Pre-analytical Sample Research Articles

Abstract 3529: Sample quality control of cell-free DNA

Abstract Sequencing of cell-free DNA (cfDNA) is possible due to the establishment of low input library protocols for next-generation sequencing workflows. Accurate quantification of cfDNA samples is essential to determine suitable input amounts for cfDNA library preparation prior to sequencing. The main component of cfDNA samples is the mononucleosome with a size around 170 bp, sometimes with additional species representing nucleosome multimers. Further, cfDNA samples may contain larger DNA fragments dependent on pre-analytical sample treatment or extraction method. High molecular weight material can negatively influence library preparation and subsequently result in lower sequencing depth. Therefore, reliable quantification of cfDNA requires a method that separates DNA fragments by size, such as electrophoresis. This poster shows the use of an automated electrophoresis platform performing cfDNA quantification with region analysis. Moreover, the results include a score to qualify cfDNA samples according to their contamination level with high molecular weight material. This allows defining a threshold for objective sample qualification prior to library preparation. The analysis features are described with examples of typical sample patterns. Citation Format: Eva Graf. Sample quality control of cell-free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3529.

Abstract 3190: Standardization and clinical implementation of liquid biopsy assays - IMI's CANCER-ID

Abstract The Innovative Medicines Initiative (IMI) project CANCER-ID (www.cancer-id.eu) is a 5 year (2015-2019) international public-private partnership of currently 40 partners from 14 countries with the aim to evaluate technologies for Circulating Tumor Cell (CTC), circulating free tumor DNA (ctDNA), microRNA (miRNA) and exosome enrichment, isolation and analysis. At the core of CANCER-ID’s activities are establishment of harmonized best practice protocols from patient sample collection, pre-analytical sample handling, sample and bioinformatics analyses down to the actionable information guiding patient selection and personalized treatment. CANCER-ID is furthermore testing and supporting development of standards for liquid biopsy as well as clinical implementation of liquid biopsy based protocols in the clinical setting. This includes interaction with regulatory bodies in Europe (EMA Innovation Task Force) and the US (FDA Public-Private Partnership liaison) to support future approval of liquid biopsies in multi-centered worldwide clinical studies. During the clinical validation phase of the project, clinical-ready liquid biopsy protocols have been implemented in an observational study on the potential predictive value of monitoring treatment response towards Immune Checkpoint Inhibition (ICI) in 180 NSCLC patients at the UMC Groningen, The Netherlands, as well as in two ICI-chemotherapy combination studies in Triple-Negative Breast Cancer and Luminal B-type breast cancer, respectively, run by the University of Oslo, Norway (ALICE NCT03164993 and ICON NCT03409198). Within both studies, blood has been collected at baseline and at follow-up visits for ctDNA and CTC analysis, including technical evaluation of CTC PD-L1 protein expression. The aim is to assess whether the allelic frequency of mutations identified by plasma NGS as a potential measure for Tumor Mutational Burden or the number of PD-L1–positive/overall CTCs at different time points is indicative of treatment success. The studies aim at providing data to assess whether clinical predictive information could be inferred from baseline number of detected mutations and PD-L1 expressing CTCs. Preliminary data of these analyses will be presented. As a follow-up activity of the IMI CANCER-ID program, the European Liquid Biopsy Society (ELBS) is currently being established by Prof. Pantel at UKE Hamburg, Germany. The ELBS will be open to all interested liquid biopsy stakeholders worldwide as a platform for scientific exchange, further efforts to standardize technologies and protocols in the field as well as for the initiation of new basic and clinical research projects with the aim to make liquid biopsies an integral part of clinical studies and patient care. This work is supported by IMI JU & EFPIA (grant no. 115749, CANCER-ID). Samples from patients and healthy volunteers, respectively, were collected under signed informed consent. Citation Format: Klaus Pantel, Leon W. Terstappen, Nicolò Manaresi, Harry J. Groen, Ed M. Schuuring, Ellen Heitzer, Michael Speicher, Bjørn Naume, Jon Amund Kyte, Thomas Schlange, for the IMI CANCER-ID consortium. Standardization and clinical implementation of liquid biopsy assays - IMI's CANCER-ID [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3190.

Determination of endocannabinoids and endocannabinoid-like substances in human K3EDTA plasma – LC-MS/MS method validation and pre-analytical characteristics

The determination of endocannabinoids and endocannabinoid-like substances in biological human samples is a vibrant field of research with great significance due to postulated relevance of these substances in diseases such as Alzheimer's disease, multiple sclerosis, cancer and cardiovascular diseases. For a possible use as biomarker in early prediction or diagnosis of a disease as well as examination of a successful treatment, the valid determination of the analytes in common accessible human samples, such as plasma or serum, is of great importance.A method for the determination of arachidonoyl ethanolamide, oleoyl ethanolamide, palmitoyl ethanolamide, 1-arachidonoyl glycerol and 2-arachidonoyl glycerol in human K3EDTA plasma using liquid-liquid-extraction in combination with liquid chromatography-tandem-mass spectrometry has been developed and validated for the quantification of the aforementioned analytes. Particular emphasis was placed on the chromatographic separation of the isomers 1-arachidonoyl glycerol and 2-arachidonoyl glycerol, arachidonoyl ethanolamide and O-arachidonoyl ethanolamine (virodhamine) as well as oleoyl ethanolamide and vaccenic acid ethanolamide.During the validation process, increasing concentrations of 1-arachidonoyl glycerol and 2-arachidonoyl glycerol while storing plasma samples were observed. In-depth investigation of pre-analytical sample handling revealed rising concentrations for both analytes in plasma and for arachidonoyl ethanolamide, oleoyl ethanolamide and palmitoyl ethanolamide in whole blood, dependent on the period and temperature of storage. Prevention of the increase in concentration was not possible, raising the question whether human K3EDTA plasma is suitable for the determination of endocannabinoids and endocannabinoid-like substances. Especially the common practice to calculate the concentration of 2-arachidonoyl glycerol as sum of 1-arachidonoyl glycerol and 2-arachidonoyl glycerol is highly questionable because the concentrations of both analytes increase unequally while storing the plasma samples in the fridge.

Impact of Pre-Analytical Differences on Biomarkers in the ADNI and PPMI Studies: Implications in the Era of Classifying Disease Based on Biomarkers.

Neurodegenerative diseases require characterization based on underlying biology using biochemical biomarkers. Mixed pathology complicates discovery of biomarkers and characterization of cohorts, but inclusion of greater numbers of patients with different, related diseases with frequently co-occurring pathology could allow better accuracy. Combining cohorts collected from different studies would be a more efficient use of resources than recruiting subjects from each population of interest for each study. To explore the possibility of combining existing datasets by controlling pre-analytic variables in the Alzheimer's Disease Neuroimaging Initiative (ADNI) and Parkinson's Progression Markers Initiative (PPMI) studies. Cerebrospinal fluid (CSF) was collected and processed from 30 subjects according to both the ADNI and PPMI protocols. Relationships between reported levels of Alzheimer's disease (AD) and Parkinson's disease (PD) biomarkers in the same subject under each protocol were examined. Protocol-related differences were observed for Aβ, but not t-tau or α-syn, and trended different for p-tau and pS129. Values of α-syn differed by platform. Conversion of α-syn values between ADNI and PPMI platforms did not completely eliminate differences in distribution. Factors not captured in the pre-analytical sample handling influence reported biomarker values. Assay standardization and better harmonized characterization of cohorts should be included in future studies of CSF biomarkers.

European survey on preanalytical sample handling - Part 1: How do European laboratories monitor the preanalytical phase? On behalf of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) Working Group for the Preanalytical Phase (WG-PRE).

IntroductionCompared to other activities of the testing process, the preanalytical phase is plagued by a lower degree of standardization, which makes it more vulnerable to errors. With the aim of providing guidelines and recommendations, the EFLM WG-PRE issued a survey across European medical laboratories, to gather information on local preanalytical practices. This is part one of two coherent articles, which covers all practices on monitoring preanalytical quality except haemolysis, icterus and lipemia (HIL).Materials and methodsAn online survey, containing 39 questions dealing with a broad spectrum of preanalytical issues, was disseminated to EFLM member countries. The survey included questions on willingness of laboratories to engage in preanalytical issues.ResultsOverall, 1405 valid responses were received from 37 countries. 1265 (94%) responders declared to monitor preanalytical errors. Assessment, documentation and further use of this information varied widely among respondents and partially among countries. Many responders were interested in a preanalytical online platform, holding information on various aspects of the preanalytical phase (N = 1177; 87%), in a guideline for measurement and evaluation of preanalytical variables (N = 1235; 92%), and in preanalytical e-learning programs or webinars (N = 1125; 84%). Fewer responders were interested in, or already participating in, preanalytical EQA programs (N = 951; 71%).ConclusionAlthough substantial heterogeneity was found across European laboratories on preanalytical phase monitoring, the interest in preanalytical issues was high. A large majority of participants indicated an interest in new guidelines regarding preanalytical variables and learning activities. This important data will be used by the WG-PRE for providing recommendations on the most critical issues.

European survey on preanalytical sample handling - Part 2: Practices of European laboratories on monitoring and processing haemolytic, icteric and lipemic samples. On behalf of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) Working Group for the Preanalytical Phase (WG-PRE).

IntroductionNo guideline currently exists on how to detect or document haemolysis, icterus or lipemia (HIL) in blood samples, nor on subsequent use of this information. The EFLM WG-PRE has performed a survey for assessing current practices of European laboratories in HIL monitoring. This second part of two coherent articles is focused on HIL.Materials and methodsAn online survey, containing 39 questions on preanalytical issues, was disseminated among EFLM member countries. Seventeen questions exclusively focused on assessment, management and follow-up actions of HIL in routine blood samples.ResultsOverall, 1405 valid responses from 37 countries were received. A total of 1160 (86%) of all responders stating to analyse blood samples - monitored HIL. HIL was mostly checked in clinical chemistry samples and less frequently in those received for coagulation, therapeutic drug monitoring and serology/infectious disease testing. HIL detection by automatic HIL indices or visual inspection, along with haemolysis cut-offs definition, varied widely among responders. A quarter of responders performing automated HIL checks used internal quality controls. In haemolytic/icteric/lipemic samples, most responders (70%) only rejected HIL-sensitive parameters, whilst about 20% released all test results with general comments. Other responders did not analysed but rejected the entire sample, while some released all tests, without comments. Overall, 26% responders who monitored HIL were using this information for monitoring phlebotomy or sample transport quality.ConclusionStrategies for monitoring and treating haemolytic, icteric or lipemic samples are quite heterogeneous in Europe. The WG-PRE will use these insights for developing and providing recommendations aimed at harmonizing strategies across Europe.

Post-mortem biochemistry differences between vitreous humour and cerebrospinal fluid

ABSTRACT Cerebrospinal fluid (CSF) and vitreous humour (VH) can be biochemically analysed post-mortem. CSF can be aspirated from the ventricular system (VA) and from lumbar puncture (LP), whereas, VH is aspirated from the orbits. This study compared the biochemical constituents between CSF and VH in 20 post-mortem subjects as well as the effect post-mortem interval and subject age have on these variables. VH samples had significantly higher sodium (Na) and chloride (Cl) and lower magnesium (Mg), potassium (K), urea (Ur) and creatinine (Cr) compared with CSF samples. No statistically significant difference was demonstrated with beta-hydroxybutyrate (BHB) and glucose levels in both VH and both CSF samples. Interestingly, some of the differences in the biochemical analysis correlated with age, but none with post-mortem interval. In addition to sampling and pre-analytical sample processing differences, there may also be ante- and post-mortem factors explaining these observations. This study suggests that post-mortem CSF and VH are biochemically different and reference ranges for VH are not recommended for use in CSF samples.

Preanalytical sample handling recommendations for Alzheimer's disease plasma biomarkers

IntroductionWe examined the influence of common preanalytical factors on the measurement of Alzheimer's disease–specific biomarkers in human plasma. MethodsAmyloid β peptides (Aβ[1-40], Aβ[1-42]) and total Tau plasma concentrations were quantified using fully automated Roche Elecsys assays. ResultsAβ(1-40), Aβ(1-42), and total Tau plasma concentrations were not affected by up to three freeze/thaw cycles, up to five tube transfers, the collection tube material, or the size; circadian rhythm had a minor effect. All three biomarkers were influenced by the anticoagulant used, particularly total Tau. Aβ concentrations began decreasing 1 hour after blood draw/before centrifugation and decreased by up to 5% and 10% at 2 and 6 hours, respectively. For separated plasma, time to measurement influenced Aβ levels by up to 7% after 6 hours and 10% after 24 hours. DiscussionOur findings provide guidance for standardizing blood sample collection, handling, and storage to ensure reliable analysis of Alzheimer's disease plasma biomarkers in routine practice and clinical trials.

Corrigendum: Akkermansia muciniphila as a Model Case for the Development of an Improved Quantitative RPA Microbiome Assay.

[This corrects the article DOI: 10.3389/fcimb.2018.00237.].

New tools for pathology: a user's review of a highly multiplexed method for in situ analysis of protein and RNA expression in tissue.

Tumor cell heterogeneity and tumor cell-stromal interactions are being explored as determinants of disease progression and treatment resistance in solid tumor and hematological malignancies. As such, tools simultaneously capable of highly multiplexed profiling of tissues' protein and RNA content, as well as interrogation of rare or single cells, are required to precisely characterize constituent tumor cell populations, infiltrating lymphocytes and stromal elements. Access to spatial relationships will enable more precise characterization of tumors, support patient stratification and may help to identify novel drug targets. Multiple platforms are being developed to address these critical unmet needs. The NanoString digital spatial profiling (DSP) platform enables highly multiplexed, spatial assessment of protein and/or RNA targets in tissues by detecting oligonucleotide barcodes conjugated via a photocleavable linker to primary antibodies or nucleic acid probes. Although this platform enables high-dimensional spatial interrogation of tissue protein and RNA expression, a detailed understanding of its composition, function and chemistry is advisable to guide experimental design and data interpretation. The purpose of this review is to provide an independent, comprehensive description of the DSP technology, including an overview of NanoString's capture and antibody barcode conjugation chemistries, experimental workflow, data output and analysis methods. The DSP technology will be discussed in the context of other highly multiplexed immunohistochemistry methods, including imaging mass cytometry and multiplexed ion beam imaging, to inform potential users of the advantages and limitations of each. Additional issues such as preanalytical variability, sampling and specimen adequacy will be considered with respect to the platforms to inform potential experimental design. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Faecal calprotectin determination: impact of preanalytical sample treatment and stool consistency on within- and between-method variability.

IntroductionWe assessed the differences in faecal calprotectin (FC) concentrations measured by two assays depending on the stool consistency and extraction method.Materials and methodsStool samples were extracted using the EliA Stool Extraction Kit, Calex® Cap extraction device and respective weighing methods, while FC concentrations were measured using the EliATM Calprotectin and Bühlmann fCAL® Turbo method and checked for within- and between-method variability with regard to extraction method and stool consistency category. Extraction yield was evaluated for impact of different sample incubation time (10 min and 1 h) in extraction buffer for both methods and for impact of different initial sample dilutions (1:50, 1:100, 1:500) for fCAL® Turbo method.ResultsResults determined from Calex® Cap extracts were higher compared to weighing method extracts (mean bias 33.3%; P < 0.001), while no significant difference was found between results obtained with EliA Stool Extraction Kit and weighing method (mean bias 0.1%; P = 0.484), in both cases irrespective of stool consistency. Bühlmann fCAL® Turbo results were higher than EliATM Calprotectin results (mean bias 32.3%, P = 0.025 weighing method; and mean bias 53.9%, P < 0.001 extraction devices), the difference is dependent on stool consistency and FC concentration. Significantly higher FC extraction yield was obtained with longer sample incubation time for both methods (P = 0.019 EliATM Calprotectin; P < 0.001 fCAL® Turbo) and with increasing initial sample dilution for fCAL® Turbo method (P < 0.001).ConclusionPreanalytical stool sample handling proved to be a crucial factor contributing to within- and between-FC assay variability. Standardization is urgently needed in order to assure comparable and reliable FC results.

Plasma free DNA: Evaluation of temperature-associated storage effects observed for Roche Cell-Free DNA collection tubes.

IntroductionStandardized pre-analytical blood sample procedures for the analysis of circulating cell-free DNA (ccfDNA) are still not available. Therefore, the present study aimed at evaluating the impact of storage conditions related to different times (24 and 48 h) and temperatures (room temperature (RT) and 4 - 8 °C) on the plasma ccfDNA concentration of blood samples drawn into Cell-Free DNA collection tubes (Roche Diagnostics GmbH, Mannheim, Germany).Materials and methodsVenous blood from 30 healthy individuals was collected into five 8.5 mL Cell-Free DNA Collection Tubes (Roche Diagnostics GmbH) each. Plasma samples were processed at time point of blood collection (tube 1), and after storage under the following conditions: 24 h at RT (tube 2) or 4-8 °C (tube 3), and 48 h at RT (tube 4) or 4 - 8 °C (tube 5). Circulating cell-free DNA concentrations were determined by EvaGreen chemistry-based droplet digital PCR (ddPCR).ResultsNo statistically significant differences between median (interquartile range) plasma ccfDNA concentrations (ng/mL) at time point of blood collection (3.17 (2.13 – 3.76)) and after storage for 24 h (RT: 3.02 (2.41 – 3.68); 4-8 °C: 3.21 (2.19 – 3.46)) and 48 h (RT: 3.13 (2.10 – 3.76); 4-8 °C: 3.09 (2.19 – 3.50)) were observed (P values from 0.102 – 0.975).ConclusionsNo unwanted release of genomic DNA from white blood cells could be detected in plasma samples after tube storage for 24 and 48 h regardless of storage temperature.

Effects of Biological Materials and Collection Media on PCR Detection of &amp;lt;i&amp;gt;Tritrichomonas foetus&amp;lt;/i&amp;gt;

Tritrichomonas foetus is an important pathogen of the bovine reproductive tract causing early embryonic death and abortion in cows and persistent, asymptomatic infection in bulls. PCR detection methods have greatly enhanced diagnostic accuracy over culture; however, pre-analytical sample handling is just as critical as technical performance in detecting this pathogen and is not well studied. The purpose of this study was to investigate the effects of biological materials present in the prepuce on PCR detection of T. foetus in a variety of collection media. Simulated preputial samples were created using InPouchTM (IP) media, lactated ringers solution (LRS), or sterile saline (SAL); inoculated with low numbers of one of three T. foetus strains; and spiked with either blood, semen, urine, or sham treatment. Samples were transported to the lab, placed in growth media (LRS and SAL samples), incubated, and tested for T. foetus by PCR. Samples containing urine had statistically significantly greater mean Ct values (P = 0.008) than samples containing other materials, seen most dramatically in IP (P < 0.0001.) Urine contamination resulted in significantly (P = 0.037) fewer samples being identified as “positive” for T. foetus. Overall, SAL collections also had significantly higher mean Ct than IP or LRS (P < 0.001), and were less likely (P = 0.018) to results in classification as a “positive” sample. Results of this study indicate that collection media and biological materials can affect T. foetus PCR detection. The presence of urine in preputial samples can result in false negative results, while blood had no detrimental effects.

Mass spectrometry based analytical quality assessment of serum and plasma specimens with patterns of endo- and exogenous peptides.

Background Inappropriate preanalytical sample handling is a major threat for any biomarker discovery approach. Blood specimens have a genuine proteolytic activity that leads to a time dependent decay of peptidic quality control markers (QCMs). The aim of this study was to identify QCMs for direct assessment of sample quality (DASQ) of serum and plasma specimens. Methods Serum and plasma specimens of healthy volunteers and tumor patients were spiked with two synthetic reporter peptides (exogenous QCMs) and aged under controlled conditions for up to 24 h. The proteolytic fragments of endogenous and exogenous QCMs were monitored for each time point by mass spectrometry (MS). The decay pattern of peptides was used for supervised classification of samples according to their respective preanalytical quality. Results The classification accuracy for fresh specimens (1 h) was 96% and 99% for serum and plasma specimens, respectively, when endo- and exogenous QCMs were used for the calculations. However, classification of older specimens was more difficult and overall classification accuracy decreased to 79%. Conclusions MALDI-TOF MS is a simple and robust method that can be used for DASQ of serum and plasma specimens in a high throughput manner. We propose DASQ as a fast and simple step that can be included in multicentric large-scale projects to ensure the homogeneity of sample quality.

Trio-R: a script for assessing maternity and paternity in trio studies performed on Agilent chromosomal microarrays

BackgroundTrio studies, which involve the testing of samples from a proband and both parents, are often used by clinical laboratories to help with the classification of genetic variants, including copy number variants. In order for the results of the trio study to be valid, the mother and father must be the true biological parents of the proband. As such, non-paternity and sample mix-ups are potential sources of error. To address these potential issues, we developed a computer script to accurately assess maternity and paternity using single nucleotide polymorphism (SNP) data generated by Agilent chromosomal microarrays, a platform-of-choice for clinical copy number testing.ResultsWe assessed the performance of the script on 10 putative trios tested at our laboratory, and found that the numbers and proportions of discordant SNPs were useful for determining parental relationships. The results of the assessment also confirmed maternity and paternity in the 10 trios tested, and by doing so essentially excluded pre-analytical sample switching in these 30 samples.ConclusionsComputational analysis of SNP data can be implemented as a quality control measure for trio testing performed on Agilent microarrays.

Plasma lactate measurement as an example of encountered gaps between routine clinical laboratory processes and manufactures' sample-handling instructions

ObjectivesDeviation from manufacturers’ pre-analytical sample handling recommendations necessitates extensive validation studies. This report uses plasma lactate testing, where a recommended 15 min room temperature sample handling limit cannot be met by the clinical laboratory, as an example for studies to bridge the gap with practice. Design and MethodsTriplicate blood samples were collected from patients (n = 51) with lactate requests by clinicians and from normal volunteers (n = 50). One tube was transported on ice (4 °C), the others were maintained at room temperature (23 °C). Tubes stored at 4 °C were processed at 30 min from collection. Tubes stored at 23 °C were processed at 15 and at 30 min from collection. Lactate levels were measured using Roche Diagnostics Cobas 6000® analyzer. ResultsLactate levels in normal subjects ranged from 0.6 to 3.1 mmol/L (median 1.1). Patient lactate levels ranged from 0.8 to 26.3 mmol/L (median 2.2). Bias in lactate levels following extended storage of samples from both normal subjects and patients ranged from − 1.3 to2.2 and from − 1.0–1.0 mmol/L when stored for 30 min at 23 °C or at 4 °C, respectively. The bias between lactate levels at 30 min at 23 °C and 4 °C was − 1.2 to − 0.5 mmol/L for both populations. Although the bias was not statistically significant for all variables, a clinically significant (>0.2 mmol/L) bias was observed in 28% of normal and 7.0% of patient samples. ConclusionExtending the pre-analytical time to 30 min at 23 °C did not significantly impact clinical utility of lactate measurement in our patient population.

Retrospective study showed that blood sampling errors risked children's well-being and safety in a Swedish paediatric tertiary care.

Blood analyses containing preanalytical errors (PAEs) are hazardous for patients. This study investigated the frequency of PAEs in blood analysis and the corresponding quality indicators of the sampling process in Swedish paediatric tertiary care. Data were retrieved from the laboratory at Astrid Lindgren Children's Hospital between 2013 and 2014. Preanalytical blood sampling performance was analysed according to the Six Sigma scale, ranging from 0 to 6 (933137-3.4 defects per million [DPM]). Of the 1148716 analyses, 61656 (5.4%) were rejected due to PAEs. The PAEs ranged between hospital specialities from 1.9 to 9.4% (p<0.001) and work shift times, from 6.0% in the day to 5.7% in the evening and 4.3% at night (p values <0.001). Clotting was the most prominent error (51.3%), affecting mostly haematology and coagulation analyses. Incorrectly filled samples represented almost 25% of all PAEs, with effects on chemistry, haematology and coagulation analyses. The sigma score for the overall preanalytical phase (3.2) corresponded to 44565 DPM. Samples with PAEs were frequently clotted and insufficiently filled, and the distribution of errors varied within working shifts and specific analyses. The overall quality control in paediatric blood sampling was barely acceptable.

Analytical performance evaluation of the new GEM® Premier™ 5000 analyzer in comparison to the GEM® Premier™ 4000 and the RapidPoint® 405 systems

Aim of the studyBlood gas analysis (BGA) is essential for the diagnosis and management of acid-base imbalances. We evaluated and compared the analytical characteristics of the new GEM® Premier™ 5000 (GP5000) (Instrumentation Laboratory, Bedford, MA, United States) BGA point-of-care (POC) device with those of the GEM® Premier™ 4000 (GP4000) (Instrumentation Laboratory, Bedford, MA, United States) and RapidPoint® 405 (RP405) (Siemens Healthcare, Milan, Italy) POC analyzers. The effect of sample mixing on patient results was also studied. Material and methodsQuantitative measurement of pH, pCO2, pO2, Na+, K+, Cl−, iCa2+, glucose, lactate, tHb, COHb, MetHb, O2Hb, HHb and Hct were carried out. The imprecision study (IS) and method comparison study (MS) were performed according to CLSI EP guidelines, using respectively internal as well as external quality controls (IS) and whole blood samples collected from the routine analysis (MS). ResultsGP5000 demonstrated satisfactory characteristics in the IS showing comparable (GM4000) or even better (RP405) imprecision results than the routine POC devices. Good performance was observed in the MS both using GP4000 and RP405 as reference instruments. Pre-analytical sample management can heavily affect the accuracy of BGA results. In the specimen mixing evaluation, a significant improvement in results accuracy was observed when mixing procedures were more meticulous. ConclusionsConsidering the overall analytical performance observed, the ease of use of the system, the rapid time-to-results and the innovative Intelligent Quality Management technology (iQM2®), GP5000 seems suitable to be used in clinical care for safe patient management. Additionally, effective sample mixing upon draw and before analysis is strongly advisable in order to ensure the most clinically reliable BGA results.

Akkermansia muciniphila as a Model Case for the Development of an Improved Quantitative RPA Microbiome Assay.

Changes in the population levels of specific bacterial species within the gut microbiome have been linked to a variety of illnesses. Most assays that determine the relative abundance of specific taxa are based on amplification and sequencing of stable phylogenetic gene regions. Such lab-based analysis requires pre-analytical sample preservation and storage that have been shown to introduce biases in the characterization of microbial profiles. Recombinase polymerase amplification (RPA) is an isothermal nucleic acid amplification method that employs commercially available, easy-to-use freeze-dried enzyme pellets that can be used to analyze specimens rapidly in the field or clinic, using a portable fluorometer. Immediate analysis of diverse bacterial communities can lead to a more accurate quantification of relative bacterial abundance. In this study, we discovered that universal bacterial 16S ribosomal DNA primers give false-positive signals in RPA analysis because manufacturing host Escherichia coli DNA is present in the RPA reagents. The manufacturer of RPA reagents advises against developing an RPA assay that detects the presence of E. coli due to the presence of contaminating E. coli DNA in the reaction buffer (www.twistdx.co.uk/). We, therefore, explored four strategies to deplete or fragment extraneous DNA in RPA reagents while preserving enzyme activity: metal-chelate affinity chromatography, sonication, DNA cleavage using methylation-dependent restriction endonucleases, and DNA depletion using anti-DNA antibodies. Removing DNA with anti-DNA antibodies enabled the development of a quantitative RPA microbiome assay capable of determining the relative abundance of the physiologically-important bacterium Akkermansia muciniphila in human feces.

Abstract 5587: Sample quality control of cell-free DNA

Abstract Sequencing of cell-free DNA (cfDNA) extracted from blood specimens or other body fluids is possible due to the establishment of low input library protocols for next-generation sequencing workflows. Accurate quantification of cfDNA samples is essential to determine suitable input amounts for cfDNA library preparation prior to sequencing. The main component of cfDNA samples is the mononucleosome with a size around 170 bp, sometimes with additional species representing nucleosome multimers. Further, cfDNA samples may contain larger DNA fragments dependent on the donor's health status, preanalytical sample treatment, or extraction method. High molecular weight material can negatively influence library preparation and subsequently result in lower sequencing depth. Therefore, reliable quantification of cfDNA requires a method that separates DNA fragments by size, such as electrophoresis. This poster shows the use of a new cfDNA assay for the 2100 Bioanalyzer system as an add-on for the High Sensitivity DNA assay. The assay enables automated cfDNA quantification with pre-defined regions. Moreover, the results include sample purity as a score to qualify cfDNA samples according to their contamination level with high molecular weight material. The features of the assay are described with examples of typical sample patterns. Citation Format: Melissa H. Liu, Eva Graf. Sample quality control of cell-free DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5587.