Accuracy of Molecular Data Generated with FFPE Biospecimens: Lessons from the Literature
- PMID: 25836717
- PMCID: PMC4636024
- DOI: 10.1158/0008-5472.CAN-14-2378
Accuracy of Molecular Data Generated with FFPE Biospecimens: Lessons from the Literature
Abstract
Formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens are a valuable resource for molecular cancer research. Although much can be gained from their use, it remains unclear whether the genomic and expression profiles obtained from FFPE biospecimens accurately reflect the physiologic condition of the patient from which they were procured, or if such profiles are confounded by biologic effects from formalin fixation and processing. To assess the physiologic accuracy of genomic and expression data generated with FFPE specimens, we surveyed the literature for articles investigating genomic and expression endpoints in case-matched FFPE and fresh or frozen human biospecimens using the National Cancer Institute's Biospecimen Research Database (http://biospecimens.cancer.gov/brd). Results of the survey revealed that the level of concordance between differentially preserved biospecimens varied among analytical parameters and platforms but also among reports, genes/transcripts of interest, and tumor status. The identified analytical techniques and parameters that resulted in strong correlations between FFPE and frozen biospecimens may provide guidance when optimizing molecular protocols for FFPE use; however, discrepancies reported for similar assays also illustrate the importance of validating protocols optimized for use with FFPE specimens with a case-matched fresh or frozen cohort for each platform, gene or transcript, and FFPE processing regime. On the basis of evidence published to date, validation of analytical parameters with a properly handled frozen cohort is necessary to ensure a high degree of concordance and confidence in the results obtained with FFPE biospecimens.
©2015 American Association for Cancer Research.
Similar articles
-
Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue.PLoS One. 2011 Feb 11;6(2):e17163. doi: 10.1371/journal.pone.0017163. PLoS One. 2011. PMID: 21347257 Free PMC article.
-
A review of preanalytical factors affecting molecular, protein, and morphological analysis of formalin-fixed, paraffin-embedded (FFPE) tissue: how well do you know your FFPE specimen?Arch Pathol Lab Med. 2014 Nov;138(11):1520-30. doi: 10.5858/arpa.2013-0691-RA. Arch Pathol Lab Med. 2014. PMID: 25357115 Review.
-
Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in Archival Formalin-Fixed Paraffin-Embedded Tissues.Toxicol Sci. 2015 Dec;148(2):460-72. doi: 10.1093/toxsci/kfv195. Epub 2015 Sep 10. Toxicol Sci. 2015. PMID: 26361796 Free PMC article.
-
Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples.PLoS One. 2009 Dec 3;4(12):e8162. doi: 10.1371/journal.pone.0008162. PLoS One. 2009. PMID: 19997620 Free PMC article.
-
Systematic review and feasibility study on pre-analytical factors and genomic analyses on archival formalin-fixed paraffin-embedded breast cancer tissue.Sci Rep. 2024 Aug 6;14(1):18275. doi: 10.1038/s41598-024-69285-8. Sci Rep. 2024. PMID: 39107471 Free PMC article.
Cited by
-
Spatial characterization and stratification of colorectal adenomas by deep visual proteomics.iScience. 2024 Jul 31;27(9):110620. doi: 10.1016/j.isci.2024.110620. eCollection 2024 Sep 20. iScience. 2024. PMID: 39252972 Free PMC article.
-
Biobanking of Fresh-Frozen Human Adenocarcinomatous and Normal Colon Tissues: Which Parameters Influence RNA Quality?PLoS One. 2016 Apr 28;11(4):e0154326. doi: 10.1371/journal.pone.0154326. eCollection 2016. PLoS One. 2016. PMID: 27124490 Free PMC article.
-
The Gastric Cancer Registry: A Genomic Translational Resource for Multidisciplinary Research in Gastric Cancer.Cancer Epidemiol Biomarkers Prev. 2022 Sep 2;31(9):1693-1700. doi: 10.1158/1055-9965.EPI-22-0308. Cancer Epidemiol Biomarkers Prev. 2022. PMID: 35771165 Free PMC article.
-
Interplay between copy number alterations and immune profiles in the early breast cancer Scandinavian Breast Group 2004-1 randomized phase II trial: results from a feasibility study.NPJ Breast Cancer. 2021 Nov 19;7(1):144. doi: 10.1038/s41523-021-00352-3. NPJ Breast Cancer. 2021. PMID: 34799582 Free PMC article.
-
Proteome profiling of formalin-fixed, paraffin-embedded lung adenocarcinoma tissues using a tandem mass tag-based quantitative proteomics approach.Oncol Lett. 2021 Oct;22(4):706. doi: 10.3892/ol.2021.12967. Epub 2021 Aug 4. Oncol Lett. 2021. PMID: 34457061 Free PMC article.
References
-
- Green TM, de Stricker K, Moller MB. Validation of putative reference genes for normalization of Q-RT-PCR data from paraffin-embedded lymphoid tissue. Diagn Mol Pathol. 2009;18(4):243–9. - PubMed
-
- Bass BP, Engel KB, Greytak SR, Moore HM. A review of pre-analytical factors affecting molecular, protein, and morphological analysis of formalin-fixed, paraffin-embedded tissue. Arch Pathol Lab Med. 2014;138(11):1520–30. - PubMed
-
- Engel KB, Moore HM. Effects of preanalytical variables on the detection of proteins by immunohistochemistry in formalin-fixed, paraffin-embedded tissue. Arch Pathol Lab Med. 2011;135(5):537–43. - PubMed
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources