Plasma lipids paediatric reference intervals: Indirect estimation using a large 14-year database

OBJECTIVES

Establishing direct reference intervals (RIs) for paediatric patients is a very challenging endeavour. Indirect RIs can address this problem, using existing clinical laboratory databases from real-world data research. Compared to the traditional direct method, the indirect approach is highly practical, widely applicable, and low-cost. Considering the relevance of dyslipidemia in the paediatric age, to provide better laboratory services to the local paediatric population, we established population-specific lipid RIs via data mining.

METHODS

Our laboratory information system was searched for cholesterol (TC), triglycerides (TG), low-density lipoprotein (LDL) and high-density lipoprotein (HDL) of patients aged less than 18 years, performed from January 2009 until December 2022. RIs were estimated using RefineR algorithm.

RESULTS

Values from 215,594 patients were initially collected. After refining data on the basis of specific exclusion criteria that left 17,933 patients, we determined the RIs for each analyte, including corresponding 95% confidence interval (95% CI). Age and sex partitions were required for proper stratification of the heterogenous subpopulations. Age-related variations in TC and TG values were observed mainly in children until 5 years. RIs were defined for children less than 3 years and for those of 3-18 years. In our population, the obtained RIs were comparable with those of the literature, but the upper TG limit in subjects under the age of 3 (2.03 mmol/L with 95% CI: 1.45-2.86) was lower than that previously reported.

CONCLUSIONS

Our RIs, necessary for paediatric lipid monitoring, are tailored to the serviced patient population as should be done whenever possible.

Quality indicators in laboratory medicine: state-of-the-art, quality specifications and future strategies

In the last few decades, quality in laboratory medicine has evolved in concert with the transformation and the changes (technological, scientific and organizational) in this sector. Laboratory professionals have faced great challenges, at times being overwhelmed, yet also involved in this progress. Worldwide, laboratory professionals and scientific societies involved in laboratory medicine have raised awareness concerning the need to identify new quality assurance tools that are effective in reducing the error rate and enhancing patient safety, in addition to Internal Quality Control (IQC) procedures and the participation in the External Quality Assessment Schemes (EQAS). The use of Quality Indicators (QIs), specifically designed for laboratory medicine are effective in assessing and monitoring all critical events occurring in the different phases of Total Testing Process (TTP), in particular, in the extra-analytical phases. The Model of Quality Indicators (MQI), proposed by the Working Group "Laboratory Errors and Patient Safety" (WG-LEPS) of the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) and validated by experts in consensus conferences, is an important window of opportunity for the medical laboratory to demonstrate the use of an effective quality assurance tool fit for this purpose. Aim of this paper is to provide an update of the state-of-the-art concerning the most used QIs data collected in 2021 and the Quality Specifications (QSs) proposed for their evaluation. Moreover, a strategy for the future is proposed in order to improve the MQI and encourage its use in medical laboratories throughout the world.

New insights into SARS-CoV-2 Lumipulse G salivary antigen testing: accuracy, safety and short TAT enhance surveillance

OBJECTIVES

The rapid, accurate and safe detection of SARS-CoV-2 is the key to improving surveillance and infection containment. The aim of the present study was to ascertain whether, after heat/chemical inactivation, SARS-CoV-2 N antigen chemiluminescence (CLEIA) assay in saliva remains a valid alternative to molecular testing.

METHODS

In 2022, 139 COVID-19 inpatients and 467 healthcare workers were enrolled. In 606 self-collected saliva samples (Salivette), SARS-CoV-2 was detected by molecular (TaqPath rRT-PCR) and chemiluminescent Ag assays (Lumipulse G). The effect of sample pre-treatment (extraction solution-ES or heating) on antigen recovery was verified.

RESULTS

Salivary SARS-CoV-2 antigen assay was highly accurate (AUC=0.959, 95% CI: 0.943-0.974), with 90% sensitivity and 92% specificity. Of the 254 antigen positive samples, 29 were false positives. We demonstrated that heterophilic antibodies could be a cause of false positive results. A significant antigen concentration decrease was observed after ES treatment (p=0.0026), with misclassification of 43 samples. Heat had a minimal impact, after treatment the correct classification of cases was maintained.

CONCLUSIONS

CLEIA SARS-CoV-2 salivary antigen provides accurate, timely and high-throughput results that remain accurate also after heat inactivation, thus ensuring a safer work environment. This supports the use of salivary antigen detection by CLEIA in surveillance programs.

Salivary proteomic analysis in asymptomatic and symptomatic SARS-CoV-2 infection: Innate immunity, taste perception and FABP5 proteins make the difference

BACKGROUND AND AIM

SARS-CoV-2 infection spawns from an asymptomatic condition to a fatal disease. Age, comorbidities, and several blood biomarkers are associated with infection outcome. We searched for biomarkers by untargeted and targeted proteomic analysis of saliva, a source of viral particles and host proteins.

METHODS

Saliva samples from 19 asymptomatic and 16 symptomatic SARS-CoV-2 infected subjects, and 20 controls were analyzed by LC-MS/MS for untargeted peptidomic (flow through of 10 kDa filter) and proteomic (trypsin digestion of filter retained proteins) profiling.

RESULTS

Peptides from 53 salivary proteins were identified. ADF was detected only in controls, while IL1RA only in infected subjects. PRPs, DSC2, FABP5, his-1, IL1RA, PRH1, STATH, SMR3B, ANXA1, MUC7, ACTN4, IGKV1-33 and TGM3 were significantly different between asymptomatic and symptomatic subjects. Retained proteins were 117, being 11 highly different between asymptomatic and symptomatic (fold change ≥2 or ≤-2). After validation by LC-MS/MS-SRM (selected reaction monitoring analysis), the most significant discriminant proteins at PCA were IL1RA, CYSTB, S100A8, S100A9, CA6, and FABP5.

CONCLUSIONS

The differentially abundant proteins involved in innate immunity (S100 proteins), taste (CA6 and cystatins), and viral binding to the host (FABP5), appear to be of interest for use as potential biomarkers and drugs targets.

Hyris bCUBE SARS-CoV-2 rapid molecular saliva testing: a POCT innovation on its way

OBJECTIVES

The reliable identification of individuals with SARS-CoV-2 infection is the cornerstone for containing viral spread. Rapid molecular point-of-care testing (POCT) of saliva might reduce analysis time, thus increasing the efficacy of contact tracing. In this study, a new POCT RT-PCR assay for the detection of SARS-CoV-2 RNA in saliva was evaluated and compared with an already validated CE-IVD method.

METHODS

An evaluation was made of 160 left-over salivary samples (27 frozen, kept at -80 °C and 133 fresh), collected using Salivette (Sarstedt, Germany). Samples were analyzed by TaqPath COVID-19 CE-IVD RT-PCR kit, QuantStudio5 Real-Time (Applied Biosystems, USA) (TaqPath) and bKIT Virus Finder COVID-19 Saliva (Hyris Global Diagnostics, Italy). Performances of three- and fivefold pooling strategies were also evaluated. Blood assay interference in saliva was also tested with Hyris.

RESULTS

On using TaqPath, SARS-CoV-2 positivity was detected in 35 samples. Another 10 positive samples were artificially-generated by blind mixing of positive with negative samples. Hyris positive and negative percentages of agreement were 97.6 (95% CI: 87.2-99.9%) and 100 (95% CI: 97.0-100%), respectively. Seventeen positive pools, evaluated for threefold strategy, were all correctly determined by both systems. For the 5-pool strategy, 94.7% (18/19) of samples resulted positive with the Hyris system, and 100% with TaqPath. The presence of 1% of blood (v/v) in saliva did not interfere with the accuracy of Hyris assay.

CONCLUSIONS

The sensitivity and specificity of the bKIT Virus Finder COVID-19 Saliva were optimal with respect to TaqPath. In view of the safe and straightforward pre-analytical procedure involved, and the small size of the Hyris bCube, the Hyris system can be used for POCT.

The University of Padua salivary-based SARS-CoV-2 surveillance program minimized viral transmission during the second and third pandemic wave

BACKGROUND

The active surveillance of students is proposed as an effective strategy to contain SARS-CoV-2 spread and prevent schools' closure. Saliva for molecular testing is as sensitive as naso-pharyngeal swab (NPS), self-collected and well accepted by participants. This prospective study aimed to verify whether the active surveillance of the Padua University employees by molecular testing of self-collected saliva is an effective and affordable strategy for limiting SARS-CoV-2 spread.

METHODS

A surveillance program based on self-collection of saliva every 2 weeks (October 2020-June 2021) was conducted. Among 8183 employees of the Padua University, a total of 6284 subjects voluntarily took part in the program. Eight collection points guaranteed the daily distribution and collection of barcoded salivary collection devices, which were delivered to the laboratory by a transport service for molecular testing. Quarantine of positive cases and contact tracing were promptly activated.

RESULTS

Among 6284 subjects, 206 individuals were SARS-CoV-2 positive (99 by salivary testing; 107 by NPS performed for contact tracing or symptoms). The cumulative SARS-CoV-2 incidence in this cohort was 3.1%, significantly lower than that of employees not in surveillance (8.0%), in Padua (7.1%) and in the Veneto region (7.2%). Employees with positive saliva results were asymptomatic or had mild symptoms. The levels of serum antibodies after 3 months from the infection were correlated with age and Ct values, being higher in older subjects with greater viral loads.

CONCLUSIONS

Salivary-based surveillance with contact tracing effectively allowed to limit SARS-CoV-2 contagion, also in a population with a high incidence.

Salivary SARS-CoV-2 antigen rapid detection: A prospective cohort study

Background and aim

SARS-CoV-2 quick testing is relevant for the containment of new pandemic waves. Antigen testing in self-collected saliva might be useful. We compared salivary and naso-pharyngeal swab (NPS) SARS-CoV-2 antigen detection by a rapid chemiluminescent assay (CLEIA) and two different point-of-care (POC) immunochromatographic assays, with results of molecular testing.

Methods

234 patients were prospectively enrolled. Paired self-collected saliva (Salivette) and NPS were obtained to perform rRT-PCR, chemiluminescent (Lumipulse G) and POC (NPS: Fujirebio and Abbott; saliva: Fujirebio) for SARS-CoV-2 antigen detection.

Results

The overall agreement between NPS and saliva rRT-PCR was 78.7%, reaching 91.7% at the first week from symptoms. SARS-CoV-2 CLEIA antigen was highly accurate in distinguishing positive and negative NPS (ROC-AUC = 0.939, 95%CI:0.903–0.977), with 81.6% sensitivity and 93.8% specificity. This assay on saliva reached the optimal value within 7 days from symptoms onset (Sensitivity: 72%; Specificity: 97%). Saliva POC antigen was limited in sensitivity (13%), performing better in NPS (Sensitivity: 48% and 66%; Specificity: 100% and 99% for Espline and Abbott respectively), depending on viral loads.

Conclusions

Self-collected saliva is a valid alternative to NPS for SARS-CoV-2 detection by molecular, but also by CLEIA antigen testing, which is therefore potentially useful for large scale screening.

SARS-CoV-2 RNA identification in nasopharyngeal swabs: issues in pre-analytics

Objectives

The direct identification of SARS-CoV-2 RNA in nasopharyngeal swabs is recommended for diagnosing the novel COVID-19 disease. Pre-analytical determinants, such as sampling procedures, time and temperature storage conditions, might impact on the end result. Our aim was to evaluate the effects of sampling procedures, time and temperature of the primary nasopharyngeal swabs storage on real-time reverse-transcription polymerase chain reaction (rRT-PCR) results.

Methods

Each nasopharyngeal swab obtained from 10 hospitalized patients for COVID-19 was subdivided in 15 aliquots: five were kept at room temperature; five were refrigerated (+4 °C); five were immediately mixed with the extraction buffer and refrigerated at +4 °C. Every day and for 5 days, one aliquot per condition was analyzed (rRT-PCR) for SARS-CoV-2 gene E and RNaseP and threshold cycles (Ct) compared. To evaluate manual sampling, 70 nasopharyngeal swabs were sampled twice by two different operators and analyzed separately one from the other.

Results

A total of 6/10 swabs were SARS-CoV-2 positive. No significant time or storage-dependent variations were observed in SARS-CoV-2 Ct. Re-sampling of swabs with SARS-CoV-2 Ct lower than 33 resulted in highly reproducible results (CV=2.9%), while a high variability was observed when Ct values were higher than 33 (CV=10.3%).

Conclusions

This study demonstrates that time and temperature of nasopharyngeal swabs storage do not significantly impact on results reproducibility. However, swabs sampling is a critical step, and especially in case of low viral load, might be a potential source of diagnostic errors.

The circulating miRNAs as diagnostic and prognostic markers

A large portion of the human genome transcribes RNA sequences that do not code for any proteins. The first of these sequences was identified in 1993, and the best known noncoding RNAs are microRNA (miRNAs). It is now fully established that miRNAs regulate approximately 30% of the known genes that codify proteins. miRNAs are involved in several biological processes, like cell proliferation, differentiation, apoptosis and metastatization. These RNA products regulate gene expression at the post-transcriptional level, modulating or inhibiting protein expression by interacting with specific sequences of mRNAs. Mature miRNAs can be detected in blood plasma, serum and also in a wide variety of biological fluids. They can be found associated with proteins, lipids as well as enclosed in exosome vesicles. We know that circulating miRNAs (C-miRNAs) can regulate several key cellular processes in tissues different from the production site. C-miRNAs behave as endogenous mediators of RNA translation, and an extraordinary knowledge on their function has been obtained in the last years. They can be secreted in different tissue cells and associated with specific pathological conditions. Significant evidence indicates that the initiation and progression of several pathologies are "highlighted" by the presence of specific C-miRNAs, underlining their potential diagnostic relevance as clinical biomarkers. Here we review the current literature on the possible use of this new class of molecules as clinical biomarkers of diseases.

The pathway for introducing novel examination procedures in routine practice in accordance with ISO 15189:2012: 17-Hydroxy progesterone, dehydroepiandrosterone sulphate and vitamin D as examples

Background

In a medical laboratory, changes may be made to the analytical phase of diagnostic testing whenever a new test or the issue of a ‘new generation’ kit or new diagnostic system is required. In such cases, ISO 15189:2012 accreditation can assist laboratory professionals. The aim of the present study was to propose a working pathway for introducing new examination procedures into clinical practice in accordance with the ISO 15189:2012 standard, through the exemplars of 17-hydroxy progesterone, dehydroepiandrosterone sulphate and vitamin D.

Methods

The working pathway includes the following steps: (i) analysing examination procedures under evaluation, (ii) analysing examination procedures currently in use, (iii) verifying metrological traceability, (iv) verifying examination procedures and (v) evaluating comparability of results.

Results

The analysis of instructions for use issued by manufacturers revealed that metrological traceability was reported only for vitamin D. The imprecision verification was satisfactory, the imprecision obtained by the laboratory in terms of total imprecision always being less than the specified total imprecision. In only one case (IQC level 1, 17-hydroxy progesterone), the total upper verification limit was calculated. The trueness verification was satisfactory for all examination procedures, except for 17-hydroxy progesterone (second material). Passing–Bablok regression analyses in the comparability study demonstrated significant differences for all the examination procedures.

Conclusions

The working pathway described for examination procedures in routine practice is in accordance with the requirements of ISO 15189:2012 accreditation and takes feasibility into account (as its main goal), based on the cost/patient benefit ratio.

Quality of plasma samples and BD Vacutainer Barricor tubes: Effects of centrifugation

BACKGROUNDS

The BD Vacutainer® Barricor™ Plasma collection tube (BD Barricor) uses an innovative non-gel separation method. This study compared the plasma residual cell count (PRCC) obtained from BD Barricor and from BD PST II plasma tubes.

METHODS

Four BD Barricors and one BD PST II were collected from 40 donors. BD PST II was centrifuged at 1300g/10 min, while the BD Barricors were centrifuged at 1800g/10 min, 4000g/3 min, 4000g/7 min and 4000g/15 min. PRCC was evaluated measuring white blood cells (WBC), red blood cells (RBC) and Platelets (PLT) counts by Siemens ADVIA 2120. Cell-free hemoglobin was quantified by haemolysis index (HI) by Roche Cobas c501.

RESULTS

BD PST II Median WBC, RBC and PLT counts were 0.38 (10⁹/L), 0.0291 (10¹²/L) and 113.5 (10⁹/L), respectively. Considering the BD PST II as reference, PRCC differences were expressed as median bias percentage. WBC showed a significant reduction at all the conditions (p < 0.01), being the reductions: 63.9% (1800g/10 min), 69.9% (4000g/3 min), 75.0% (4000g/7 min) and 82.7% (4000g/15 min). RBC reductions 29.7% (1800g/10 min), 33.8% (4000g/3 min), 39.6% (4000g/7 min) and 66.4 (4000g/15 min) were all significant (p < 0.01). PLT reductions were 1.6% at 1800g/10 min (p = ns), 1.2% at 4000g/3 min (p = ns), 27.1% at 4000g/7 min (p = 0.046) and 46.6% at 4000g/15 min (p = 0.005). BD Barricor centrifuged for 7 and 15 min at 4000g showed an increased haemolysis.

CONCLUSIONS

BD Barricors plasma quality improved with increasing the centrifugation times but already at 4000g/3 min, the suggested centrifugation condition, a significant improvement was achieved.

Extra-analytical quality indicators – where to now?

A large body of evidence collected in recent years demonstrates the vulnerability of the extra-analytical phases of the total testing process (TTP) and the need to promote quality and harmonization in each and every step of the testing cycle. Quality indicators (QIs), which play a key role in documenting and improving quality in TTP, are essential requirements for clinical laboratory accreditation. In the last few years, wide consensus has been achieved on the need to adopt universal QIs and common terminology and to harmonize the management procedure concerning their use by adopting a common metric and reporting system. This, in turn, has led to the definition of performance specifications for extra-analytical phases based on the state of the art as indicated by data collected on QIs, particularly by clinical laboratories attending the Model of Quality Indicators program launched by the Working Group “Laboratory Errors and Patient Safety” of the International Federation of Clinical Chemistry and Laboratory Medicine. Harmonization plays a fundamental role defining not only the list of QIs to use but also performance specifications based on the state of the art, thus providing a valuable interlaboratory benchmark and tools for continuous improvement programs.

Verification of examination procedures in clinical laboratory for imprecision, trueness and diagnostic accuracy according to ISO 15189:2012: a pragmatic approach

Background The International Standard ISO 15189 is recognized as a valuable guide in ensuring high quality clinical laboratory services and promoting the harmonization of accreditation programmes in laboratory medicine. Examination procedures must be verified in order to guarantee that their performance characteristics are congruent with the intended scope of the test. The aim of the present study was to propose a practice model for implementing procedures employed for the verification of validated examination procedures already used for at least 2 years in our laboratory, in agreement with the ISO 15189 requirement at the Section 5.5.1.2. Methods In order to identify the operative procedure to be used, approved documents were identified, together with the definition of performance characteristics to be evaluated for the different methods; the examination procedures used in laboratory were analyzed and checked for performance specifications reported by manufacturers. Then, operative flow charts were identified to compare the laboratory performance characteristics with those declared by manufacturers. Results The choice of performance characteristics for verification was based on approved documents used as guidance, and the specific purpose tests undertaken, a consideration being made of: imprecision and trueness for quantitative methods; diagnostic accuracy for qualitative methods; imprecision together with diagnostic accuracy for semi-quantitative methods. Conclusions The described approach, balancing technological possibilities, risks and costs and assuring the compliance of the fundamental component of result accuracy, appears promising as an easily applicable and flexible procedure helping laboratories to comply with the ISO 15189 requirements.

PDAC-derived exosomes enrich the microenvironment in MDSCs in a SMAD4-dependent manner through a new calcium related axis

Tumor genetics and escape from immune surveillance concur in the poor prognosis of PDAC. In this study an experimental model was set up to verify whether SMAD4, deleted in about 55% PDAC and associated with poor prognosis, is involved in determining immunosuppression through Exosomes (Exo). Potential mechanisms and mediators underlying SMAD4-dependent immunosuppression were evaluated by studying intracellular calcium (Fluo-4), Exo-miRNAs (microarray) and Exo-proteins (SILAC). Two PDAC cell lines expressing (BxPC3-SMAD4+) or not-expressing (BxPC3) SMAD4 were used to prepare Exo-enriched conditioned media, employed in experiments with blood donors PBMCs. Exo expanded myeloid derived suppressor cells (gMDSC and mMDSC, flow cytometry) and altered intracellular calcium fluxes in an SMAD4 dependent manner. BxPC3-SMAD4+, but mainly BxPC3 Exo, increased calcium fluxes of PBMCs (p = 0.007) and this increased intracellular calcium trafficking characterized mMDSCs. The analysis of de-regulated Exo-miRNAs and transfection experiments revealed hsa-miR-494-3p and has-miR-1260a as potential mediators of SMAD4-associated de-regulated calcium fluxes. Eleven main biological processes were identified by the analysis of SMAD4-associated de-regulated Exo-proteins, including translation, cell adhesion, cell signaling and glycolysis. A reverse Warburg effect was observed by treating PBMCs with PDAC-derived Exo: BxPC3 Exo induced a higher glucose consumption and lactate production than BxPC3-SMAD4+ Exo. Conclusion: PDAC-derived Exo from cells with, but mainly from those without SMAD4 expression, create an immunosuppressive myeloid cell background by increasing calcium fluxes and glycolysis through the transfer of SMAD4-related differentially expressed miRNAs and proteins.

An approach for estimating measurement uncertainty in medical laboratories using data from long-term quality control and external quality assessment schemes

Background:

The present study was prompted by the ISO 15189 requirements that medical laboratories should estimate measurement uncertainty (MU).

Methods:

The method used to estimate MU included the: a) identification of quantitative tests, b) classification of tests in relation to their clinical purpose, and c) identification of criteria to estimate the different MU components. Imprecision was estimated using long-term internal quality control (IQC) results of the year 2016, while external quality assessment schemes (EQAs) results obtained in the period 2015–2016 were used to estimate bias and bias uncertainty.

Results:

A total of 263 measurement procedures (MPs) were analyzed. On the basis of test purpose, in 51 MPs imprecision only was used to estimate MU; in the remaining MPs, the bias component was not estimable for 22 MPs because EQAs results did not provide reliable statistics. For a total of 28 MPs, two or more MU values were calculated on the basis of analyte concentration levels. Overall, results showed that uncertainty of bias is a minor factor contributing to MU, the bias component being the most relevant contributor to all the studied sample matrices.

Conclusions:

The model chosen for MU estimation allowed us to derive a standardized approach for bias calculation, with respect to the fitness-for-purpose of test results. Measurement uncertainty estimation could readily be implemented in medical laboratories as a useful tool in monitoring the analytical quality of test results since they are calculated using a combination of both the long-term imprecision IQC results and bias, on the basis of EQAs results.

Performance criteria and quality indicators for the post-analytical phase

Quality indicators (QIs) used as performance measurements are an effective tool in accurately estimating quality, identifying problems that may need to be addressed, and monitoring the processes over time. In Laboratory Medicine, QIs should cover all steps of the testing process, as error studies have confirmed that most errors occur in the pre- and post-analytical phase of testing. Aim of the present study is to provide preliminary results on QIs and related performance criteria in the post-analytical phase.

This work was conducted according to a previously described study design based on the voluntary participation of clinical laboratories in the project on QIs of the Working Group “Laboratory Errors and Patient Safety” (WG-LEPS) of the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC).

Overall, data collected highlighted an improvement or stability in performances over time for all reported indicators thus demonstrating that the use of QIs is effective in the quality improvement strategy. Moreover, QIs data are an important source for defining the state-of-the-art concerning the error rate in the total testing process. The definition of performance specifications based on the state-of-the-art, as suggested by consensus documents, is a valuable benchmark point in evaluating the performance of each laboratory.

Laboratory tests play a relevant role in the monitoring and evaluation of the efficacy of patient outcome thus assisting clinicians in decision-making. Laboratory performance evaluation is therefore crucial to providing patients with safe, effective and efficient care.

TNFA Haplotype Genetic Testing Improves HLA in Estimating the Risk of Celiac Disease in Children

Background

TNF-α and IFN-γ play a role in the development of mucosal damage in celiac disease (CD). Polymorphisms of TNFA and IFNG genes, as well as of the TNFRSF1A gene, encoding the TNF-α receptor 1, might underlie different inter-individual disease susceptibility over a common HLA risk background. The aims of this study were to ascertain whether five SNPs in the TNFA promoter (-1031T>C,-857C>T,-376G>A,-308G>A,-238G>A), sequence variants of the TNFRSF1A gene and IFNG +874A>T polymorphism are associated with CD in a HLA independent manner.

Methods

511 children (244 CD, 267 controls) were genotyped for HLA, TNFA and INFG (Real Time PCR). TNFRSF1A variants were studied (DHPLC and sequence).

Results

Only the rare TNFA-1031C (OR=0.65, 95% CI:0.44-0.95), -857T (OR=0.42, 95% CI:0.27-0.65), -376A (OR=2.25, 95% CI:1.12-4.51) and -308A (OR=4.76, 95% CI:3.12-7.26) alleles were significantly associated with CD. One TNFRSF1A variant was identified (c.625+10A>G, rs1800693), but not associated with CD. The CD-correlated TNFA SNPs resulted in six haplotypes. Two haplotypes were control-associated (CCGG and TTGG) and three were CD-associated (CCAG, TCGA and CCGA). The seventeen inferred haplotype combinations were grouped (A to E) based on their frequencies among CD. Binary logistic regression analysis documented a strong association between CD and HLA (OR for intermediate risk haplotypes=178; 95% CI:24-1317; OR for high risk haplotypes=2752; 95% CI:287-26387), but also an HLA-independent correlation between CD and TNFA haplotype combination groups. The CD risk for patients carrying an intermediate risk HLA haplotype could be sub-stratified by TNFA haplotype combinations.

Conclusion

TNFA promoter haplotypes associate with CD independently from HLA. We suggest that their evaluation might enhance the accuracy in estimating the CD genetic risk.

The novel S59P mutation in the TNFRSF1A gene identified in an adult onset TNF receptor associated periodic syndrome (TRAPS) constitutively activates NF-κB pathway

Introduction

Mutations in the TNFRSF1A gene, encoding tumor necrosis factor receptor 1 (TNF-R1), are associated with the autosomal dominant autoinflammatory disorder, called TNF receptor associated periodic syndrome (TRAPS). TRAPS is clinically characterized by recurrent episodes of long-lasting fever and systemic inflammation. A novel mutation (c.262 T > C; S59P) in the TNFRSF1A gene at residue 88 of the mature protein was recently identified in our laboratory in an adult TRAPS patient. The aim of this study was to functionally characterize this novel TNFRSF1A mutation evaluating its effects on the TNF-R1-associated signaling pathways, firstly NF-κB, under particular conditions and comparing the results with suitable control mutations.

Methods

HEK-293 cell line was transfected with pCMV6-AC construct expressing wild-type (WT) or c.262 T > C (S59P), c.362G > A (R92Q), c.236C > T (T50M) TNFRSF1A mutants. Peripheral blood mononuclear cells (PBMCs) were instead isolated from two TRAPS patients carrying S59P and R92Q mutations and from five healthy subjects. Both transfected HEK-293 and PBMCs were stimulated with tumor necrosis factor (TNF) or interleukin 1β (IL-1β) to evaluate the expression of TNF-R1, the activation of TNF-R1-associated downstream pathways and the pro-inflammatory cytokines by means of immunofluorescent assay, array-based technique, immunoblotting and immunometric assay, respectively.

Results

TNF induced cytoplasmic accumulation of TNF-R1 in all mutant cells. Furthermore, all mutants presented a particular set of active TNF-R1 downstream pathways. S59P constitutively activated IL-1β, MAPK and SRC/JAK/STAT3 pathways and inhibited apoptosis. Also, NF-κB pathway involvement was demonstrated in vitro by the enhancement of p-IκB-α and p65 nuclear subunit of NF-κB expression in all mutants in the presence of TNF or IL-1β stimulation. These in vitro results correlated with patients’ data from PBMCs. Concerning the pro-inflammatory cytokines secretion, mainly IL-1β induced a significant and persistent enhancement of IL-6 and IL-8 in PBMCs carrying the S59P mutation.

Conclusions

The novel S59P mutation leads to defective cellular trafficking and to constitutive activation of TNF-R1. This mutation also determines constitutive activation of the IL-1R pathway, inhibition of apoptosis and enhanced and persistent NF-κB activation and cytokine secretion in response to IL-1β stimulation.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0604-7) contains supplementary material, which is available to authorized users.

Performance criteria and quality indicators for the pre-analytical phase

The definition, implementation and monitoring of valuable analytical quality specifications have played a fundamental role in improving the quality of laboratory services and reducing the rates of analytical errors. However, a body of evidence has been accumulated on the relevance of the extra-analytical phases, namely the pre-analytical steps, their vulnerability and impact on the overall quality of the laboratory information. The identification and establishment of valueable quality indicators (QIs) represents a promising strategy for collecting data on quality in the total testing process (TTP) and, particularly, for detecting any mistakes made in the individual steps of the pre-analytical phase, thus providing useful information for quality improvement projects. The consensus achieved on the developed list of harmonized QIs is a premise for the further step: the identification of achievable and realistic performance targets based on the knowledge of the state-of-the-art. Data collected by several clinical laboratories worldwide allow the classification of performances for available QIs into three levels: optimum, desirable and minimum, in agreement with the widely accepted proposal for analytical quality specifications.

Harmonization of pre-analytical quality indicators

Quality indicators (QIs) measure the extent to which set targets are attained and provide a quantitative basis for achieving improvement in care and, in particular, laboratory services. A body of evidence collected in recent years has demonstrated that most errors fall outside the analytical phase, while the pre- and post-analytical steps have been found to be more vulnerable to the risk of error. However, the current lack of attention to extra-laboratory factors and related QIs prevent clinical laboratories from effectively improving total quality and reducing errors. Errors in the pre-analytical phase, which account for 50% to 75% of all laboratory errors, have long been included in the ‘identification and sample problems’ category. However, according to the International Standard for medical laboratory accreditation and a patient-centered view, some additional QIs are needed. In particular, there is a need to measure the appropriateness of all test request and request forms, as well as the quality of sample transportation. The QIs model developed by a working group of the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) is a valuable starting point for promoting the harmonization of available QIs, but further efforts should be made to achieve a consensus on the road map for harmonization.