Transcriptomics

Dataset Information

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Transcription profiling by array of formalin-fixed paraffin-embedded or fresh frozen human tumor samples


ABSTRACT: Background: To date, few studies have systematically characterized microarray gene expression signal performance with degraded RNA from formalin-fixed paraffin-embedded (FFPE) specimens in comparison to intact RNA from unfixed fresh-frozen (FF) specimens. Methodology: RNA was extracted and isolated from paired tumor and normal samples from both FFPE and FF kidney, lung and colon tissue specimens. Microarray signal dynamics on both the raw probe and probeset level were evaluated. A contrast metric was developed to directly compare microarray signal derived from RNA extracted from matched FFPE and FF specimens. Gene-level summaries were then compared to determine the degree of overlap in expression profiles. Results: RNA extracted from FFPE material was more degraded and fragmented than FF, resulting in reduced dynamic range of expression signal. It was found that probe performance is not affected uniformly and declines sharply toward 5¬タル end of genes. The most significant differences in FFPE vs. FF signal were consistent across three tissue types and enriched with ribosomal genes. Significance: Our results show that archived FFPE samples can be used to profile for expression signatures and assess differential expression similar to unfixed tissue sources. This study provides guidelines for application of these methods in the discovery, validation, and clinical application of microarray expression profiling with FFPE material. 53 samples: 16 FF colon, 7 FFPE colon, 6 FF lung, 8 FFPE lung, 8 FF kidney, and 8 FFPE kidney specimens. Samples are paired tumor and normal tissue. 1-4 biological replicates.

REANALYSED by: E-GEOD-19249

ORGANISM(S): Homo sapiens  

SUBMITTER: Diana Abdueva  Michele Wing   Elai Davicioni   Betty Schaub   Timothy Triche    

PROVIDER: E-GEOD-19249 | ArrayExpress | 2010-11-25

SECONDARY ACCESSION(S): GSE19249PRJNA120789

REPOSITORIES: GEO, ArrayExpress

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Publications

Quantitative expression profiling in formalin-fixed paraffin-embedded samples by affymetrix microarrays.

Abdueva Diana D   Wing Michele M   Schaub Betty B   Triche Timothy T   Davicioni Elai E  

The Journal of molecular diagnostics : JMD 20100603 4


To date, few studies have systematically characterized microarray gene expression signal performance with degraded RNA from fixed (FFPE) in comparison with intact RNA from unfixed fresh-frozen (FF) specimens. RNA was extracted and isolated from paired tumor and normal samples from both FFPE and FF kidney, lung, and colon tissue specimens and microarray signal dynamics on both the raw probe and probeset level were evaluated. A contrast metric was developed to directly compare microarray signal de  ...[more]

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