Next-generation sequencing (NGS) analyses on DNA derived from archived Formalin-Fixed Paraffin-Embedded (FFPE) clinical material can provide a powerful tool in oncology research and clinical diagnostics. Although several studies have established that NGS can be performed using DNA from FFPE tissue, the accuracy and reproducibility of such analyses, as well as their robustness to the biomolecular quality of the samples used, remains a matter of debate. Excellent reviews have recently been published, providing evidence-based best practices for FFPE DNA extraction. Alternative fixatives exist, although their implementation in clinical practice is difficult. In this article, we present (i) a review of fixed tissue DNA preanalytics with a special focus on DNA extraction and fixed tissue sample qualification and (ii) results from comparisons between different methods of DNA extraction from tissue samples that have been fixed or stabilized by different methods, in terms of NGS metrics and different DNA quality metrics.

Collection of human whole blood for genomic DNA extraction is part of numerous clinical studies. Since DNA extraction cannot always be performed at the time of sample collection, whole blood samples may be stored for years before being processed. The use of appropriate storage conditions is then critical to obtain DNA in sufficient quantity and of adequate quality in order to obtain reliable results from the subsequent molecular biological analyses. In this study, EDTA whole blood samples were collected from 8 healthy volunteers, and different durations (up to 1 year) and temperatures (room temperature, 4°C, -20°C, and -80°C) of storage were compared. The effect of the addition of a DNA preservative agent was also assessed before and after storage. DNA concentrations measured by UV spectrophotometry and spectrofluorometry were used to calculate DNA extraction yields and double-strand DNA ratios. DNA integrity was controlled by agarose gel electrophoresis and long-range polymerase chain reaction. The impact of storage conditions on DNA methylation was also evaluated. Results showed that certain storage conditions have a significant impact on the DNA extraction yield but little or no effect on DNA integrity and methylation. Storage of EDTA blood at -80°C guarantees high-quality DNA with a good yield. Higher DNA extraction yields were obtained with the addition of a DNA preservative agent before thawing EDTA blood stored at -20°C or -80°C. Long-term storage at room temperature in the presence of a DNA preservative agent also appeared to be a reliable procedure.

Background: This is the third in a series of publications presenting formal method validation for biospecimen processing in the context of accreditation in laboratories and biobanks. We report here optimization of a stool processing protocol validated for fitness-for-purpose in terms of downstream DNA-based analyses.Methods: Stool collection was initially optimized in terms of sample input quantity and supernatant volume using canine stool. Three DNA extraction methods (PerkinElmer MSM I-(R), Norgen Biotek All-In-One((R)), MoBio PowerMag((R))) and six collection container types were evaluated with human stool in terms of DNA quantity and quality, DNA yield, and its reproducibility by spectrophotometry, spectrofluorometry, and quantitative PCR, DNA purity, SPUD assay, and 16S rRNA gene sequence-based taxonomic signatures.Results: The optimal MSM I protocol involves a 0.2 g stool sample and 1000 mu L supernatant. The MSM I extraction was superior in terms of DNA quantity and quality when compared to the other two methods tested. Optimal results were obtained with plain Sarstedt tubes (without stabilizer, requiring immediate freezing and storage at -20 degrees C or -80 degrees C) and Genotek tubes (with stabilizer and RT storage) in terms of DNA yields (total, human, bacterial, and double-stranded) according to spectrophotometry and spectrofluorometry, with low yield variability and good DNA purity. No inhibitors were identified at 25 ng/mu L. The protocol was reproducible in terms of DNA yield among different stool aliquots.Conclusions: We validated a stool collection method suitable for downstream DNA metagenomic analysis. DNA extraction with the MSM I method using Genotek tubes was considered optimal, with simple logistics in terms of collection and shipment and offers the possibility of automation. Laboratories and biobanks should ensure protocol conditions are systematically recorded in the scope of accreditation.

Until now, proficiency testing programs have not existed for the quality assessment of biospecimens that are used in basic, translational, and clinical research studies, yet the discovery, validation, and clinical evaluation of biomarkers necessary for the advancement of global health depend upon the availability of a large number of standardized specimens. To meet this void, ISBER has launched a biorepository Proficiency Testing (PT) Program in partnership with the Integrated Biobank of Luxembourg (IBBL). The ISBER PT Program belongs to the category of interlaboratory comparison ‘‘schemes’’ involving simultaneous participation of biorepository laboratories located in different countries. Randomly selected aliquots from a source material prepared at IBBL (the test items) are being distributed and tested concurrently by all registered participants. After the completion of the testing, the participants’ results will be returned to the Proficiency Testing provider (ISBER) and compared with the assigned value(s) derived from the reference laboratories to give an indication of the performance of the individual participants and of the group as a whole. The ISBER PT Program allows biorepositories performing quality control assays and/or characterization of the biospecimens to assess the accuracy of their testing and to compare their results with those obtained in other laboratories around the world. It has been designed to include four schemes: DNA quantification and purity, RNA integrity, cell viability, and tissue antigenicity. The first two schemes were open for participation in the latter part of 2011. The cell viability and tissue antigenicity schemes will be added to the program in 2012.