bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inter-Laboratory Robustness of Next-Generation Bile Acid Study in Mice and Humans: International Ring Trial Involving 12 Laboratories
Authors: Pham Hai T , Arnhard Kathrin , Asad Yasmin J , Deng Lu , Felder Thomas K , St John-Williams Lisa , Kaever Volkhard , Leadley Michael , Mitro Nico , Muccio Stephane , Prehn Cornelia , Rauh Manfred , Rolle-Kampczyk Ulrike , Thompson J Will , Uhl Olaf , Ulaszewska Maria , Vogeser Michael , Wishart David S , Koal Therese 
Published: July 2018

Abstract

Background
The increasing relevance of individual bile acids quantification in biological samples requires analytical standardization to guarantee robustness and reliability of laboratory results. We have organized the first international ring trial, carried out in 12 laboratories, to evaluate the newly developed LC-MS/MS–based test kit for bile acid analysis.

Methods
Each laboratory received a Biocrates® Bile Acids Kit including system suitability test (SST) protocol. The kit is designed to analyze 16 individual human and 19 mouse bile acids. A set of 9 human and mouse plasma samples was measured in replicates. Laboratories were first required to pass the acceptance criteria for the SST. Within the subset of laboratories passing SST criteria, we evaluated how many laboratories met the target criteria of 80% of reported values with a relative accuracy within the 70%–130% range and analytical precisions (%CV) below 30%.

Results
A total of 12 of 16 participating laboratories passed the SST as the prerequisite to enter the ring trial. All 12 laboratories were then able to successfully run the kit and ring trial samples. Of the overall reported values, 94% were within 70%–130% relative accuracy range. Mean precision was 8.3% CV. The condition of CV &lt;30% was fulfilled by 99% of the reported values.

Conclusions
The first publically available interlaboratory ring trial for standardized bile acids quantification in human and mouse plasma samples showed very good analytical performance, within acceptance criteria typically applied in the preclinical environment. The kit is therefore suitable for standardized quantitative bile acid analysis and the establishment of reference values.
Verification of Claimed Limit of Detection in Molecular Diagnostics
Authors: Vaks Jeffrey E , Hemyari Parichehr , Rullkoetter Matthias , Santulli Michael J , Schoenbrunner Nancy 
Published: July 2018

Abstract

Background
Limit of detection (LOD) is an important performance characteristic of clinical laboratory tests. Verification, as recommended by the CLSI EP17-A2 guideline, is done by testing a sample with a claimed LOD concentration. Claimed LOD is verified if the 95% CI for the population proportion, calculated from observed proportion of positive results, contains the expected detection rate of 95% (CLSI EP17-A2; Clin Chem 2004;50:732–40). Claimed LOD, verification sample concentration, and observed rate of positive results are subjects to systematic and random errors that can cause false failure or false acceptance of the LOD verification. The aim of this study was to assess the probability to pass or fail verification of claimed LOD with various numbers of tests as function of the ratio of test sample concentration and actual LOD for PCR-based molecular diagnostics tests and provide recommendations for study design.

Methods
A method of calculating the probability of passing the claimed LOD verification following CLSI EP17-A2 guideline recommendations, based on the Poisson–binomial probability model, have been developed for PCR-based assays.

Results
Calculations and graphs have shown that the probability of passing LOD verification depends on the number of tests and has local minima and maxima between 0.975 and 0.995 for the number of tests from 20 to 1000 on samples having actual LOD concentration. The probability of detecting the difference between claimed LOD and actual LOD increases with the number of tests performed. Graphs and tables with examples are included.

Conclusions
Method, tables, and graphs helping in planning LOD verification study in molecular diagnostics are provided along with the recommendations on what to do in case of failure to verify the LOD claim.
Lipoprotein Biomarkers and Risk of Cardiovascular Disease: A Laboratory Medicine Best Practices (LMBP) Systematic Review
Authors: Sandhu Paramjit K , Musaad Salma M A , Remaley Alan T , Buehler Stephanie S , Strider Sonya , Derzon James H , Vesper Hubert W , Ranne Anne , Shaw Colleen S , Christenson Robert H 
Published: July 2018

Abstract

Background
Controversy exists about the incremental utility of nontraditional lipid biomarkers [e.g., apolipoprotein (apo) B, apo A-I, and non-HDL-C] in improving cardiovascular disease (CVD) risk prediction when added to a conventional model of traditional risk factors (e.g., total cholesterol, LDL cholesterol, HDL cholesterol, sex, age, smoking status, and blood pressure). Here we present a systematic review that was conducted to assess the use of nontraditional lipid biomarkers including apo B, apo A-I, apo B/A-I ratio, and non-HDL-C in improving CVD risk prediction after controlling for the traditional risk factors in populations at risk for cardiovascular events.

Content
This systematic review used the Laboratory Medicine Best Practices (LMBP™) A-6 methods. A total of 9 relevant studies published before and including July 2015 comprised the evidence base for this review. Results from this systematic review indicated that after the adjustment for standard nonlipid and lipid CVD risk factors, nontraditional apolipoprotein biomarkers apo B (overall effect = relative risk: 1.31; 95% CI, 1.22–1.40; 4 studies) and apo B/apo A-I ratio (overall effect = relative risk: 1.31; 95% CI, 1.11–1.38; 7 studies) resulted in significant improvement in long-term CVD risk assessment.

Summary
Available evidence showed that nontraditional lipid biomarkers apo B and apo B/apo I ratio can improve the risk prediction for cardiovascular events after controlling for the traditional risk factors for the populations at risk. However, because of insufficient evidence, no conclusions could be made for the effectiveness of apo A-I and non-HDL-C lipid markers to predict the CVD events, indicating a need for more research in this field.
Score Using Measurements of Plasma Midregional Pro–Atrial Natriuretic Peptide to Estimate the Duration of Atrial Fibrillation
Authors: Legallois Damien , Sorbets Emmanuel , Chenevier-Gobeaux Camille , Hallouche Maya , Boubaya Marouane , Charnaux Nathalie , Lebon Alain , Levy Vincent , Beygui Farzin , Meune Christophe 
Published: July 2018

Abstract

Background
An accurate estimate of the duration of atrial fibrillation (AF) is critical for its safe and successful management. We examined the ability of midregional pro–atrial natriuretic peptide (MR-proANP) to identify patients presenting with AF of ≤48 vs &gt;48 h in duration.

Methods
We prospectively studied 106 patients presenting with AF of known duration. We examined the predictive values of MR-proANP and N-terminal pro–brain natriuretic peptide (NT-proBNP) in the detection of recent-onset AF, in addition to other factors identified by multiple variable analyses.

Results
In patients presenting with AF of ≤48 vs &gt;48 h in duration, the median MR-proANP plasma concentration was 147.7 [95.3–197.4] pmol/L vs 220.4 [154.0–303.1] pmol/L (P &lt;0.001). MR-proANP and NT-proBNP were correlated (r = 0.5, P &lt;10−7), but MR-proANP tended to better discriminate AF of ≤48 h in duration than NT-proBNP (P = 0.09). A score including heart rate, dyspnea, and MR-proANP concentration accurately detected AF of ≤48 h in duration (area under the curve = 0.890; 95% CI, 0.828–0.952). A score of 98 points was an optimal cutoff that excluded AF of ≤48 h in duration with a sensitivity of 95%, while a score of 132.5 points was an optimal cutoff that confirmed AF of ≤48 h in duration with a sensitivity of 95%. Overall, a score ≤98 or ≥132.5 identified AF of ≤48 h in duration in 56% of patients.

Conclusions
A score based on a model including heart rate, dyspnea, and plasma MR-proANP concentration was helpful in identifying AF of ≤48 h in duration.
Frequency that Laboratory Tests Influence Medical Decisions
Authors: Ngo Andy , Gandhi Paras , Miller W Greg 
Published: July 2018

Abstract

Background
Among the variables that influence medical decisions, laboratory tests are considered to be among the most important and frequently used. The influence of laboratory tests on medical decisions has been difficult to estimate. The goal of this study was to estimate the number of patient encounters that included a laboratory test.

Methods
We extracted information for 72196 patient encounters from 1-week intervals each quarter of a year from our comprehensive academic medical center electronic medical record. The patients examined represent a comprehensive range of clinical conditions and medical services. We determined for which encounters laboratory and other orders existed.

Results
Overall 35% of encounters had 1 or more laboratory tests ordered. However, the percent varied markedly with patient care areas. For inpatient, emergency department, and outpatient populations, 98%, 56%, and 29%, respectively, had 1 or more laboratory tests ordered.

Conclusions
Our observations support that it is not possible to use a single number to categorize the frequency with which laboratory tests occur in patient encounters. Utilization of laboratory tests varied with type of medical service with almost all inpatients, approximately half of emergency department patients, and nearly one-third of outpatients having laboratory tests during their healthcare visit.
Renal Function Influences Diagnostic Markers in Serum and Urine: A Study of Guanidinoacetate, Creatine, Human Epididymis Protein 4, and Neutrophil Gelatinase–Associated Lipocalin in Children
Authors: Salvador Cathrin L , Tøndel Camilla , Rowe Alexander D , Bjerre Anna , Brun Atle , Brackman Damien , Bolstad Nils , Mørkrid Lars 
Published: July 2018

AbstractBackgroundImpaired renal function may affect the level of diagnostic disease markers. The aim of the study was to investigate the effect of measured glomerular filtration rate (GFR) on 4 diagnostic markers in blood and urine—guanidinoacetate (GAA), creatine (CRE), human epididymis protein 4 (HE4), and neutrophil gelatinase–associated lipocalin (NGAL)—and how this could affect the decision and reference limits.MethodsWe examined 96 children (median age 9.2 years, range 0.25–17.5) with different stages of chronic kidney disease (CKD). GFR [median 65.9 mL · min−1 · (1.73 m2)−1, range 6.3–153] was measured by iohexol clearance using 7 venous blood samples after iohexol injection. Fasting serum and urinary GAA, CRE, HE4, NGAL, and creatinine (crn) were analyzed. After appropriate transformation of the markers, a multiple linear regression analysis examined the influence of age, sex, and measured GFR.ResultsThe level of GFR significantly affected S-GAA (P = 2 × 10−4) and U-GAA/crn (P = 5 ×10−11), leading to decreased values in renal impairment. GFR did not correlate significantly with the level of CRE and to a minor degree did the U-CRE/crn ratio (P = 0.54 and 0.01, respectively). The level of GFR significantly affected S-HE4 (P = 4 × 10−31) and U-HE4/S-HE4 ratio (P = 2 × 10−21) with increased serum values and decreased U-HE4/S-HE4 ratio in renal impairment. S-NGAL increased with decreasing kidney function (P = 2 × 10−19).ConclusionsDiagnostic disease markers may be influenced by the renal function, and this must be taken into account when interpreting test results. Decreased renal function could change the level of the marker above or below decision limits, leading to diagnostic misinterpretation.Clinical Trial RegistrationClinicalTrials.gov, Identifier NCT01092260, https://clinicaltrials.gov/ct2/show/NCT01092260?term=tondel&rank=2
Validation of an Automated Assay for Levetiracetam (Keppra) on Vitros 5600
Authors: Ali Mahesheema , Tam Estella , Roper Stephen M , Cao Jing , Devaraj Sridevi 
Published: July 2018

Abstract

Objective
Levetiracetam (also known as Keppra™) is an antiepileptic drug that has been demonstrated as an effective adjunctive therapy in the treatment of partial onset of seizures, primary generalized tonic-clonic seizures, and myoclonic seizures. The aim of our study was to validate an automated quantitative immunoassay for levetiracetam at Texas Children's Hospital.

Method
We validated the analytical performance of ARK™ Levetiracetam Assay on an Ortho Clinical Diagnostic Vitros 5600 Analyzer at Texas Children's Hospital. Analytical performance parameters included precision, linearity, sensitivity, accuracy, and effect of common interferents (free hemoglobin, bilirubin, triglycerides). We also tested common drug interferents on the ARK Levetiracetam Assay.

Results
The assay showed good precision with &lt;4% coefficient of variation (%CV) for intraassay and &lt;7% for interassay precision, respectively. The assay was linear across the measurement range (0.0–100.00 μg/mL). No significant effect was seen with common interferents or commonly co-used drugs.

Conclusions
The ARK Levetiracetam Assay on Ortho Clinical Diagnostic Vitros 5600 can be used for routine determination of levetiracetam for conducting therapeutic drug monitoring and optimizing individual dosage regimen.
Cyanide-Nitroprusside Colorimetric Assay: A Rapid Colorimetric Screen for Urinary Cystine
Authors: Brady Clayton T , Giesen Callen D , Voskoboev Nikolay , Chirackal Robin S , Gavrilov Dimitar K , Flanagan Ryan M , Lieske John C 
Published: July 2018

Abstract

Background
Cystinuria is an autosomal recessive disorder resulting in poor proximal tubule reabsorption of cystine in the nephron, increasing the risk of cystine stone formation. A fast, inexpensive assay to screen for urinary cystine is needed because cystine stones are difficult to noninvasively differentiate from more common calcium-containing ones. Tandem mass spectrometry (MS/MS) is sensitive and specific but is labor-intensive and costly. Alternatively, a colorimetric assay is fast and cost-effective; however, creatinine interference is an issue.

Methods
A published cyanide-nitroprusside colorimetric assay was modified for a high-throughput microplate format. Creatinine interference was reduced using 0.1 mol/L PBS and a standard reaction time of 60 s and was further corrected using a formula derived from the slope of multiple creatinine standard curves.

Results
The limit of blank was determined to be 2.6 mg/L, the limit of detection 11.9 mg/L, and the limit of quantitation 15.3 mg/L. The analytic measurement range was established as 15.3–100 mg/L cystine. Intraassay and interassay CV was calculated to be 9.6% and 8.0%, respectively, for a high-level cystine concentration (83.6 mg/L). Low-level cystine (36.4 mg/L) intraassay and interassay CV was determined to be 18.1% and 17.6%, respectively. Passing–Bablok regression analysis of colorimetric vs LC-MS/MS results revealed a slope of 1.10 and y intercept of −7.14 mg/L, with an overall bias of 2% by Bland–Altman plot analysis.

Conclusions
We analytically validated a rapid colorimetric assay suitable to quantify urinary cystine. The effect of thiol drugs on this assay remains to be determined.
Comparison of 13 Commercially Available Cardiac Troponin Assays in a Multicenter North American Study
Authors: Christenson Robert H , Jacobs Ellis , Uettwiller-Geiger Denise , Estey Mathew P , Lewandrowski Kent , Koshy Thomas I , Kupfer Kenneth , Li Yin , Wesenberg James C 
Published: July 2018

Abstract

Background
We examined the concordance of 13 commercial cardiac troponin (cTn) assays [point-of-care, high-sensitivity (hs), and conventional] using samples distributed across a continuum of results.

Methods
cTnI (11 assays) and cTnT (2 assays) were measured in 191 samples from 128 volunteers. cTn assays included Abbott (iSTAT, STAT, and hs), Alere (Cardio 3), Beckman (AccuTnI+3), Pathfast (cTnI-II), Ortho (Vitros), Siemens (LOCI, cTnI-Ultra, Xpand, Stratus CS), and Roche [4th Generation (Gen), hs]. Manufacturer-derived 99th percentile cutoffs were used to classify results as positive or negative. Alternative 99th percentile cutoffs were tested for some assays. Correlation was assessed using Passing–Bablok linear regression, bias was examined using Bland–Altman difference plots, and concordance/discordance of each method comparison was determined using the McNemar method.

Results
Regression slopes ranged from 0.63 to 1.87, y-intercepts from 0.00 to 0.03 ng/mL, and r values from 0.93 to 0.99. The cTnT methods had a slope of 0.93, y-intercept of 0.02 ng/mL, and r value of 0.99. For the cTnI assays, positive, negative, and overall concordance was 76.2%–100%, 66.0%–100%, and 82.9%–98.4%, respectively. Overall concordance between the 4th Gen cTnT and hsTnT assays was 88.9%. A total of 30 of the 78 method comparisons showed significant differences in classification of samples (P &lt;0.001); the iSTAT showed 10, hsTnT showed 9, AccuTnI+3 showed 5, Xpand showed 5, and Stratus CS showed 1. Using alternative 99th percentile cutoffs to those listed by manufacturers lowered the method discordance by 6-fold, from 30 to 5 (all involved iSTAT).

Conclusions
These data provide insight into characteristics of cTn methods and will assist the healthcare community in setting expectations for relationships among commercial cTn assays.
Biological Variation of Donor-Derived Cell-Free DNA in Renal Transplant Recipients: Clinical Implications
Authors: Bromberg Jonathan S , Brennan Daniel C , Poggio Emilio , Bunnapradist Suphamai , Langone Anthony , Sood Puneet , Matas Arthur J , Mannon Roslyn B , Mehta Shikha , Sharfuddin Asif , Fischbach Bernard , Narayanan Mohanram , Jordan Stanley C , Cohen David J , Zaky Ziad S , Hiller David , Woodward Robert N , Grskovic Marica , Sninsky John J , Yee James P , Bloom Roy D 
Published: July 2018

Abstract

Background
Previous studies have demonstrated that donor-derived cell-free DNA (dd-cfDNA) found in circulating blood of transplant recipients may serve as a noninvasive biomarker of allograft rejection. To better interpret the clinical meaning of dd-cfDNA, it is essential to understand the biological variation of this biomarker in stable healthy recipients. This report establishes the biological variation and clinical reference intervals of dd-cfDNA in renal transplant recipients by using an analytically validated assay that has a CV of 6.8%.

Methods
We sampled venous blood at patient surveillance visits (typically at posttransplant months 1–4, 6, 9, and 12) in a 14-center observational study. Patients with stable renal allograft function spanning ≥3 serial visits were selected. We used AlloSure®, a targeted next-generation sequencing-based approach, to measure dd-cfDNA in the plasma and computed the intraindividual CV (CVI) and interindividual CV (CVG), the index of individuality (II), and reference change value (RCV).

Results
Of 93 patients, 61% were men, 56% were Caucasian, mean age was 49 years, and 63% were deceased donor kidney recipients. Of 380 blood samples, the dd-cfDNA median value was 0.21% (interquartile range 0.12%–0.39%) and the 97.5th percentile was 1.20%. In 18 patients with an average of 4.1 tests, the CVI was 21%, CVG was 37%, II was 0.57, and RCV was 61%.

Conclusions
In a renal transplant recipient, a dd-cfDNA level above 1.2% is out of range and potentially abnormal. A serial increase of up to 61% in level of dd-cfDNA in a patient may be attributable to biological variation.
Clinicaltrials.gov Identifier: NCT02424227
Use of Biosynthetic Controls as Performance Standards for Next-Generation Sequencing Assays of Somatic Tumors: A Multilaboratory Study
Authors: De Abreu Francine B , Peterson Jason D , Deharvengt Sophie J , Daber Robert , Sarsani Vishal K , Spotlow Vanessa , Harrington Robin D , Lih Chih-Jian , Williams P Mickey , Bouk Courtney H , Konigshofer Yves , Huang Catherine , Anekella Bharathi , Davis Lorn , Garlick Russell K , Ferreira-Gonzalez Andrea , Dumur Catherine I , Fernandes Helen , Haralampu Stephen , Tsongalis Gregory J 
Published: July 2018

Abstract

Background
Next-generation sequencing (NGS) assays are highly complex tests that can vary substantially in both their design and intended application. Despite their innumerous advantages, NGS assays present some unique challenges associated with the preanalytical process, library preparation, data analysis, and reporting. According to a number of professional laboratory organization, control materials should be included both during the analytical validation phase and in routine clinical use to guarantee highly accurate results. The SeraseqTM Solid Tumor Mutation Mix AF10 and AF20 control materials consist of 26 biosynthetic DNA constructs in a genomic DNA background, each containing a specific variant or mutation of interest and an internal quality marker at 2 distinct allelic frequencies of 10% and 20%, respectively. The goal of this interlaboratory study was to evaluate the Seraseq AF10 and AF20 control materials by verifying their performance as control materials and by evaluating their ability to measure quality metrics essential to a clinical test.

Methods
Performance characteristics were assessed within and between 6 CLIA-accredited laboratories and 1 research laboratory.

Results
Most laboratories detected all 26 mutations of interest; however, some discrepancies involving the internal quality markers were observed.

Conclusion
This interlaboratory study showed that the Seraseq AF10 and AF20 control materials have high quality, stability, and genomic complexity in variant types that are well suited for assisting in NGS assay analytical validation and monitoring routine clinical applications.
The Case Back on the TRAIL: Death Receptors as Markers for rhTRAIL Sensitivity
Authors: Turner Katherine A , Kalafatis Michael 
Published: July 2018

AbstractBackgroundPersonalized cancer treatments can be applied to the clinical use of recombinant human tumor necrosis factor-related apoptosis-inducing ligand (rhTRAIL). rhTRAIL holds great promise because of its selectivity for cancer cells. However, rhTRAIL clinical trials were conducted without the screening of patients' tumors for rhTRAIL-binding death receptor (DR)4 and DR5, and the unselected treatment resulted in a lack of clinical benefit. Here we propose an in vitro test to analyze tumor cells isolated from patients for the membrane expression of DRs to determine patient suitability for rhTRAIL treatment.MethodsUsing a panel of malignant melanoma cell lines, the correlation between DR membrane expression and rhTRAIL sensitivity was evaluated. The membrane expression of DR4 and DR5 was examined through staining with anti-DR4 and -DR5 antibodies followed by fluorescence-activated cell sorting. rhTRAIL sensitivity was determined through Annexin-V and propidium iodide staining and Western blotting after rhTRAIL treatment.ResultsHere we show a direct correlation between the membrane expression of DRs and rhTRAIL sensitivity. rhTRAIL-sensitive melanoma lines, on average, had nearly 4-fold more DR4 and &gt;2-fold more DR5 than rhTRAIL-resistant lines. For a cancer cell to display rhTRAIL sensitivity, the optimum expression of DRs is essential. To overcome the apoptotic threshold, cancer cells must express DRs &gt;2-fold higher compared with their benign counterpart.ConclusionThese data show the potential of this flow cytometry-based assay for the analysis of isolated tumor cells for DR membrane expression. By first determining a patient's susceptibility to rhTRAIL-based treatments, they can be more appropriately placed in rhTRAIL clinical trials and improve rhTRAIL as an anticancer therapeutic.