Making clinical samples fit for research (3/3) – Selecting suitable techniques for nucleic acid extraction

Clinical biospecimens are the most commonly used sample-type for research purposes, but are often of poor quality given their susceptibility to uncontrolled and unrecorded preanalytical variables. IBBL’s Biorefinery Department carries out biospecimen research to guide researchers in their sample preparation, selection and processing decisions. Recently, Dr. William Mathieson and his colleagues assessed the impact of automated DNA extraction and SpeedVac concentration on the quality and fitness-for-purpose of the extracted nucleic acids, with the aim of providing better insight into these sample processing techniques.

DNA extracted from FFPE tissue blocks is increasingly being used for applications such as next generation sequencing to determine patients’ therapeutic treatment. Automated robots that simultaneously extract DNA from multiple FFPE tissue blocks are commonly used by high-throughput laboratories such as IBBL. However, many smaller institutes still rely on manual extractions.

To assess whether DNA quality is compromised by the choice of particular manual or automated extractions, the IBBL team, collaborating with Imperial College London, extracted DNA from 42 FFPE tissue blocks using two automated platforms and a manual method. Results show that both integrity and yield were slightly higher in the manual extractions, while automated techniques allowed for slightly better reproducibility and required much less intervention by technicians. “The extraction methods have different strengths and weaknesses. The choice of which to use therefore depends on the specific requirements of the users. However, our findings are particularly relevant to smaller laboratories which cannot necessarily invest in expensive automated technologies, since we confirm the high reliability and quality of manual extractions”, explains Dr. Mathieson.

Following extraction from FFPE tissues, DNA and RNA are often too dilute to be further analysed, and need to be concentrated, usually by applying vacuum centrifugal concentration (SpeedVac). IBBL researchers assessed the impact of this technique by concentrating the nucleic acids extracted from FFPE tissues with SpeedVac at different times and temperatures and measuring the changes in quantity, purity and integrity. The study showed that SpeedVac has no negative effects on the DNA and RNA. In addition to reassuring researchers in their choice of concentration procedure, these findings can be used by biobanks seeking ISO 20387 accreditation to validate their processing methods. “Our goal is to continuously expand the value that tissue banks can offer. By providing researchers with biospecimens of known quality, and by understanding what drives poor quality, tissue banks play a crucial role in curing disease”, Dr. Mathieson concludes.

The detailed results of the two studies on automated DNA extraction and SpeedVac concentration can be accessed in the respective full papers.