ArticleBreast cancer research and treatment2011
Gene expression array testing of FFPE archival breast tumor samples: an optimized protocol for WG-DASL sample preparation.
Article in Breast cancer research and treatment, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 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
- A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples.PloS one · 2017Article
- Secreted factors derived from obese visceral adipose tissue regulate the expression of breast malignant transformation genes.International journal of obesity (2005) · 2016Article
- Article
- Quality assessment metrics for whole genome gene expression profiling of paraffin embedded samples.BMC research notes · 2013Article
- Heterogeneity of gene expression in murine squamous cell carcinoma development-the same tumor by different means.PloS one · 2013Article
- Molecular Signatures of Recurrent Hepatocellular Carcinoma Secondary to Hepatitis C Virus following Liver Transplantation.Journal of transplantation · 2013Article
- Quality assurance of RNA expression profiling in clinical laboratories.The Journal of molecular diagnostics : JMD · 2012Review
- Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens.BMC cancer · 2011Article
- Article
- Clinical implementation of RNA signatures for pharmacogenomic decision-making.Pharmacogenomics and personalized medicine · 2011Article
- Prognostic and diagnostic value of spontaneous tumor-related antibodies.Clinical & developmental immunology · 2010Review
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Archived formalin-fixed, paraffin embedded (FFPE) tissues constitute a vast, well-annotated, but underexploited resource for the molecular study of cancer progression, largely because degradation, chemical modification, and cross-linking, render FFPE RNA a suboptimal substrate for conventional analytical methods. We report here a modified protocol for RNA extraction from FFPE tissues which maximized the success rate (with 100% of samples) in the expression profiling of a set of 60 breast cancer samples on the WG-DASL platform; yielding data of sufficient quality such that in hierarchical clustering (a) 12/12 (100%) replicates correctly identified their respective counterparts, with a high self-correlation (r = 0.979), and (b) the overall sample set grouped with high specificity into ER+ (38/40; 95%) and ER- (18/20; 90%) subtypes. These results indicate that a large fraction of decade-old FFPE samples, of diverse institutional origins and processing histories, can yield RNA suitable for gene expression profiling experiments.
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