ArticleBritish journal of cancer2008
Acquisition of biologically relevant gene expression data by Affymetrix microarray analysis of archival formalin-fixed paraffin-embedded tumours.
Article in British journal of cancer, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 43 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
43 citing papers in PubMed, 76 citations in OpenAlex.
- Intrinsic molecular subtypes of glioma are prognostic and predict benefit from adjuvant procarbazine, lomustine, and vincristine chemotherapy in combination with other prognostic factors in anaplastic oligodendroglial brain tumors: a report from EORTC study 26951.Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2013Trial
- Role of the human cytochrome b561 family in iron metabolism and tumors (Review).Oncology letters · 2025Review
- Storage, Retention, and Use of Leftover Pathology Specimens: The Underestimated Treasures.Cureus · 2024Review
- LncRNA HOXD-AS1 affects proliferation and apoptosis of cervical cancer cells by promoting FRRS1 expression via transcription factor ELF1.Cell cycle (Georgetown, Tex.) · 2022Article
- Practical tips to using formalin-fixed paraffin-embedded tissue archives for molecular diagnostics in a South African setting.African journal of laboratory medicine · 2022Article
- Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches.BMC bioinformatics · 2020Article
- Screening of core genes and pathways in breast cancer development via comprehensive analysis of multi gene expression datasets.Oncology letters · 2019Article
- Genome-wide analysis of canine oral malignant melanoma metastasis-associated gene expression.Scientific reports · 2019Article
- Article
- Identification of molecular genetic contributants to canine cutaneous mast cell tumour metastasis by global gene expression analysis.PloS one · 2018Article
- The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies.International journal of genomics · 2017Review
- Reliable gene expression profiling of formalin-fixed paraffin-embedded breast cancer tissue (FFPE) using cDNA-mediated annealing, extension, selection, and ligation whole-genome (DASL WG) assay.BMC medical genomics · 2016Article
- Organocatalytic removal of formaldehyde adducts from RNA and DNA bases.Nature chemistry · 2015Article
- Mitochondrial DNA variants can mediate methylation status of inflammation, angiogenesis and signaling genes.Human molecular genetics · 2015Article
- Accuracy of Molecular Data Generated with FFPE Biospecimens: Lessons from the Literature.Cancer research · 2015Review
- The PFA-AMeX method achieves a good balance between the morphology of tissues and the quality of RNA content in DNA microarray analysis with laser-capture microdissection samples.Journal of toxicologic pathology · 2015Article
- Article
- Use of formalin-fixed paraffin-embedded samples for gene expression studies in breast cancer patients.PloS one · 2015Article
- Isolation of microarray-quality RNA from primary human cells after intracellular immunostaining and fluorescence-activated cell sorting.Journal of immunological methods · 2013Article
- An optimized workflow for improved gene expression profiling for formalin-fixed, paraffin-embedded tumor samples.Journal of clinical bioinformatics · 2013Article
Corrections and comments
- Erratum issued
Authors and funding
12 authors at 4 institutions in 1 country.
Funding
Abstract
Robust protocols for microarray gene expression profiling of archival formalin-fixed paraffin-embedded tissue (FFPET) are needed to facilitate research when availability of fresh-frozen tissue is limited. Recent reports attest to the feasibility of this approach, but the clinical value of these data is poorly understood. We employed state-of-the-art RNA extraction and Affymetrix microarray technology to examine 34 archival FFPET primary extremity soft tissue sarcomas. Nineteen arrays met stringent QC criteria and were used to model prognostic signatures for metastatic recurrence. Arrays from two paired frozen and FFPET samples were compared: although FFPET sensitivity was low ( approximately 50%), high specificity (95%) and positive predictive value (92%) suggest that transcript detection is reliable. Good agreement between arrays and real time (RT)-PCR was confirmed, especially for abundant transcripts, and RT-PCR validated the regulation pattern for 19 of 24 candidate genes (overall R(2)=0.4662). RT-PCR and immunohistochemistry on independent cases validated prognostic significance for several genes including RECQL4, FRRS1, CFH and MET - whose combined expression carried greater prognostic value than tumour grade - and cmet and TRKB proteins. These molecules warrant further evaluation in larger series. Reliable clinically relevant data can be obtained from archival FFPET, but protocol amendments are needed to improve the sensitivity and broad application of this approach.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.