ArticleNucleic acids research2007
Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT).
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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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.
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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
17 citing papers in PubMed, 1 synthesis or guideline pooled it, 37 citations in OpenAlex.
- Systematic review and feasibility study on pre-analytical factors and genomic analyses on archival formalin-fixed paraffin-embedded breast cancer tissue.Scientific reports · 2024Pooled it
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- MiRNA expression deregulation correlates with the Oncotype DXBreast cancer research : BCR · 2022Article
- An AIB1 Isoform Alters Enhancer Access and Enables Progression of Early-Stage Triple-Negative Breast Cancer.Cancer research · 2021Article
- The ZNF217 Biomarker Predicts Low- and High-Risk Oncotype DXFrontiers in pharmacology · 2019Article
- Understanding preanalytical variables and their effects on clinical biomarkers of oncology and immunotherapy.Seminars in cancer biology · 2018Review
- Article
- MicroRNA expression in benign breast tissue and risk of subsequent invasive breast cancer.PloS one · 2018Article
- Apolipoprotein E Promotes Invasion in Oral Squamous Cell Carcinoma.The American journal of pathology · 2017Article
- Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens.International journal of molecular sciences · 2017Article
- Coextraction and PCR Based Analysis of Nucleic Acids From Formalin-Fixed Paraffin-Embedded Specimens.Journal of clinical laboratory analysis · 2015Article
- Accuracy of Molecular Data Generated with FFPE Biospecimens: Lessons from the Literature.Cancer research · 2015Review
- The clinico-pathologic role of microRNAs miR-9 and miR-151-5p in breast cancer metastasis.Molecular diagnosis & therapy · 2012Article
- Effective DNA/RNA co-extraction for analysis of microRNAs, mRNAs, and genomic DNA from formalin-fixed paraffin-embedded specimens.PloS one · 2012Article
- Robust gene expression signature from formalin-fixed paraffin-embedded samples predicts prognosis of non-small-cell lung cancer patients.Clinical cancer research : an official journal of the American Association for Cancer Research · 2011Article
- Quantitative expression profiling in formalin-fixed paraffin-embedded samples by affymetrix microarrays.The Journal of molecular diagnostics : JMD · 2010Article
- A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens.Journal of molecular medicine (Berlin, Germany) · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene expression profiling of formalin-fixed and paraffin-embedded (FFPE) specimens, banked from completed clinical trials and routine clinical care, has the potential to yield valuable information implicating and linking genes with clinical parameters. In order to prepare high-quality cDNA from highly fragmented FFPE-RNA, previously precluded from high-throughput analyses, we have designed a novel strategy based on the nucleic acid restoration of incomplete cDNA sequences prior to T7 in vitro transcription (IVT) amplification. We describe this strategy as complementary-template reverse-transcription (CT-RT) because short single-stranded T7-oligo-dT24-VN-DNA sequences, obtained from FFPE-RNA, are used as primers for the RT of complementary RNA templates contained in a sense-RNA library. We validated our assay by determining the correlation between expression profiles of a matched 10-year-old frozen and FFPE breast cancer sample. We show that T7 IVT-amplification of cDNA transcripts restored by CT-RT is a specific and reliable process that allows recovery of transcriptional features undetectable by direct T7 IVT-amplification of FFPE-RNA. Furthermore, CT-RT restored 35-41% of the transcripts from archived breast and cervical specimens when compared to matched frozen tissue; and profiles included tissue-specific transcripts. Our results indicate that CT-RT allows microarray profiling of severely degraded RNA that could not be analyzed by previous methods.
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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.