Transcriptome profiling of archived sectioned formalin-fixed paraffin-embedded (AS-FFPE) tissue for disease classification.
Author(s): Kojima K, April C, Canasto-Chibuque C, Chen X, Deshmukh M, Venkatesh A, Tan PS, Kobayashi M, Kumada H, Fan JB, Hoshida Y
Publication: PLoS One, 2014, Vol. 9, Page e86961
PubMed ID: 24498002 PubMed Review Paper? No
Purpose of Paper
This paper compared the percentage of formalin-fixed paraffin-embedded (FFPE) specimens that could be successfully used for transcriptome profiling by DASL or the nCounter assay (Nanostring) when sections were freshly cut from archival blocks or stored as slide-mounted sections for 6 to 7 years.
Conclusion of Paper
RIN values and RIN reproducibility were comparable among slide-mounted FFPE sections stored for 6-7 years and freshly cut sections that generated intermediate to low quality whole-transcriptome profiles. While use of different assay platforms precludes direct comparisons, archived sections displayed a wider range of percent present calls and inter-sample correlation of expression profiles than freshly cut sections. Patient classification of hepatocellular carcinoma specimens into three subclasses was concordant among archived and freshly cut FFPE sections for 86% specimens. Similarly, prognosis prediction was concordant among archived and freshly cut FFPE sections in 67% liver cirrhosis specimens by both DASL and the nCounter assay.
Studies
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Study Purpose
This study compared the percentage of FFPE specimens that could be successfully used for transcriptome profiling by DASL or the nCounter assay (Nanostring) when sections were freshly cut from archival blocks or stored as slide-mounted sections for 6 to 7 years. FFPE liver specimens from 83 patients diagnosed with hepatocellular carcinoma and 47 patients diagnosed with cirrhosis were used for analysis. These archival FFPE blocks were stored for 5 to 16 years at the time of the study. FFPE slide-mounted sections stored for an additional 6-7 years at room temperature in sealed bags with a drying reagent were compared to freshly cut sections from the same archival FFPE blocks. Total RNA was extracted from 1-3 10 µm thick sections with Trizol after deparaffinization with CitriSolve. RNA quality was assessed by bioanalyzer and transcriptome profiles were assessed using wither the HumanHT-12 whole genome DASL beadarray or Nanostring's nCounter assay. Details on formalin fixation and processing were not provided.
Summary of Findings:
Comparable RIN values (2.40-2.50 vs. 2.40-3.10) and RIN reproducibility (0.91-0.93 vs. 0.92-0.98) were obtained for slide-mounted FFPE sections stored for 6-7 years and freshly cut sections that generated intermediate to low quality whole-transcriptome profiles. While use of different assay platforms precludes direct comparisons, archived sections displayed a wider range of percent present calls (the proportion of probes for which a signal was detectable)(10-60%) compared to freshly cut sections from the same block (70-90%), and a wider range of inter-sample correlation of expression profiles (0.4-0.9) than freshly cut sections (0.6-1.0). Patient classification of hepatocellular carcinoma specimens into three subclasses was concordant among archived and freshly cut FFPE sections for 86% (55/64) specimens. Similarly, prognosis prediction based on gene expression signatures of 186 genes was concordant among archived and freshly cut FFPE sections in 67% (24/36) of liver cirrhosis specimens. When the same 186 genes were analyzed in liver cirrhosis specimens with the nCounter assay, predictions in archived and freshly cut FFPE sections were concordant for 67% (16/36) of specimens.
Biospecimens
Preservative Types
- Formalin
Diagnoses:
- Cirrhosis
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform RNA Automated electrophoresis/Bioanalyzer RNA DNA microarray RNA DASL Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Storage Storage duration Fresh
6-7 y