ArticleBMC clinical pathology2015
Comparing gene expression data from formalin-fixed, paraffin embedded tissues and qPCR with that from snap-frozen tissue and microarrays for modeling outcomes of patients with ovarian carcinoma.
Article in BMC clinical pathology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
7 citing papers in PubMed, 1 synthesis or guideline pooled it, 11 citations in OpenAlex.
- Replication Study:eLife · 2018Pooled it
- Precision diagnostics in transplanted organs using microarray-assessed gene expression: concepts and technical methods of the Molecular Microscope® Diagnostic System (MMDx).Clinical science (London, England : 1979) · 2024Review
- Association between colorectal cancer and Fusobacterium nucleatum and Bacteroides fragilis bacteria in Iranian patients: a preliminary study.Infectious agents and cancer · 2021Article
- Article
- Targeted Transcriptional Profiling of Kidney Transplant Biopsies.Kidney international reports · 2018Article
- The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies.International journal of genomics · 2017Review
- A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay.International journal of molecular sciences · 2016Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundPreviously, we have used clinical and gene expression data from The Cancer Genome Atlas (TCGA) to model a pathway-based index predicting outcomes in ovarian carcinoma. This data were obtained from snap-frozen tissue measured with the Affymetrix U133 platform. In the current study, we correlate the data used to model with data derived from TaqMan qPCR both snap frozen and paraffin embedded (FFPE) samples.
methodsTo compare the effect of preservation methods on gene expression measured by qPCR, we assessed 18 patient and tumor sample matched snap-frozen and FFPE ovarian carcinoma samples. To compare gene measurement technologies, we correlated qPCR data from 10 patients with tumor sample matched snap-frozen ovarian carcinoma samples with the microarray data from TCGA. We normalized results to the average expression of three housekeeping genes. We scaled and centered the data for comparison to the Affymetrix output.
resultsFor the 18 specimens, gene expression data obtained from snap-frozen tissue correlated highly with that from FFPE samples in our TaqMan assay (r > 0.82). For the 10 duplicate TCGA specimens, the reported microarray data correlated well (r = 0.6) with our qPCR data, and ranges of expression along pathways were similar.
conclusionsGene expression data obtained by qPCR from FFPE serous ovarian carcinoma samples can be used to assess in the pathway-based predictive model. The normalization procedures described control variations in expression, and the range calculated along a specific pathway can be interpreted for a patient's risk profile.
Identifiers
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Registered trials
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