Second SPIDIA-DNA External Quality Assessment (EQA): Influence of pre-analytical phase of blood samples on genomic DNA quality

A pocket companion to cell-free DNA (cfDNA) preanalytics

The cumulative pool of cell-free DNA (cfDNA) molecules within bodily fluids represents a highly dense and multidimensional information repository. This "biological mirror" provides real-time insights into the composition, function, and dynamics of the diverse genomes within the body, enabling significant advancements in personalized molecular medicine. However, effective use of this information necessitates meticulous classification of distinct cfDNA subtypes with exceptional precision. While cfDNA molecules originating from different sources exhibit numerous genetic, epigenetic, and physico-chemical variations, they also share common features that complicate analyses. Considerable progress has been achieved in mapping the landscape of cfDNA features, their clinical correlations, and optimizing extraction procedures, analytical approaches, bioinformatics pipelines, and machine learning algorithms. Nevertheless, preanalytical workflows, despite their profound impact on cfDNA measurements, have not progressed at a corresponding pace. In this perspective article, we emphasize the pivotal role of robust preanalytical procedures in the development and clinical integration of cfDNA assays, highlighting persistent obstacles and emerging challenges.

The changing face of circulating tumor DNA (ctDNA) profiling: Factors that shape the landscape of methodologies, technologies, and commercialization

Liquid biopsies, in particular the profiling of circulating tumor DNA (ctDNA), have long held promise as transformative tools in cancer precision medicine. Despite a prolonged incubation phase, ctDNA profiling has recently experienced a strong wave of development and innovation, indicating its imminent integration into the cancer management toolbox. Various advancements in mutation-based ctDNA analysis methodologies and technologies have greatly improved sensitivity and specificity of ctDNA assays, such as optimized preanalytics, size-based pre-enrichment strategies, targeted sequencing, enhanced library preparation methods, sequencing error suppression, integrated bioinformatics and machine learning. Moreover, research breakthroughs have expanded the scope of ctDNA analysis beyond hotspot mutational profiling of plasma-derived apoptotic, mono-nucleosomal ctDNA fragments. This broader perspective considers alternative genetic features of cancer, genome-wide characterization, classical and newly discovered epigenetic modifications, structural variations, diverse cellular and mechanistic ctDNA origins, and alternative biospecimen types. These developments have maximized the utility of ctDNA, facilitating landmark research, clinical trials, and the commercialization of ctDNA assays, technologies, and products. Consequently, ctDNA tests are increasingly recognized as an important part of patient guidance and are being implemented in clinical practice. Although reimbursement for ctDNA tests by healthcare providers still lags behind, it is gaining greater acceptance. In this work, we provide a comprehensive exploration of the extensive landscape of ctDNA profiling methodologies, considering the multitude of factors that influence its development and evolution. By illuminating the broader aspects of ctDNA profiling, the aim is to provide multiple entry points for understanding and navigating the vast and rapidly evolving landscape of ctDNA methodologies, applications, and technologies.

The Significance of External Quality Assessment Schemes for Molecular Testing in Clinical Laboratories

Simple Summary

Patients and clinicians often rely on the outcome of laboratory tests, but can we really trust these test results? Good quality management is key for laboratories to guarantee reliable test results. This review focusses on external quality assessment (EQA) schemes which are a tool for laboratories to examine and improve the quality of their testing routines. In this review, an overview of the role and importance of EQA schemes for clinical laboratories is given, and different types of EQA schemes and EQA providers available on the market are discussed, as well as recent developments in the EQA landscape.

Abstract

External quality assessment (EQA) schemes are a tool for clinical laboratories to evaluate and manage the quality of laboratory practice with the support of an independent party (i.e., an EQA provider). Depending on the context, there are different types of EQA schemes available, as well as various EQA providers, each with its own field of expertise. In this review, an overview of the general requirements for EQA schemes and EQA providers based on international guidelines is provided. The clinical and scientific value of these kinds of schemes for clinical laboratories, clinicians and patients are highlighted, in addition to the support EQA can provide to other types of laboratories, e.g., laboratories affiliated to biotech companies. Finally, recent developments and challenges in laboratory medicine and quality management, for example, the introduction of artificial intelligence in the laboratory and the shift to a more individual-approach instead of a laboratory-focused approach, are discussed. EQA schemes should represent current laboratory practice as much as possible, which poses the need for EQA providers to introduce latest laboratory innovations in their schemes and to apply up-to-date guidelines. By incorporating these state-of-the-art techniques, EQA aims to contribute to continuous learning.

Concentration of cell-free DNA in different tumor types

Introduction: Cell-free DNA (cfDNA) circulates in the blood for a long time. The levels of cfDNA in the blood are assayed in cancer diagnostics because they are closely related to the tumor burden of patients.Areas covered: cfDNA escapes the action of DNA-hydrolyzing enzymes, being a part of supramolecular complexes or interacting with the plasma membrane of blood cells. cfDNA has heterogeneous size and composition, which impose various restrictions on both isolation methods and subsequent analysis. cfDNA concentration and structural changes with the development of diseases highlight the high potential of cfDNA as a diagnostic and prognostic marker. The concentration of cfDNA released in the blood by tumor cells determines the specificity of such diagnostics and the required blood volume. The present review aimed to synthesize the available data on cfDNA concentration in the cancer patient's blood as well as pre-analytical, analytical, and biological factors, which interfere with cfDNA concentration.Expert opinion: The concentration of cfDNA and tumor cell DNA (ctDNA), and the over-presentation of DNA loci in cfDNA must be considered when looking for tumor markers. Some inconsistent data on cfDNA concentrations (like those obtained by different methods) suggest that the study of cfDNA should be continued.

Size profile of cell-free DNA: A beacon guiding the practice and innovation of clinical testing

Cell-free DNA (cfDNA) has pioneered the development of noninvasive prenatal testing and liquid biopsy, its emerging applications include organ transplantation, autoimmune diseases, and many other disorders; size profile of cfDNA is a crucial biological property and is essential for its clinical applications. Therefore, a thorough mastery of the characteristic and potential applications of cfDNA size profile is needed. Methods: Based on the recent researches, we summarized the size profile of cfDNA in pregnant women, tumor patients, transplant recipients and systemic lupus erythematosus (SLE) patients to explore the common features. We also concluded the applications of size profile in pre-analytical phases, analytical phases for novel assays, and preparation of quality control materials (QCMs). Results: The size profile of cfDNA shared common features in different populations, and was distributed as a "ladder" pattern with a dominant peak at ~166 bp. However, cfDNA entailed slightly discrepant characteristics due to specific tissues of origin. The dominant peaks of fetal and maternal cfDNA fragments in pregnant women were at 143 bp and 166 bp, respectively. The plasma cfDNA in tumor patients, transplant recipients, and SLE patients had a peak of around 166 bp. In pre-analytical phases, size profile served as a vital indicator to judge the eligibility of specimens, thus ensuring the successful implementation of assays. More importantly, the size profile had the potential to enrich short fragments, calculate fetal fraction, detect fetal abnormalities, predict tumor progress in analytical phase and to guide the preparation of QCMs. Conclusions: Our finding summarized the characteristics and potential applications of cfDNA size profile, providing clinical researchers with novel assays by the extensive application of cfDNA.

Exploring DNA quantity and quality from raw materials to botanical extracts

OBJECTIVES

The aim of this study was to explore the variability in DNA quality and quantity along a gradient of industrial processing of botanical ingredients from raw materials to extracts.

METHODS

A data matrix was assembled for 1242 botanical ingredient samples along a gradient of industrial processing commonly used in the Natural Health Product (NHP) industry. Multivariate statistics was used to explore dependant variables for quality and quantity. The success of attaining a positive DNA test result along a gradient of industrial processing was compared among four biotechnologies: DNA barcoding, NGS, Sanger sequencing and qPCR.

RESULTS

There was considerable variance in DNA quality and quantity among the samples, which could be interpreted along a gradient from raw materials with greater quantities (50-120 ng/μL) of DNA and longer DNA (400-500bp) sequences to extracts, which were characterized by lower quantities (0.1-10.0 ng/μL) and short fragments (50-150bp).

CONCLUSIONS

Targeted molecular diagnostic tests for species identity can be used in the NHP industry for raw and processed samples. Non-targeted tests or the use of NGS for any identity test needs considerable research and development and must be validated before it can be used in commercial operations as these methods are subject to considerable risk of false negative and positive results. Proper use of these tools can be used to ensure ingredient authenticity, and to avert adulteration, and contamination with plants that are a health concern. Lastly these tools can be used to prevent the exploitation of rare herbal species and the harvesting of native biodiversity for commercial purposes.

Methodological and statistical issues in developing an External Quality Assessment scheme in laboratory medicine: Focus on biomarker research

External Quality Assessment (EQA) schemes are well-established tools with which to evaluate, monitor and improve the output quality of clinical laboratories, recognising that high quality laboratory medicine is essential for patient care. EQA programs involve the testing of multiple laboratories and the statistical comparison of their results, according to a multistep workflow. New clinical laboratory activities, such as biomarker research, require new EQA schemes. Critical elements in designing EQA programs are choosing the statistical methods and defining reference values and control limits. This article summarizes the key features of an EQA scheme, including designing the study, identifying reference values and control limits for qualitative and quantitative data, and graphically reporting laboratory performance statistics. These steps are illustrated with examples taken from the authors' experience in national and international quality assessment schemes for biomarker research.

The emerging role of cell-free DNA as a molecular marker for cancer management

An increasing number of studies demonstrate the potential use of cell-free DNA (cfDNA) as a surrogate marker for multiple indications in cancer, including diagnosis, prognosis, and monitoring. However, harnessing the full potential of cfDNA requires (i) the optimization and standardization of preanalytical steps, (ii) refinement of current analysis strategies, and, perhaps most importantly, (iii) significant improvements in our understanding of its origin, physical properties, and dynamics in circulation. The latter knowledge is crucial for interpreting the associations between changes in the baseline characteristics of cfDNA and the clinical manifestations of cancer. In this review we explore recent advancements and highlight the current gaps in our knowledge concerning each point of contact between cfDNA analysis and the different stages of cancer management.

High DNA stability in white blood cells and buffy coat lysates stored at ambient temperature under anoxic and anhydrous atmosphere

Conventional storage of blood-derived fractions relies on cold. However, lately, ambient temperature preservation has been evaluated by several independent institutions that see economic and logistic advantages in getting rid of the cold chain. Here we validated a novel procedure for ambient temperature preservation of DNA in white blood cell and buffy coat lysates based on the confinement of the desiccated biospecimens under anoxic and anhydrous atmosphere in original hermetic minicapsules. For this validation we stored encapsulated samples either at ambient temperature or at several elevated temperatures to accelerate aging. We found that DNA extracted from stored samples was of good quality with a yield of extraction as expected. Degradation rates were estimated from the average fragment size of denatured DNA run on agarose gels and from qPCR reactions. At ambient temperature, these rates were too low to be measured but the degradation rate dependence on temperature followed Arrhenius’ law, making it possible to extrapolate degradation rates at 25°C. According to these values, the DNA stored in the encapsulated blood products would remain larger than 20 kb after one century at ambient temperature. At last, qPCR experiments demonstrated the compatibility of extracted DNA with routine DNA downstream analyses. Altogether, these results showed that this novel storage method provides an adequate environment for ambient temperature long term storage of high molecular weight DNA in dehydrated lysates of white blood cells and buffy coats.

"Nuts and Bolts" of Laboratory Evaluation of Angioedema

Angioedema, as a distinct disease entity, often becomes a clinical challenge for physicians, because it may cause a life-threatening condition, whereas prompt and accurate laboratory diagnostics may not be available. Although the bedside diagnosis needs to be established based on clinical symptoms and signs, family history, and the therapeutic response, later, laboratory tests are available. Currently, only for five out of the nine different types of angioedema can be diagnosed by laboratory testing, and these occur only in a minority of the patient population. Hereditary angioedema with C1-inhibitor (C1-INH) deficiency type I can be diagnosed by the low C1-INH function and concentration, whereas in type II, C1-INH function is low, but its concentration is normal or even elevated. C1q concentration is normal in both forms. Acquired angioedema with C1-INH deficiency type I is characterized by the low C1-INH function and concentration; however, C1q concentration is also low, and autoantibodies against C1-INH cannot be detected. Complement profile of acquired angioedema with C1-INH deficiency type II is similar to that of type I, but in this form, autoantibodies against C1-INH are present. Hereditary angioedema due to a mutation of the coagulation factor XII can be diagnosed exclusively by mutation analysis of FXII gene. Diagnostic metrics are not available for idiopathic histaminergic acquired angioedema, idiopathic non-histaminergic acquired angioedema, acquired angioedema related to angiotensin-converting enzyme inhibitor, and hereditary angioedema of unknown origin; these angioedemas can be diagnosed by medical and family history, clinical symptoms, and therapeutic response and by excluding the forms previously described. Several potential biomarkers of angioedema are used to date only in research. In the future, they could be utilized into the clinical practice to improve the differential diagnosis, therapy, as well as the prognosis of angioedema.

Data and performances evaluation of the SPIDIA-DNA Pan-European External Quality Assessment: 2nd SPIDIA-DNA laboratory report

Within the EU-SPIDIA project (www.spidia.eu), the quality parameters of blood genomic DNA were defined [SPIDIA-DNA: an External Quality Assessment for the pre-analytical phase of blood samples used for DNA-based analyses - [1]; Influence of pre-analytical procedures on genomic DNA integrity in blood samples: the SPIDIA experience - [2]; Combining qualitative and quantitative imaging evaluation for the assessment of genomic DNA integrity: the SPIDIA experience - [3]. DNA quality parameters were used to evaluate the laboratory performance within an External Quality Assessment (EQA) [Second SPIDIA-DNA External Quality Assessment (EQA): Influence of pre-analytical phase of blood samples on genomic DNA quality - [4]. These parameters included DNA purity and yield by UV spectrophotometric measurements, the presence of PCR interferences by Kineret software and genomic DNA integrity analysis by Pulsed Field Gel Electrophoresis. Here we present the specific laboratory report of the 2nd SPIDIA-DNA EQA as an example of data and performances evaluation.