Quantity and quality of nucleic acids extracted from archival formalin fixed paraffin embedded prostate biopsies

Abstract

BackgroundIn Sweden, human tissue samples obtained from diagnostic and surgical procedures have for decades been routinely stored in a formalin-fixed, paraffin-embedded, form. Through linkage with nationwide registers, these samples are available for molecular studies to identify biomarkers predicting mortality even in slow-progressing prostate cancer. However, tissue fixation causes modifications of nucleic acids, making it challenging to extract high-quality nucleic acids from formalin fixated tissues.MethodsIn this study, the efficiency of five commercial nucleic acid extraction kits was compared on 30 prostate biopsies with normal histology, and the quantity and quality of the products were compared using spectrophotometry and Agilent’s BioAnalyzer. Student’s t-test’s and Bland-Altman analyses were performed in order to investigate differences in nucleic acid quantity and quality between the five kits. The best performing extraction kits were subsequently tested on an additional 84 prostate tumor tissues. A Spearman’s correlation test and linear regression analyses were performed in order to investigate the impact of tissue age and amount of tissue on nucleic acid quantity and quality.ResultsNucleic acids extracted with RNeasy® FFPE and QIAamp® DNA FFPE Tissue kit had the highest quantity and quality, and was used for extraction from 84 tumor tissues. Nucleic acids were successfully extracted from all biopsies, and the amount of tumor (in millimeter) was found to have the strongest association with quantity and quality of nucleic acids.ConclusionsTo conclude, this study shows that the choice of nucleic acid extraction kit affects the quantity and quality of extracted products. Furthermore, we show that extraction of nucleic acids from archival formalin-fixed prostate biopsies is possible, allowing molecular studies to be performed on this valuable sample collection.

Expression of selected microRNAs in pancreatic ductal adenocarcinoma: is there a relation to tumor morphology, progression, and patient’s outcome?

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Estimation of Relative and Absolute Risks in a Competing-Risks Setting Using a Nested Case-Control Study Design: Example From the ProMort Study

“…Because of the limited amount of tissue available for molecular analysis, we conducted 2 pilot studies to 1) determine the best-performing DNA/RNA extraction kit in terms of the amount of tissue needed for the extraction and the quality of the extracted DNA/RNA ( 25 ) and 2) estimate the number and thickness of slices that could be cut from the tissue blocks and the minimum amount of cancer tissue (mm) needed to extract a sufficient amount of DNA/RNA for molecular analyses. Based on the outcome of these pilot studies and on a parallel systematic literature review, the most promising molecular markers for lethal prostate cancer will be prioritized for the main tissue analyses.…”

Frequent high-risk HPV co-infections excluding types 16 or 18 in cervical neoplasia in Guadeloupe

“…All previous work on HPV epidemiology in Guadeloupe were performed on fresh samples [ 14 , 19 , 20 ]. Archiving paraffin embedded blocks in tropical regions with humid weather, is known to hamper DNA extraction and amplification during HPV genotyping [ 21 ]. In our study, the samples were kept in designated areas before de-archiving.…”