SynthesisClinical cancer research : an official journal of the American Association for Cancer Research2012
Expression profiling of archival tumors for long-term health studies.
Synthesis in Clinical cancer research : an official journal of the American Association for Cancer Research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it, 31 citations in OpenAlex.
- Continuity of transcriptomes among colorectal cancer subtypes based on meta-analysis.Genome biology · 2018Pooled it
- Integrated Analysis of Bulk and Single-Cell Transcriptomics Identifies Prognostic Biomarkers in Breast Cancer Metastasis.Biochemical genetics · 2026Article
- Tumour-associated high endothelial venules drive portal-specific immune evasion in lymph nodes via ALOX12.Nature communications · 2026Article
- Pathology Laboratory Archives: Conservation Quality of Nucleic Acids and Proteins for NSCLC Molecular Testing.Journal of personalized medicine · 2024Article
- PRECISION.seq: An R Package for Benchmarking Depth Normalization in microRNA Sequencing.Frontiers in genetics · 2021Article
- A qualitative transcriptional signature for predicting the biochemical recurrence risk of prostate cancer patients after radical prostatectomy.The Prostate · 2020Article
- MMP9 modulates the metastatic cascade and immune landscape for breast cancer anti-metastatic therapy.Life science alliance · 2019Article
- Article
- Leveraging Spatial Variation in Tumor Purity for Improved Somatic Variant Calling of Archival Tumor Only Samples.Frontiers in oncology · 2019Article
- Robust transcriptional tumor signatures applicable to both formalin-fixed paraffin-embedded and fresh-frozen samples.Oncotarget · 2017Article
- 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
- Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues.The Journal of molecular diagnostics : JMD · 2015Article
- Prognostic stromal gene signatures in breast cancer.Breast cancer research : BCR · 2015Article
- Use of formalin-fixed paraffin-embedded samples for gene expression studies in breast cancer patients.PloS one · 2015Article
- Progress and opportunities in molecular pathological epidemiology of colorectal premalignant lesions.The American journal of gastroenterology · 2014Review
- Review
- Differential Gene Expression Landscape of Co-Existing Cervical Pre-Cancer Lesions Using RNA-seq.Frontiers in oncology · 2014Article
- Transcriptome profiling of archived sectioned formalin-fixed paraffin-embedded (AS-FFPE) tissue for disease classification.PloS one · 2014Article
- Molecular pathological epidemiology of epigenetics: emerging integrative science to analyze environment, host, and disease.Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2013Review
- Feasibility of RNA and DNA extraction from fresh pipelle and archival endometrial tissues for use in gene expression and SNP arrays.Obstetrics and gynecology international · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
19 authors at 7 institutions in 2 countries.
Funding
Abstract
purposeMore than 20 million archival tissue samples are stored annually in the United States as formalin-fixed, paraffin-embedded (FFPE) blocks, but RNA degradation during fixation and storage has prevented their use for transcriptional profiling. New and highly sensitive assays for whole-transcriptome microarray analysis of FFPE tissues are now available, but resulting data include noise and variability for which previous expression array methods are inadequate. EXPERIMENTAL
designWe present the two largest whole-genome expression studies from FFPE tissues to date, comprising 1,003 colorectal cancer (CRC) and 168 breast cancer samples, combined with a meta-analysis of 14 new and published FFPE microarray datasets. We develop and validate quality control (QC) methods through technical replication, independent samples, comparison to results from fresh-frozen tissue, and recovery of expected associations between gene expression and protein abundance.
resultsArchival tissues from large, multicenter studies showed a much wider range of transcriptional data quality relative to smaller or frozen tissue studies and required stringent QC for subsequent analysis. We developed novel methods for such QC of archival tissue expression profiles based on sample dynamic range and per-study median profile. This enabled validated identification of gene signatures of microsatellite instability and additional features of CRC, and improved recovery of associations between gene expression and protein abundance of MLH1, FASN, CDX2, MGMT, and SIRT1 in CRC tumors.
conclusionsThese methods for large-scale QC of FFPE expression profiles enable study of the cancer transcriptome in relation to extensive clinicopathological information, tumor molecular biomarkers, and long-term lifestyle and outcome data.
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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.