Paraffin treasures: do they last forever?
Author(s): Ademà V, Torres E, Solé F, Serrano S, Bellosillo B
Publication: Biopreserv Biobank, 2014, Vol. 12, Page 281-3
PubMed ID: 25075953 PubMed Review Paper? No
Purpose of Paper
The purpose of this paper was to assess if DNA integrity is adversely affected by long term storage of FFPE blocks.
Conclusion of Paper
Prolonged storage of FFPE blocks adversely and significantly affected DNA integrity in case-matched lymph node specimens. Amplicons were longer in the majority of specimens (88%, 38/43) when samples were stored for 8 years as extracted DNA at -20°C than as FFPE blocks. Longer amplicons were generated in of specimens when DNA was extracted from FFPE blocks (p<0.001). Maximal amplicon length was also greater when DNA was extracted within 1 month of embedding and stored (600 bp) than when specimens were stored as FFPE blocks (400 bp). Maximum amplicon lengths were comparable among the additional three specimens that were analyzed immediately after extraction 8 years prior and after 8 years of storage at -20°C, indicating that DNA degradation in frozen samples was minimal. The authors did not discuss the potential impact of the different DNA extraction methods used.
Studies
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Study Purpose
This study examined the integrity of DNA isolated from FFPE blocks stored for less than 1 month or after 8 years. Specimens included 43 randomly selected FFPE blocks that contained biopsies of lymph nodes subjected to a cold ischemia time of 5-30 min and fixed in 10% neutral buffered formalin. DNA was extracted from two 15 µm thick sections per block within 1 month and after 8 years using the QIAamp DNA mini kit and the Qiacube robot, respectively. While extracted DNA was stored at -20°C until analysis for the majority of specimens, which introduces frozen storage as a potentially confounding variable, three specimens that were analyzed immediately after extraction at each timepoint were also included. DNA integrity was assessed by multiplex PCR that produced five different sized amplicons from four genes, which were not specified.
Summary of Findings:
Prolonged storage of FFPE blocks adversely and significantly affected DNA integrity, as longer amplicons were generated in 88% (38/43) of specimens when extraction occurred within 1 month of embedding (DNA was then stored at -20°C for 8 years) than in case-matched FFPE blocks that were stored for 8 years before DNA extraction(p<0.001). For the remaining five cases, comparable multiplex PCR results were obtained between samples stored as extracted DNA at -20°C and as FFPE blocks. Maximal amplicon length was greater when DNA was immediately extracted and stored (600 bp) than when specimens were stored as FFPE blocks (400 bp). Maximum amplicon lengths were comparable among the additional three specimens that were analyzed immediately after extraction 8 years prior and after 8 years of storage at -20°C, indicating that DNA degradation in frozen samples was minimal. The authors did not discuss the potential impact of the different DNA extraction methods used.
Biospecimens
Preservative Types
- Formalin
Diagnoses:
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform DNA PCR Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Storage Storage duration < 1 month
8 years
PCR Specific Length of gene fragment 100 bp
200 bp
300 bp
400 bp
600 bp
Analyte Extraction and Purification Analyte isolation method Manual (QIAamp DNA Mini Kit)
Automated (Qiacube robot)