10 years of IBBL publications (2/4) – Quality Control assays: available tools and remaining gaps

IBBL recently celebrated 10 years of service to the national and international scientific community through the publication of its 100th scientific paper, sharing its knowledge and expertise in biobanking and biospecimen research to promote the standardisation of biobanking practices and ultimately advance biomedical research. To provide a thorough insight into the assays that can be performed to objectively evaluate the quality of biospecimens, IBBL and the International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group carried out two comprehensive literature reviews, compiling all the most promising markers and assays that can be used to assess preanalytical variations for both fluid and solid samples.

Preanalytical variables, such as warm or cold ischemia times, delays in processing or storage conditions, can have major repercussions on the biomolecular integrity of biological samples. In order to control such variables and minimise their impact on sample quality and on the reliability of downstream analyses, specific tests or markers to assess the quality of the biospecimen are needed. There are currently few appropriate quality control (QC) tools that are either diagnostic of upstream collection, processing, and/or storage conditions, or predictive of the feasibility and/or validity of downstream analysis performed with the samples. In order to provide the biospecimen science community with a comprehensive view of the existing QC assays that can be used to assess sample integrity and quality, the ISBER Biospecimen Science Working Group (BSWG), chaired by IBBL’s Chief Scientific Officer Dr. Fay Betsou, reviewed in 2013 and 2016 all the main publications dealing with biomolecules and biospecimen analytical behavior to identify the most promising QC tools. Their findings were published in two key review articles.

The first paper, published in 2013 in the ‘Journal of Molecular Diagnostics’, aimed to identify either novel markers/analytes that are particularly unstable and sensitive to specific preanalytical variations, displaying on/off responses, or functional assays that can be used to assess such variations. Based on the findings from the literature review, the ISBER BSWG evaluated the usefulness of the marker tools according to four criteria: type of QC tool (either diagnostic or predictive), evidence base, applicability grade (immediate, potential and no applicability) and accessibility grade (readily, potentially and not immediately accessible). This analysis allowed the authors to compile a comprehensive list of the most readily applicable and accessible evidence-based QC tools/markers. For instance, in terms of diagnostic QC assays for the qualification of serum and plasma biospecimens, the ISBER BSWG identified analytes including ascorbic acid, potassium, CD40L, interleukin cytokines and vitamin E as markers for the evaluation of preanalytical variables such as precentrifugation delays, storage conditions, exposure to room temperature and freeze-thawing. Concerning the qualification of urine specimens, analytes such as tumour necrosis factor alpha (TNF-α), epinephrine and dopamine were found to be reliable markers for preprocessing delays and storage conditions, while various proteins and RNA transcripts are indicative of warm and cold ischemia times in solid tissue-derived specimens. In terms of predictive QC tools, various PCR-based assays as well as the predictive value of the RNA Integrity Number (RIN) on the performance of gene expression microarrays were highlighted.

The second review article, published in 2016 in the journal ‘Biopreservation and Biobanking’, aimed to provide up to date information that can be used for the qualification (i.e. the assessment of the suitability of a specimen for research purposes) but also for the quality stratification (i.e. specimen classification into distinct categories corresponding to a specific in vivo biological characteristic or ex vivo pre-analytical condition) of fluid, tissue and cytological specimens, in the context of different types of downstream analyses.

The two reviews show that many QC tools are already available and can be used for specimen qualification and quality stratification. However, there are still several gaps in the area of qualification of specimens used in specific downstream analyses. For instance, there are currently no reliable assays for the qualification of urine, saliva or frozen tissue for use in proteomic analyses, or for the qualification of DNA to be used in methylation analyses. Moreover, only a few markers have been identified which have a known threshold for the preanalytical variation and a known reference range. Knowing the baseline reference ranges is crucial to define the lower threshold value of the analyte, beyond which it can be said with certainty that the biospecimen underwent preanalytical stress. The reviews have also elucidated the fact that a single ‘universal’ marker/QC assay cannot provide all of the information required regarding sample quality or cover all aspects of biospecimen characterisation. Therefore, a panel of QC markers is needed to comprehensively assess biospecimen quality.

In order to address these issues and fill the gaps, Dr. Fay Betsou and her Biorefinery team at IBBL have been working on the development of evidence-based and reliable assays that can be used with confidence to qualify a variety of different biospecimen types. The next article in this series will focus specifically on QC assays devised by the IBBL team to qualify serum, plasma, FFPE tissue and peripheral blood mononuclear cell (PBMC) samples. Stay tuned!