Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples: a comparison to snap-frozen material using oligonucleotide microarrays.

Author(s): Frank M, Döring C, Metzler D, Eckerle S, Hansmann ML

Publication: Virchows Arch, 2007, Vol. 450, Page 699-711

PubMed ID: 17479285 PubMed Review Paper? No

Purpose of Paper

This paper conducted a comparison of oligonucleotide microarray results obtained from two different tissue/tumor types that were differentially preserved by snap freezing or formalin fixation and paraffin embedding (FFPE) to determine if biological relevance was preserved.

Conclusion of Paper

A direct comparison of microarray results among differentially preserved specimens yielded a correlation coefficient of 0.86 for signal intensity, and low percentages (52-61%) of concomitantly expressed genes that were elevated 5-fold or greater among different tissue/tumor types. The authors conclude that while FFPE archival specimens retain biologically relevant information regarding gene expression, a direct comparison to frozen specimens is precluded.

Studies

Study Purpose

The purpose of this study was to compare quality and degradation among RNA extracted from two different tissue and tumor types that had been snap frozen or FFPE. Tissue types employed were large B-cell lymphoma and follicular thyroid carcinoma.

Summary of Findings:

RNA quality was high in snap frozen specimens, as determined by a bioanalyzer; while RNA degradation among FFPE specimens, determined by real-time quantitative RT-PCR (qRT-PCR) amplification of 5' and 3' regions of beta-actin, was more prevalent and variable. The degree of degradation of RNA extracted from FFPE specimens appeared to be related to the duration of paraffin block storage.

Biospecimens

Preservative Types

Formalin
Frozen

Diagnoses:

Neoplastic - Carcinoma
Neoplastic - Lymphoma

Platform:

Analyte	Technology Platform
RNA	Automated electrophoresis/Bioanalyzer
RNA	Real-time qRT-PCR

Pre-analytical Factors:

Classification	Pre-analytical Factor	Value(s)
Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Snap frozen
Biospecimen Acquisition	Biospecimen location	Lymph node Thyroid
Storage	Storage duration	< 1 yr 3.5 yr 4.9 yr

Study Purpose

The purpose of this study was to compare oligonucleotide microarray results obtained from two different tissue/tumor types that were differentially preserved by snap freezing or formalin fixation and paraffin embedding (FFPE) to determine if biological relevance was preserved.

Summary of Findings:

The percent present call average was comparable among snap frozen and FFPE specimens, 22% versus 26%, respectively. However, a comparison of signal intensities among preservation methods revealed a correlation coefficient of 0.86, indicating a source of bias that precludes direct comparison. Hierarchical clustering separated results first by tissue/tumor type followed by preservation method, indicating biologically relevant gene expression differences were preserved to some degree after formalin fixation and paraffin embedding. Of the genes that exhibited a 5-fold increase or greater in expression among tissue/tumor types, only 52-61% were concomitantly detected among snap frozen and FFPE specimens.

Biospecimens

Preservative Types

Formalin
Frozen

Diagnoses:

Neoplastic - Carcinoma
Neoplastic - Lymphoma

Platform:

Analyte	Technology Platform
RNA	DNA microarray

Pre-analytical Factors:

Classification	Pre-analytical Factor	Value(s)
Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Snap frozen
Biospecimen Acquisition	Biospecimen location	Lymph node Thyroid

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