validation of an estrogen receptor status classifier derived in frozen samples. The approach is therefore suitable to profile formalin-fixed paraffin-embedded samples collected in clinical trials, provided that quality controls are run both before (sample pre-assessment) and after hybridization on the array.This publication has 48 references indexed in Scilit:
- An optimized workflow for improved gene expression profiling for formalin-fixed, paraffin-embedded tumor samplesJournal of Clinical Bioinformatics, 2013
- The Colorectal cancer disease-specific transcriptome may facilitate the discovery of more biologically and clinically relevant informationBMC Cancer, 2010
- Identification of methods for use of formalin-fixed, paraffin-embedded tissue samples in RNA expression profilingGenomics, 2009
- Impact of biospecimens handling on biomarker research in breast cancerBMC Cancer, 2009
- Gene Expression Profiling of Paraffin-Embedded Primary Melanoma Using the DASL Assay Identifies Increased Osteopontin Expression as Predictive of Reduced Relapse-Free SurvivalClinical Cancer Research, 2009
- Use of Archived Specimens in Evaluation of Prognostic and Predictive BiomarkersJNCI Journal of the National Cancer Institute, 2009
- Gene Expression in Fixed Tissues and Outcome in Hepatocellular CarcinomaThe New England Journal of Medicine, 2008
- Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumoursBritish Journal of Cancer, 2008
- Quantitative Expression Profiling of RNA from Formalin-Fixed, Paraffin-Embedded Tissues Using Randomly Assembled Bead ArraysMethods in molecular biology (Clifton, N.J.), 2008
- RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologiesBMC Molecular Biology, 2007