3'-end sequencing for expression quantification (3SEQ) from archival tumor samples.

Author(s): Beck AH, Weng Z, Witten DM, Zhu S, Foley JW, Lacroute P, Smith CL, Tibshirani R, van de Rijn M, Sidow A, West RB

Publication: PLoS One, 2010, Vol. 5, Page e8768

PubMed ID: 20098735 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine the effects of formalin fixation on gene expression analysis in solitary fibrous tumors (SFT) and desmoid type fibromatosis (DTF) by 3SEQ and microarray.

   Summary of Findings:

   A total of approximately 27,000 genes were identified in at least 1 3SEQ read (frozen and FFPE tissues combined) and approximately 18,000 genes had more than 25 reads. By comparison approximately 24,000 genes were quantified by microarray, of which approximately 12,000 were also read by 3SEQ. Gene expression between FFPE and frozen specimens had a mean correlation of 0.76 by 3SEQ, but by microarray, the mean correlation was 0.46 (p=0.0008). The authors report no effect of storage duration on the correlation of frozen and FFPE tissues by 3SEQ or microarray. The differential expression test statistical comparisons of DTF and SFT showed a correlation of 0.82 between frozen and FFPE tissues by 3SEQ, but the correlation was 0.54 using microarray. When a cutoff FDR of less than 0.01 was applied, 9,645 and 8,137 genes were identified as differentially expressed between tumor types by 3SEQ in frozen and FFPE specimens, respectively. Importantly, 82% of genes found to be differentially expressed in frozen tumors were also found in FFPE tissues by 3SEQ. In contrast, when a FDR of less than 0.01 was applied to microarray data, 4,574 and 64 genes were identified from frozen and FFPE specimens, respectively. Further analysis showed that 3SEQ was able to identify biological pathways differentially regulated between DTF and SFT tumors using FFPE or frozen tissues.

   Biospecimens

   • Tissue - Other

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Neoplastic - Benign
   • Neoplastic

   Platform:

   Analyte	Technology Platform
   RNA	DNA sequencing
   RNA	DNA microarray

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Frozen
   DNA microarray Specific	Technology platform	Microarray 3' end next generation sequencing
   Preaquisition	Diagnosis/ patient condition	Solitary fibrous tumor Desmoid type fibromatosis
   Storage	Storage duration	1-8 y 0-15 y
   Storage	Storage temperature	Room temperature -80 degrees C

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