ArticleJournal of molecular medicine (Berlin, Germany)2009
A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens.
Article in Journal of molecular medicine (Berlin, Germany), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Expression profiling of archival tumors for long-term health studies.Clinical cancer research : an official journal of the American Association for Cancer Research · 2012Pooled it
- MicroRNA-193b acts as a tumor suppressor in colon cancer progression via targeting RAB22A.Experimental and therapeutic medicine · 2019Article
- Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays.PloS one · 2018Article
- TargetClone: A multi-sample approach for reconstructing subclonal evolution of tumors.PloS one · 2018Article
- Usefulness of miRNA profiles for predicting pathological responses to neoadjuvant chemotherapy in patients with human epidermal growth factor receptor 2-positive breast cancer.Oncology letters · 2017Article
- The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies.International journal of genomics · 2017Review
- Article
- An optimized workflow for improved gene expression profiling for formalin-fixed, paraffin-embedded tumor samples.Journal of clinical bioinformatics · 2013Article
- Gene expression profiling of breast cancer survivability by pooled cDNA microarray analysis using logistic regression, artificial neural networks and decision trees.BMC bioinformatics · 2013Article
- Three-dimensional mRNA measurements reveal minimal regional heterogeneity in esophageal squamous cell carcinoma.The American journal of pathology · 2013Article
- miRNA expressions in rectal cancer as predictors of response to neoadjuvant chemoradiation therapy.International journal of colorectal disease · 2013Article
- Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity.BMC genomics · 2013Article
- Whole genome and transcriptome amplification: practicable tools for sustainable tissue biobanking?Virchows Archiv : an international journal of pathology · 2012Article
- Loss-of-heterozygosity on chromosome 19q in early-stage serous ovarian cancer is associated with recurrent disease.BMC cancer · 2012Article
- Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens.BMC cancer · 2011Article
- Validation and reproducibility of a microarray-based gene expression test for tumor identification in formalin-fixed, paraffin-embedded specimens.The Journal of molecular diagnostics : JMD · 2011Article
- Genomic markers for decision making: what is preventing us from using markers?Nature reviews. Clinical oncology · 2010Review
- Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples.PloS one · 2009Article
- Microarray analysis of RNA extracted from formalin-fixed, paraffin-embedded and matched fresh-frozen ovarian adenocarcinomas.BMC medical genomics · 2009Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a novel approach for microarray analysis of RNA derived from microdissected cells of routinely formalin-fixed and paraffin-embedded (FFPE) cancer resection specimens. Subsequent to RNA sample preparation and hybridization to standard GeneChips (Affymetrix), RNA samples yielded 36.43 +/- 9.60% (FFPE), 49.90 +/- 4.43% (fresh-frozen), and 53.9% (cell line) present calls. Quality control parameters and Q-RT-PCR validation demonstrated reliability of results. Microarray datasets of FFPE samples were informative and comparable to those of fresh-frozen samples. A systematic measurement difference of differentially processed tissues was eliminated by a correction step for comparative unsupervised data analysis of fresh-frozen and FFPE samples. Within FFPE samples, unsupervised clustering analyses clearly distinguished between normal and malignant tissues as well as to further separate tumor samples according to histological World Health Organization (WHO) subtypes. In summary, our approach represents a major step towards integration of microarrays into retrospective studies and enables further investigation of the relevance of microarray analysis for clinico-pathological diagnostics.
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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.