ArticlePloS one2014
Transcriptome profiling of archived sectioned formalin-fixed paraffin-embedded (AS-FFPE) tissue for disease classification.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
29 citing papers in PubMed, 50 citations in OpenAlex.
- NanoCMSer: a consensus molecular subtype stratification tool for fresh-frozen and paraffin-embedded colorectal cancer samples.Molecular oncology · 2025Article
- The effect of storage time and temperature on the proteomic analysis of FFPE tissue sections.Clinical proteomics · 2025Article
- Role of Epigenetic Factors in Determining the Biological Behavior and Prognosis of Hepatocellular Carcinoma.Diagnostics (Basel, Switzerland) · 2024Article
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- Hepatocellular carcinoma chemoprevention by targeting the angiotensin-converting enzyme and EGFR transactivation.JCI insight · 2022Article
- Hormone and receptor activator of NF-κB (RANK) pathway gene expression in plasma and mammographic breast density in postmenopausal women.Breast cancer research : BCR · 2022Article
- A germinal center-associated microenvironmental signature reflects malignant phenotype and outcome of DLBCL.Blood advances · 2022Article
- A human liver cell-based system modeling a clinical prognostic liver signature for therapeutic discovery.Nature communications · 2021Article
- Transcription factors linked to the molecular signatures in the development of hepatocellular carcinoma on a cirrhotic background.Medical oncology (Northwood, London, England) · 2021Article
- GJA1 promotes hepatocellular carcinoma progression by mediating TGF-β-induced activation and the epithelial-mesenchymal transition of hepatic stellate cells.Open medicine (Warsaw, Poland) · 2021Article
- PRELP has prognostic value and regulates cell proliferation and migration in hepatocellular carcinoma.Journal of Cancer · 2020Article
- Data mining of the expression and regulatory role of BCAT1 in hepatocellular carcinoma.Oncology letters · 2019Article
- Molecular profiling of radical prostatectomy tissue from patients with no sign of progression identifiesOncotarget · 2019Article
- Microenvironmental immune cell signatures dictate clinical outcomes for PTCL-NOS.Blood advances · 2018Article
- Article
- A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.PloS one · 2017Article
- Clinicopathological indices to predict hepatocellular carcinoma molecular classification.Liver international : official journal of the International Association for the Study of the Liver · 2016Article
- Comparison of Nanostring nCounter® Data on FFPE Colon Cancer Samples and Affymetrix Microarray Data on Matched Frozen Tissues.PloS one · 2016Article
- Molecular prognostic prediction in liver cirrhosis.World journal of gastroenterology · 2015Review
Corrections and comments
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Authors and funding
11 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundArchived tissues from previously completed prospective trials represent invaluable resource for biomarker development. However, such specimens are often stored as sections on glass slides, in which RNA is severely degraded due to prolonged air exposure. We evaluated whether a proportion of archived sectioned formalin-fixed paraffin-embedded (AS-FFPE) tissues yield transcriptome profiles comparable to freshly cut (FC) FFPE tissues, which can be used for retrospective class prediction analysis.
methodsGenome-wide transcriptome profiles of 6 to 7-year-old AS-FFPE tissue sections (generated from 5 to 16-year-old blocks) of 83 hepatocellular carcinoma (HCC) and 47 liver cirrhosis samples were generated by using whole-genome DASL assay (Illumina) and digital transcript counting (nCounter) assay (NanoString), and gene signature-based prediction of HCC subclasses and prognosis was compared with previously generated FC-FFPE profiles from the same tissue blocks.
resultsRNA quality and assay reproducibility of AS-FFPE RNA were comparable to intermediate to poor quality FC-FFPE samples (RNA Integrity Number: up to 2.50, R-square for technical replicates: up to 0.93). Analyzable transcriptome profiles were obtained in 64 (77%) HCC and 36 (77%) cirrhosis samples. Statistically more confident predictions based on random resampling-based method (nearest template prediction) were obtained in 37 (58%) HCC and 13 (36%) cirrhosis samples. Predictions made in FC-FFPE profiles were reproduced in 36 (97%) HCC and 11 (85%) cirrhosis AS-FFPE profiles. nCounter assay was tested in 24 cirrhosis samples, which yielded confident prediction in 15 samples (63%), of which 10 samples (67%) showed concordant predictions with FC-FFPE profiles.
conclusionsAS-FFPE tissues yielded poorer quality RNA and transcriptome profiles compared to FC-FFPE tissues. Statistically more confident class prediction was feasible in 37 of 83 HCC samples and 13 of 47 cirrhosis samples. These results suggest that AS-FFPE tissues can be regarded as a resource for retrospective transcriptome-based class prediction analysis when they are the only available materials.
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