Effect of preservation time of formalin-fixed paraffin-embedded tissues on extractable DNA and RNA quantity

Abstract

Objectives This study aimed to investigate the factors affecting the quantity of DNA and RNA extractable from human formalin-fixed paraffin-embedded (FFPE) tissues stored for different lengths of time. Methods We randomly selected 20 FFPE specimens harvested from hysteromyoma patients with uterine fibroids during 2010, 2015, and 2017 at the Department of Pathology, Jiading District Central Hospital Affiliated Shanghai University of Medicine and Health Sciences. DNA and RNA extractions were performed using a DNA/RNA FFPE kit. DNA and RNA concentrations and their OD260/OD280 ratios were determined by a NanoDrop 2000 spectrophotometer. The human β-globin gene and aldehyde dehydrogenase-2 (ALDH2) gene were amplified from nucleic acids using a LightCycler 480 Real-Time PCR System, and PCR amplification products were electrophoresed on 1% agarose gels. Results Specimens that were stored for longer showed more degradation and a reduced concentration of DNA and RNA after nucleic acid extraction. However, there was no significant difference in DNA or RNA purity. β-globin and ALDH2 genes could be amplified from more than 99% of specimens. Conclusion We found that FFPE tissues stored for longer had a reduced quantity of extractable DNA and RNA. However, these tissues could be used for the analysis of some small target genes.

Non-Small Cell Lung Cancer Harboring Concurrent EGFR Genomic Alterations: A Systematic Review and Critical Appraisal of the Double Dilemma

“…Most of the results of our systematic review consisted in articles and reports on Asian population. This is consistent with the major prevalence of EGFR genomic alteration in NSCLC Asian patients [114,115]. Notable, Asian patients appeared to display better response comparing to Caucasian cohorts (see Table 2); this finding shows racial differences in genetic pathways and prompts further studies on this field of research.…”

Evaluation of DNA Isolation and Amplification from Various Organs Preserved through Frozen, Formalin-Fixed and Paraffin-Embedded Tissue Sample method

“…This method can be used for long-term storage from 1 month up to 5 years, at room temperature. According to Yi (2020), the paraffin-embedded tissue preservation method did not show any significant difference in extracted DNA and RNA purity as compared to the other method. Further, small-sized extracted DNA fragments were successfully amplified from most paraffin block samples for several years at room temperature (Nam et al 2014).…”

Practical tips to using formalin-fixed paraffin-embedded tissue archives for molecular diagnostics in a South African setting

“…Thus far, FFPE tissue archives in most African forensic pathology departments have been an underexploited resource for conducting large retrospective and prospective genetic epidemiological studies. 14 , 15 , 16 It is time to utilise these resources at our disposal to the advantage of the African population. The most significant benefit of post-mortem molecular testing is the high disease-specific diagnostic, therapeutic, and prognostic benefits derivable from subsequent genetic analysis.…”

“… 9 , 11 , 12 , 13 Although blood collected in ethylenediaminetetraacetic acid or fresh frozen tissue samples are the best source of DNA and the preferred material used for genetic testing, numerous studies have reported on the successful use of FFPE tissue samples. 2 , 14 , 15 The successful use of FFPE tissue samples is particularly encouraging because African forensic pathology still faces the dire reality of inadequate funding and resource allocation required to maintain freezer preservation systems for routine collection and storage of blood or tissue samples. 15 , 16 , 17 …”

“…Consequently, the increased caseload delays case investigation, prolonging formalin fixation times by days, weeks, and even months. 26 , 27 , 28 According to recommended guidelines for optimised molecular testing, tissue samples should be fixed in 10% buffered formalin for 14 h – 24 h. 9 , 14 Hence, most forensic pathology departments doubt the value and efficacy of their decades worth of FFPE tissue archives in the context of molecular diagnostic applications or research. 9 , 15 , 20…”