scholarly journals Determining Plasma Protein Variation Parameters as a Prerequisite for Biomarker Studies—A TMT-Based LC-MSMS Proteome Investigation

Proteomes ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 47
Author(s):  
Lou-Ann C. Andersen ◽  
Nicolai Bjødstrup Palstrøm ◽  
Axel Diederichsen ◽  
Jes Sanddal Lindholt ◽  
Lars Melholt Rasmussen ◽  
...  
Keyword(s):  
Sample Size ◽  
Plasma Protein ◽  
Plasma Proteins ◽  
Clinical Chemistry ◽  
Biological Variation ◽  
Sample Size Determination ◽  
Clinical Proteomics ◽  
European Federation ◽  
Plasma Samples ◽  
Proteomic Approach

Specific plasma proteins serve as valuable markers for various diseases and are in many cases routinely measured in clinical laboratories by fully automated systems. For safe diagnostics and monitoring using these markers, it is important to ensure an analytical quality in line with clinical needs. For this purpose, information on the analytical and the biological variation of the measured plasma protein, also in the context of the discovery and validation of novel, disease protein biomarkers, is important, particularly in relation to for sample size calculations in clinical studies. Nevertheless, information on the biological variation of the majority of medium-to-high abundant plasma proteins is largely absent. In this study, we hypothesized that it is possible to generate data on inter-individual biological variation in combination with analytical variation of several hundred abundant plasma proteins, by applying LC-MS/MS in combination with relative quantification using isobaric tagging (10-plex TMT-labeling) to plasma samples. Using this analytical proteomic approach, we analyzed 42 plasma samples prepared in doublets, and estimated the technical, inter-individual biological, and total variation of 265 of the most abundant proteins present in human plasma thereby creating the prerequisites for power analysis and sample size determination in future clinical proteomics studies. Our results demonstrated that only five samples per group may provide sufficient statistical power for most of the analyzed proteins if relative changes in abundances >1.5-fold are expected. Seventeen of the measured proteins are present in the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) Biological Variation Database, and demonstrated remarkably similar biological CV’s to the corresponding CV’s listed in the EFLM database suggesting that the generated proteomic determined variation knowledge is useful for large-scale determination of plasma protein variations.

scholarly journals An overview of EFLM harmonization activities in Europe

2018 ◽  
Vol 56 (10) ◽  
pp. 1591-1597 ◽  
Author(s):  
Eric S. Kilpatrick ◽  
Sverre Sandberg
Keyword(s):  
Best Practice ◽  
Clinical Chemistry ◽  
Laboratory Medicine ◽  
Biological Variation ◽  
European Federation ◽  
Eu Countries ◽  
European Guidelines ◽  
Common Basis ◽  
Evaluation Procedures ◽  
E Learning

Abstract The European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) has initiated many harmonization activities in all phases of the examination process. The EFLM is dealing with both the scientific and the educational aspects of harmonization, with the intention of disseminating best practice in laboratory medicine throughout Europe. Priorities have been given (1) to establish a standard for conducting and assessing biological variation studies and to construct an evidence based EFLM webpage on biological variation data, (2) to harmonize preanalytical procedures by producing European guidelines, (3) to improve test ordering and interpretation, (4) to produce other common European guidelines for laboratory medicine and play an active part in development of clinical guidelines, (5) to establish a common basis for communicating laboratory results to patients, (6) to harmonize units of measurement throughout Europe, (7) to harmonize preanalytical procedures in molecular diagnostics and (8) to harmonize and optimize test evaluation procedures. The EFLM is also now launching the 5th version of the European Syllabus to help the education of European Specialists in Laboratory Medicine (EuSpLM), which is being supported by the development of e-learning courses. A register of EuSpLM is already established for members of National Societies in EU countries, and a similar register will be established for specialists in non-EU countries.

scholarly journals The EuBIVAS Project: Within- and Between-Subject Biological Variation Data for Serum Creatinine Using Enzymatic and Alkaline Picrate Methods and Implications for Monitoring

2017 ◽  
Vol 63 (9) ◽  
pp. 1527-1536 ◽  
Author(s):  
Anna Carobene ◽  
Irene Marino ◽  
Abdurrahman Coşkun ◽  
Mustafa Serteser ◽  
Ibrahim Unsal ◽  
...  
Keyword(s):  
Serum Creatinine ◽  
Clinical Chemistry ◽  
Biological Variation ◽  
European Federation ◽  
Healthy Individuals ◽  
Homogeneity Analysis ◽  
Variation Data ◽  
Performance Specifications ◽  
Age Range ◽  
Analytical Variation

Abstract BACKGROUND The European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) European Biological Variation Study (EuBIVAS) has been established to deliver rigorously determined biological variation (BV) indices. EuBIVAS determined BV for serum creatinine using the enzymatic and alkaline picrate measurement methods. METHOD In total, 91 healthy individuals (38 males, 53 females; age range, 21–69 years) were bled for 10 consecutive weeks at 6 European laboratories. An equivalent protocol was followed at each center. Sera were stored at −80 °C before analysis. Analyses for each patient were performed in duplicate within a single run on an ADVIA 2400 system (San Raffaele Hospital, Milan). The data were subjected to outlier and homogeneity analysis before performing CV-ANOVA to determine BV and analytical variation (CVA) estimates with confidence intervals (CI). RESULTS The within-subject BV estimates [CVI (95% CI)] were similar for enzymatic [4.4% (4.2–4.7)] and alkaline picrate [4.7% (4.4–4.9)] methods and lower than the estimate presently available online (CVI = 5.9%). No significant male/female BV differences were found. Significant differences were observed in mean creatinine values between men and women and between Turkish individuals and those of other nationalities. Between-subject BV (CVG) estimates, stratified accordingly, produced CVG values similar to historical BV data. CVA was 1.1% for the enzymatic and 4.4% for alkaline picrate methods, indicating that alkaline picrate methods fail to fulfill analytical performance specifications for imprecision (CVAPS). CONCLUSIONS The serum creatinine CVI obtained by EuBIVAS specifies a more stringent CVAPS than previously identified. The alkaline picrate method failed to meet this CVAPS, raising questions regarding its future use.

scholarly journals ROC Curves in Clinical Chemistry: Uses, Misuses, and Possible Solutions

2004 ◽  
Vol 50 (7) ◽  
pp. 1118-1125 ◽  
Author(s):  
Nancy A Obuchowski ◽  
Michael L Lieber ◽  
Frank H Wians
Keyword(s):  
Phase I ◽  
Sample Size ◽  
Gold Standard ◽  
Diagnostic Tests ◽  
Clinical Laboratory ◽  
Clinical Chemistry ◽  
Roc Curves ◽  
Sample Size Determination ◽  
Phase Iii ◽  
Test Accuracy

Abstract Background: ROC curves have become the standard for describing and comparing the accuracy of diagnostic tests. Not surprisingly, ROC curves are used often by clinical chemists. Our aims were to observe how the accuracy of clinical laboratory diagnostic tests is assessed, compared, and reported in the literature; to identify common problems with the use of ROC curves; and to offer some possible solutions. Methods: We reviewed every original work using ROC curves and published in Clinical Chemistry in 2001 or 2002. For each article we recorded phase of the research, prospective or retrospective design, sample size, presence/absence of confidence intervals (CIs), nature of the statistical analysis, and major analysis problems. Results: Of 58 articles, 31% were phase I (exploratory), 50% were phase II (challenge), and 19% were phase III (advanced) studies. The studies increased in sample size from phase I to III and showed a progression in the use of prospective designs. Most phase I studies were powered to assess diagnostic tests with ROC areas ≥0.70. Thirty-eight percent of studies failed to include CIs for diagnostic test accuracy or the CIs were constructed inappropriately. Thirty-three percent of studies provided insufficient analysis for comparing diagnostic tests. Other problems included dichotomization of the gold standard scale and inappropriate analysis of the equivalence of two diagnostic tests. Conclusion: We identify available software and make some suggestions for sample size determination, testing for equivalence in diagnostic accuracy, and alternatives to a dichotomous classification of a continuous-scale gold standard. More methodologic research is needed in areas specific to clinical chemistry.

Sample collections from healthy volunteers for biological variation estimates’ update: a new project undertaken by the Working Group on Biological Variation established by the European Federation of Clinical Chemistry and Laboratory Medicine

2016 ◽  
Vol 54 (10) ◽  
Author(s):  
Anna Carobene ◽  
Marta Strollo ◽  
Niels Jonker ◽  
Gerhard Barla ◽  
William A. Bartlett ◽  
...  
Keyword(s):  
Working Group ◽  
Clinical Chemistry ◽  
Laboratory Medicine ◽  
Biological Variation ◽  
European Federation ◽  
Laboratory Measurements ◽  
Controlled Conditions ◽  
Edta Plasma ◽  
Blood Specimens

AbstractBackground:Biological variation (BV) data have many fundamental applications in laboratory medicine. At the 1st Strategic Conference of the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) the reliability and limitations of current BV data were discussed. The EFLM Working Group on Biological Variation is working to increase the quality of BV data by developing a European project to establish a biobank of samples from healthy subjects to be used to produce high quality BV data.Methods:The project involved six European laboratories (Milan, Italy; Bergen, Norway; Madrid, Spain; Padua, Italy; Istanbul, Turkey; Assen, The Netherlands). Blood samples were collected from 97 volunteers (44 men, aged 20–60 years; 43 women, aged 20–50 years; 10 women, aged 55–69 years). Initial subject inclusion required that participants completed an enrolment questionnaire to verify their health status. The volunteers provided blood specimens once per week for 10 weeks. A short questionnaire was completed and some laboratory tests were performed at each sampling consisting of blood collected under controlled conditions to provide serum, KResults:Samples from six out of the 97 enroled subjects were discarded as a consequence of abnormal laboratory measurements. A biobank of 18,000 aliquots was established consisting of 120 aliquots of serum, 40 of EDTA-plasma, and 40 of citrated-plasma from each subject. The samples were stored at –80 °C.Conclusions:A biobank of well-characterised samples collected under controlled conditions has been established delivering a European resource to enable production of contemporary BV data.

Long-term biological variation estimates of 13 hematological parameters in healthy Chinese subjects

2020 ◽  
Vol 58 (8) ◽  
pp. 1282-1290 ◽  
Author(s):  
Chenbin Li ◽  
Mingting Peng ◽  
Ji Wu ◽  
Zhongli Du ◽  
Hong Lu ◽  
...  
Keyword(s):  
Complete Blood Count ◽  
Clinical Chemistry ◽  
Hematological Parameters ◽  
Age Distribution ◽  
Turnover Time ◽  
Biological Variation ◽  
European Federation ◽  
Mean Values ◽  
Healthy Chinese ◽  
Chinese Subjects

AbstractBackgroundThe complete blood count (CBC) is a basic test routinely ordered by physicians as a part of initial diagnostic work-up on their patients. To ensure safe clinical application of the CBC, reliable biological variation (BV) data are needed to establish analytical performance specifications. Our aim was to define the BV of CBC parameters using a rigorous protocol that is compliant with the Biological Variation Data Critical Appraisal Checklist (BIVAC) provided by the European Federation of Clinical Chemistry and Laboratory Medicine.MethodsBlood samples drawn from 41 healthy Chinese subjects (22 females and 19 males; 23–59 years of age) once monthly for 6 consecutive months were analyzed using an ABX Pentra 80 instrument. The instrument was precisely calibrated. All samples were analyzed in duplicate for 13 CBC parameters. The data were assessed for outliers, normality, and variance homogeneity prior to nested ANOVA. Gender-stratified within-subject (CVI) and between-subject (CVG) BV estimates were calculated.ResultsThe number of remaining data for each subject was 442–484 after removing outliers. No significant differences existed between female/male CVI estimates. Except for leukocytes, neutrophils, and lymphocytes, the mean values of 10 parameters differed significantly between genders, rendering partitioning of CVG data between genders. No significant differences were detected between most BV estimates and recently published estimates representing a Europid population.ConclusionsMost BV estimates in BIVAC-compliant studies are similar. The turnover time of blood cells and age distribution of participants should be considered in a CBC BV study. Our study will contribute to global BV estimates and future studies.

scholarly journals The EuBIVAS: Within- and Between-Subject Biological Variation Data for Electrolytes, Lipids, Urea, Uric Acid, Total Protein, Total Bilirubin, Direct Bilirubin, and Glucose

2018 ◽  
Vol 64 (9) ◽  
pp. 1380-1393 ◽  
Author(s):  
Aasne K Aarsand ◽  
Jorge Díaz-Garzón ◽  
Pilar Fernandez-Calle ◽  
Elena Guerra ◽  
Massimo Locatelli ◽  
...  
Keyword(s):  
Uric Acid ◽  
Total Protein ◽  
Total Bilirubin ◽  
Service Providers ◽  
Clinical Chemistry ◽  
Hdl Cholesterol ◽  
Biological Variation ◽  
Direct Bilirubin ◽  
European Federation ◽  
Variation Data

Abstract BACKGROUND The European Federation of Clinical Chemistry and Laboratory Medicine European Biological Variation Study (EuBIVAS) has been established to deliver rigorously determined data describing biological variation (BV) of clinically important measurands. Here, EuBIVAS-based BV estimates of serum electrolytes, lipids, urea, uric acid, total protein, total bilirubin, direct bilirubin, and glucose, as well as their associated analytical performance specifications (APSs), are presented. METHOD Samples were drawn from 91 healthy individuals (38 male, 53 female; age range, 21–69 years) for 10 consecutive weeks at 6 European laboratories. Samples were stored at −80 °C before duplicate analysis of all samples on an ADVIA 2400 (Siemens Healthineers). Outlier and homogeneity analyses were performed, followed by CV-ANOVA on trend-corrected data, when relevant, to determine BV estimates with CIs. RESULTS The within-subject BV (CVI) estimates of all measurands, except for urea and LDL cholesterol, were lower than estimates available in an online BV database, with differences being most pronounced for HDL cholesterol, glucose, and direct bilirubin. Significant differences in CVI for men and women/women <50 years of age were evident for uric acid, triglycerides, and urea. The CVA obtained for sodium and magnesium exceeded the EuBIVAS-based APS for imprecision. CONCLUSIONS The EuBIVAS, which is fully compliant with the recently published Biological Variation Data Critical Appraisal Checklist, has produced well-characterized, high-quality BV estimates utilizing a stringent experimental protocol. These new reference data deliver revised and more exacting APS and reference change values for commonly used clinically important measurands, thus having direct relevance to diagnostics manufacturers, service providers, clinical users, and ultimately patients.

scholarly journals Identification of plasma biomarker candidates in glioblastoma using an antibody-array-based proteomic approach

2014 ◽  
Vol 48 (3) ◽  
pp. 257-266 ◽  
Author(s):  
Klemen Zupancic ◽  
Andrej Blejec ◽  
Ana Herman ◽  
Matija Veber ◽  
Urska Verbovsek ◽  
...  
Keyword(s):  
Blood Plasma ◽  
Plasma Proteins ◽  
Cell Signalling ◽  
Therapy Response ◽  
Small Scale ◽  
Antibody Array ◽  
Plasma Samples ◽  
Guanine Nucleotide Binding Protein ◽  
Proteomic Approach ◽  
The Impact

Abstract Background. Glioblastoma multiforme (GBM) is a brain tumour with a very high patient mortality rate, with a median survival of 47 weeks. This might be improved by the identification of novel diagnostic, prognostic and predictive therapy-response biomarkers, preferentially through the monitoring of the patient blood. The aim of this study was to define the impact of GBM in terms of alterations of the plasma protein levels in these patients. Materials and methods. We used a commercially available antibody array that includes 656 antibodies to analyse blood plasma samples from 17 healthy volunteers in comparison with 17 blood plasma samples from patients with GBM. Results. We identified 11 plasma proteins that are statistically most strongly associated with the presence of GBM. These proteins belong to three functional signalling pathways: T-cell signalling and immune responses; cell adhesion and migration; and cell-cycle control and apoptosis. Thus, we can consider this identified set of proteins as potential diagnostic biomarker candidates for GBM. In addition, a set of 16 plasma proteins were significantly associated with the overall survival of these patients with GBM. Guanine nucleotide binding protein alpha (GNAO1) was associated with both GBM presence and survival of patients with GBM. Conclusions. Antibody array analysis represents a useful tool for the screening of plasma samples for potential cancer biomarker candidates in small-scale exploratory experiments; however, clinical validation of these candidates requires their further evaluation in a larger study on an independent cohort of patients.

scholarly journals The Biological Variation Data Critical Appraisal Checklist: A Standard for Evaluating Studies on Biological Variation

2018 ◽  
Vol 64 (3) ◽  
pp. 501-514 ◽  
Author(s):  
Aasne K Aarsand ◽  
Thomas Røraas ◽  
Pilar Fernandez-Calle ◽  
Carmen Ricos ◽  
Jorge Díaz-Garzón ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Critical Appraisal ◽  
Clinical Chemistry ◽  
Essential Elements ◽  
Biological Variation ◽  
European Federation ◽  
Variation Data ◽  
Global Estimates ◽  
Variance Homogeneity

Abstract BACKGROUND Concern has been raised about the quality of available biological variation (BV) estimates and the effect of their application in clinical practice. A European Federation of Clinical Chemistry and Laboratory Medicine Task and Finish Group has addressed this issue. The aim of this report is to (a) describe the Biological Variation Data Critical Appraisal Checklist (BIVAC), which verifies whether publications have included all essential elements that may impact the veracity of associated BV estimates, (b) use the BIVAC to critically appraise existing BV publications on enzymes, lipids, kidney, and diabetes-related measurands, and (c) apply metaanalysis to deliver a global within-subject BV (CVI) estimate for alanine aminotransferase (ALT). METHODS In the BIVAC, publications were rated as A, B, C, or D, indicating descending compliance for 14 BIVAC quality items, focusing on study design, methodology, and statistical handling. A D grade indicated that associated BV estimates should not be applied in clinical practice. Systematic searches were applied to identify BV studies for 28 different measurands. RESULTS In total, 128 publications were identified, providing 935 different BV estimates. Nine percent achieved D scores. Outlier analysis and variance homogeneity testing were scored as C in >60% of 847 cases. Metaanalysis delivered a CVI estimate for ALT of 15.4%. CONCLUSIONS Application of BIVAC to BV publications identified deficiencies in required study detail and delivery, especially for statistical analysis. Those deficiencies impact the veracity of BV estimates. BV data from BIVAC-compliant studies can be combined to deliver robust global estimates for safe clinical application.

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