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Updated: Aug 5, 2026
Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
Published on: August 21, 2016
DNA Extracted From Aged Formalin-Fixed Paraffin-Embedded Specimens of Patients With Papillary Thyroid Carcinomas Can
Kousuke Tanimoto1,2,3, Tomonori Hayashi1,2,4, Hidewaki Nakagawa5
1Department of Molecular Biosciences, Radiation Effects Research Foundation, Hiroshima, Hiroshima, Japan.
Background:
In Hiroshima, thyroid cancer tissue samples from A-bomb survivors have been preserved since 1958. However, the feasibility of using these old formalin-fixed paraffin-embedded (FFPE) specimens for genetic analysis has not been fully evaluated. Here, we aimed to assess the quality of DNA extracted from long-term stored FFPE specimens obtained from patients with papillary thyroid carcinoma (PTC) in Hiroshima and to evaluate their applicability to whole exome sequencing (WES).
Methods:
We extracted DNA from tumor and adjacent normal regions of FFPE thyroid tumor specimens from 57 cases stored for up to 55 years at three hospitals in Hiroshima and confirmed the quality of the extracted DNA. From this cohort, tumor and paired normal samples from 24 patients with PTC were selected for WES, and sequencing metrics were evaluated.
Results:
Both DNA yield and DNA integrity number were negatively correlated with storage duration. WES analysis showed that storage duration was also negatively correlated with mean insert size and normalized read depth. In contrast, the uniformity score, which reflects the evenness of sequence coverage across targeted regions, did not show a significant correlation with storage duration. Among the 22 BRAF V600E-positive cases identified by droplet digital PCR, 18 cases (82%) had at least one sequencing read supporting the mutation.
Conclusions:
These findings suggest that FFPE samples preserved for up to 55 years may be amenable to sequencing with increased read depth. However, the progressive decline in DNA quality with longer storage periods indicates that careful interpretation of sequencing results is warranted.
