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Accurate data processing improves the reliability of Affymetrix gene expression profiles from FFPE samples.
- Source :
-
PloS one [PLoS One] 2014 Jan 29; Vol. 9 (1), pp. e86511. Date of Electronic Publication: 2014 Jan 29 (Print Publication: 2014). - Publication Year :
- 2014
-
Abstract
- Formalin fixed paraffin-embedded (FFPE) tumor specimens are the conventionally archived material in clinical practice, representing an invaluable tissue source for biomarkers development, validation and routine implementation. For many prospective clinical trials, this material has been collected allowing for a prospective-retrospective study design which represents a successful strategy to define clinical utility for candidate markers. Gene expression data can be obtained even from FFPE specimens with the broadly used Affymetrix HG-U133 Plus 2.0 microarray platform. Nevertheless, important major discrepancies remain in expression data obtained from FFPE compared to fresh-frozen samples, prompting the need for appropriate data processing which could help to obtain more consistent results in downstream analyses. In a publicly available dataset of matched frozen and FFPE expression data, the performances of different normalization methods and specifically designed Chip Description Files (CDFs) were compared. The use of an alternative CDFs together with fRMA normalization significantly improved frozen-FFPE sample correlations, frozen-FFPE probeset correlations and agreement of differential analysis between different tumor subtypes. The relevance of our optimized data processing was assessed and validated using two independent datasets. In this study we demonstrated that an appropriate data processing can significantly improve the reliability of gene expression data derived from FFPE tissues using the standard Affymetrix platform. Tools for the implementation of our data processing algorithm are made publicly available at http://www.biocut.unito.it/cdf-ffpe/.
- Subjects :
- Algorithms
Breast Neoplasms pathology
Databases, Factual
Female
Formaldehyde
Gene Expression Profiling instrumentation
Gene Expression Profiling methods
Humans
Lymphoma, B-Cell pathology
Paraffin Embedding
Tissue Fixation
Breast Neoplasms genetics
Gene Expression
Gene Expression Profiling statistics & numerical data
Lymphoma, B-Cell genetics
Tissue Array Analysis statistics & numerical data
Subjects
Details
- Language :
- English
- ISSN :
- 1932-6203
- Volume :
- 9
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- PloS one
- Publication Type :
- Academic Journal
- Accession number :
- 24489733
- Full Text :
- https://doi.org/10.1371/journal.pone.0086511