External Proficiency Testing Program Research Articles

Proficiency testing for SARS-CoV-2 whole genome sequencing

Extensive studies and analyses into the molecular features of severe acute respiratory syndrome related coronavirus 2 (SARS-CoV-2) have enhanced the surveillance and investigation of its clusters and transmission worldwide. The whole genome sequencing (WGS) approach is crucial in identifying the source of infection and transmission routes by monitoring the emergence of variants over time and through communities. Varying SARS-CoV-2 genomics capacity and capability levels have been established in public health laboratories across different Australian states and territories. Therefore, laboratories performing SARS-CoV-2 WGS for public health purposes are recommended to participate in an external proficiency testing program (PTP). This study describes the development of a SARS-CoV-2 WGS PTP. The PTP assessed the performance of laboratories while providing valuable insight into the current state of SARS-CoV-2 genomics in public health across Australia. Part 1 of the PTP contained eight simulated SARS-CoV-2 positive and negative specimens to assess laboratories' wet and dry laboratory capacity. Part 2 involved the analysis of a genomic dataset that consisted of a multi-FASTA file of 70 consensus genomes of SARS-CoV-2. Participating laboratories were required to (1) submit raw data for independent bioinformatics analysis, (2) analyse the data with their processes, and (3) answer relevant questions about the data. The performance of the laboratories was commendable, despite some variation in the reported results due to the different sequencing and bioinformatics approaches used by laboratories. The overall outcome is positive and demonstrates the critical role of the PTP in supporting the implementation and validation of SARS-CoV-2 WGS processes. The data derived from this PTP will contribute to the development of SARS-CoV-2 bioinformatic quality control (QC) and performance benchmarking for accreditation.

NordiQC Assessments of Synaptophysin Immunoassays.

This paper is number 8 in a series developed through a partnership between ISIMM and NordiQC with the purpose of reporting research assessing the performance characteristics of immunoassays in an external proficiency testing program.

Quality assurance and harmonization for targeted biomonitoring measurements of environmental organic chemicals across the Children's Health Exposure Analysis Resource laboratory network.

A consortium of laboratories established under the Children's Health Exposure Analysis Resource (CHEAR) used a multifaceted quality assurance program to promote measurement harmonization for trace organics analyses of human biospecimens that included: (1) participation in external quality assurance (EQA)/proficiency testing (PT) programs; (2) analyses of a urine-based CHEAR common quality control (QC) pool with each analytical batch across all participating laboratories; (3) method validation against NIST Standard Reference Materials® (SRMs); and (4) analyses of blinded duplicates and other project-specific QC samples. The capability of five CHEAR laboratories in organic chemical analysis increased across the 4-year period, and performance in the external PT program improved over time - recent challenges reporting >90% analytes with satisfactory performance. The CHEAR QC pools were analyzed for several classes of organic chemicals including phthalate metabolites and environmental phenols by the participating laboratories with every batch of project samples, which provided a rich source of measurement data for the assessment of intra- and inter-laboratory variance. Within-laboratory and overall variabilities in measurements across laboratories were calculated for target chemicals in urine QC pools; the coefficient of variation (CV) was generally below 25% across batches, studies and laboratories and indicated acceptable analytical imprecision. The suite of organic chemicals analyzed in the CHEAR QC pool was broader than those reported for commercially available reference materials. The accuracy of each of the laboratories' methods was verified through the analysis of several NIST SRMs and was, for example, 97±5.2% for environmental phenols and 95±11% for phthalates. Analysis of blinded duplicate samples showed excellent agreement and reliability of measurements. The intra-class correlation coefficients (ICC) for phthalate metabolites analyzed in various batches across three CHEAR laboratories showed excellent reliability (typically >0.90). Overall, the multifaceted quality assurance protocols followed among the CHEAR laboratories ensured reliable and reproducible data quality for several classes of organic chemicals. Increased participation in external PT programs through inclusion of additional target analytes will further enhance the confidence in data quality.

A Comprehensive Quality Assurance Platform in Canada for National Point-of-Care Chronic Kidney Disease Screening: The Kidney Check Program

A Comprehensive Quality Assurance Platform in Canada for National Point-of-Care Chronic Kidney Disease Screening: The Kidney Check Program

NordiQC Assessments of Keratin 5 Immunoassays.

This paper is number 7 in a series developed through a partnership between ISIMM and NordiQC with the purpose of reporting research assessing the performance characteristics of immunoassays in an external proficiency testing program.

NordiQC Assessments of Chromogranin A Immunoassays.

This paper is number 6 in a series developed through a partnership between ISIMM and Nordic IHC Quality Control with the purpose of reporting research assessing the performance characteristics of immunoassays in an external proficiency testing program.

NordiQC Assessments of CD117 Immunoassays.

This paper is the number 5 in a series developed through a partnership between ISIMM and NordiQC for the purpose of reporting research assessing the performance characteristics of immunoassays in an external proficiency-testing program.

NordiQC Assessments of MSH6 Immunoassays.

This paper is number 4 in a series developed through a partnership between ISIMM and Nordic immunohistochemical Quality Control for the purpose of reporting research assessing the performance characteristics of immunoassays in an external proficiency testing program.

NordiQC Assessments of PAX8 Immunoassays.

This paper is number 3 in a series developed through a partnership between ISIMM and NordiQC for the purpose of reporting research assessing the performance characteristics of immunoassays in an external proficiency testing program.

NordiQC Assessments of Low Molecular Weight Keratin 8/18 Immunoassays.

This paper is number 2 in a series developed through a partnership between ISIMM and NordiQC for the purpose of reporting research assessing the performance characteristics of immunoassays in an external proficiency testing program.

NordiQC Assessments of SOX10 Immunoassays.

This paper is number 1 in a series developed through a partnership between ISIMM and NordiQC for the purpose of reporting research assessing the performance characteristics of immunoassays in an external proficiency testing program.

The Nanjing Glycated Hemoglobin Standardization Program: 2012 to 2015

PurposeThis study aims to investigate glycosylated hemoglobin (HbA1c), between-laboratory imprecision (%CV), and pass rates from 2012 to 2015 in Nanjing to provide evidence for improving the HbA1c measurement. MethodsThis was a retrospective, descriptive analysis of HbA1c levels obtained from participating hospitals in Nanjing from 2012 to 2015. The HbA1c levels of fresh whole blood samples taken from healthy and diabetic adults were determined within 24 hours. HbA1c levels (low level: 4.0%−6.0% HbA1c; medium level: 6.1%−8.0% HbA1c; and high level: 8.1%−10.0%) were grouped. Meanwhile, the target values were determined and assigned by a Level I−certified laboratory to assess the accuracy. Results as %HbA1c and related detection information, such as methods, were collected from all participants, then evaluated after each survey part of the program. FindingsOverall, the %CVs acquired by HPLC methods were lower than those determined by other methods. Pass rates ranged from 62.9% to 100%, depending on the HbA1c level, and overall pass rates increased from 54.3% to 94.4% for those laboratories passing the 3 HbA1c levels. In addition, the top-grade hospital-based laboratories had better performances than the secondary hospital-based laboratories in 2012 to 2015. ImplicationsThe use of accuracy-based proficiency testing with stringent quality-control management has greatly improved the performance of HbA1c testing. The Nanjing Glycated Hemoglobin Standardization Program (NJGHSP) played an important role in this improvement by encouraging use of more rigorous quality control, participation in external proficiency testing programs, and providing education.

Report From the First and Second Spanish Killer Immunoglobulin-Like Receptor Genotyping Workshops: External Quality Control for Natural Killer Alloreactive Donor Selection in Haploidentical Stem Cell Transplantation

An important factor affecting the success in the setting of related haploidentical hematopoietic stem cell transplantation (HSCT) is the graft-versus-leukemia effect mediated by natural killer (NK) cells when the donor displays NK alloreactivity versus the recipient. NK cell function is regulated by killer immunoglobulin-like receptors (KIR) and it has been described that donor KIR genotype influences transplantation outcome. This has led to a requirement of laboratories to have a quality assurance program for validation and control of their KIR genotyping methods. The goal of the 1st and 2nd Spanish KIR Genotyping Workshops was to provide an external proficiency testing program in KIR genotyping for Spanish immunology and transplant laboratories. These workshops were conducted during the years 2014–2016 and consisted of 17 participating laboratories typing a set of 20 samples. The presence/absence of 16 mandatory KIR loci (2DL1, 2DL2, 2DL3, 2DL4, 2DL5, 2DS1, 2DS2, 2DS3, 2DS4, 2DS5, 2DP1, 3DL1, 3DL2, 3DL3, 3DS1, and 3DP1) was evaluated per sample. Methods for KIR genotyping included polymerase chain reaction with the use of sequence-specific primers and sequence-specific oligoprobes. Consensus typing was reached in all samples, and the performance of laboratories in external proficiency testing was satisfactory in all cases. The polymorphism detected in the small sample studied in both workshops is indicative of an ample variety of KIR gene profiles in the Spanish population.

Validation Study of Inter-Laboratory Haematology Results in Enugu, Nigeria.

Background: A reliable and reproducible Medical Laboratory (Haematology) result needs internal and external quality control within the Medical Laboratory facilities and participation in external proficiency testing program such as this validation checks of inter-laboratory haematology results in Enugu – Nigeria. Objectives: This study was done to assess haematology laboratory performance and uniformity of results through comparison of manual and automated methods by participating laboratories in reporting test samples sent for complete blood counts and CD4–T-cell counts. Materials and Method: A total number of 10 subjects (males and females) were selected for this research study. Blood samples were collected from each of these subjects and were aliquoted each and distributed to 11 laboratories for analysis. The result generated from each laboratory was subjected to robust statistical analysis. Results and Discussions:The result revealed a significant statistical difference (P 0.05) observed in white blood cell count, lymphocytes count, mean cell haemoglobin concentration, total white blood cell count, Granulocytes, Haemoglobin, Haematocrit, mean cell volume, platelets count, Red blood cell count, and CD4 – cell counts between the automated techniques. There was a significant difference (p<0.05) in the mean lymphocyte counts, Haemoglobin concentration and mean cell haemoglobin concentrations when manual and automated methods where compared. These inverse correlations existing in the correlation of different results gotten from different laboratory facilities and different methods of haematological analysis may pose great diagnostic challenges in the clinical management / treatment of various disease conditions such as iron deficiency anaemia, etc. Conclusion: Report showed that inter-laboratory differences exist in Haematology.

Results from an external proficiency testing program: 11 years of molecular genetics testing for myotonic dystrophy type 1.

The aim of this study was to examine the performance of laboratories offering assessment for myotonic dystrophy type 1 (DM1) using external proficiency testing samples. DM1, a dominant disorder, has a prevalence of 1:20,000 due to the expansion of CTG trinucleotide repeats in the DMPK gene. External proficiency testing administered by the College of American Pathologists/American College of Medical Genetics and Genomics distributes three samples twice yearly. Responses from 2003 through the first distribution of 2013 were analyzed after stratification by location (United States/international). Both the repeat sizes (analytic validity) and clinical interpretations were assessed. Over the 21 distributions, 45 US and 29 international laboratories participated. Analytic sensitivity for detecting and reporting expanded repeats (≥50) was 99.2% (382/385 challenges) and 97.1% (133/137 challenges), respectively. Analytic specificity (to within two repeats of the consensus) was 99.2% (1,790/1,805 alleles) and 98.6% (702/712 alleles), respectively. Clinical interpretations were correct for 99.3% (450/453) and 98.2% (224/228) of positive challenges and in 99.9% (936/937) and 99.6% (455/457) of negative challenges, respectively. Of four incorrect interpretations made in the United States, two were probably due to sample mix-up. This review of laboratory performance regarding laboratory-developed genetic tests indicates very high performance for both the analytic and interpretative challenges for DM1.Genet Med 18 12, 1290-1294.

Utilizing global data to estimate analytical performance on the Sigma scale: A global comparative analysis of methods, instruments, and manufacturers through external quality assurance and proficiency testing programs

ObjectiveTo assess the analytical performance of instruments and methods through external quality assessment and proficiency testing data on the Sigma scale. Design and methodsA representative report from five different EQA/PT programs around the world (2 US, 1 Canadian, 1 UK, and 1 Australasian) was accessed. The instrument group standard deviations were used as surrogate estimates of instrument imprecision. Performance specifications from the US CLIA proficiency testing criteria were used to establish a common quality goal. Then Sigma-metrics were calculated to grade the analytical performance. ResultsDifferent methods have different Sigma-metrics for each analyte reviewed. Summary Sigma-metrics estimate the percentage of the chemistry analytes that are expected to perform above Five Sigma, which is where optimized QC design can be implemented. The range of performance varies from 37% to 88%, exhibiting significant differentiation between instruments and manufacturers. Median Sigmas for the different manufacturers in three analytes (albumin, glucose, sodium) showed significant differentiation. ConclusionsChemistry tests are not commodities. Quality varies significantly from manufacturer to manufacturer, instrument to instrument, and method to method. The Sigma-assessments from multiple EQA/PT programs provide more insight into the performance of methods and instruments than any single program by itself. It is possible to produce a ranking of performance by manufacturer, instrument and individual method. Laboratories seeking optimal instrumentation would do well to consult this data as part of their decision-making process. To confirm that these assessments are stable and reliable, a longer term study should be conducted that examines more results over a longer time period.

Leukopak PBMC sample processing for preparing quality control material to support proficiency testing programs

External proficiency testing programs designed to evaluate the performance of end-point laboratories involved in vaccine and therapeutic clinical trials form an important part of clinical trial quality assurance. Good clinical laboratory practice (GCLP) guidelines recommend both assay validation and proficiency testing for assays being used in clinical trials, and such testing is facilitated by the availability of large numbers of well-characterized test samples. These samples can be distributed to laboratories participating in these programs and allow monitoring of laboratory performance over time and among participating sites when results are obtained with samples derived from a large master set. The leukapheresis procedure provides an ideal way to collect samples from participants that can meet the required number of cells to support these activities. The collection and processing of leukapheresis samples require tight coordination between the clinical and laboratory teams to collect, process, and cryopreserve large number of samples within the established ideal time of ≤8hours. Here, we describe our experience with a leukapheresis cryopreseration program that has been able to preserve the functionality of cellular subsets and that provides the sample numbers necessary to run an external proficiency testing program.

Screening for Down Syndrome in the United States: Results of Surveys in 2011 and 2012

Participants in a College of American Pathologists external proficiency testing program for first and second trimester Down syndrome screening. To determine the number of women screened for Down syndrome in the United States, along with the type of test received and to compare those results to earlier surveys in 1988 and 1992. Questionnaires regarding the type and number of Down syndrome tests performed per month were completed by participants in early 2011 and again in early 2012. After accounting for some of the missing responses, data from up to 131 laboratories indicated that 67% (2 764 020 of 4 130 000) to 72% (2012: 2 963 592 of 4 130 000) of US pregnancies received prenatal screening for Down syndrome. Second trimester tests were most common (2012: 60%; 1 770 024 of 2 963 592), followed by integrated (2012: 21%; 627 876 of 2 963 592), and first trimester (2012: 19%; 565 692 of 2 963 592). The 6 largest laboratories tested 61% of screened pregnancies and offered the widest array of tests, while the smallest 32 tested 1% and almost always offered only second trimester tests. The current population estimate of 72% pregnancies screened annually is higher than estimates from 1988 (25%) and 1992 (50%). Available testing choices are also more varied, and all testing methods perform better than those methods available 10 years ago. Clinicians should ensure that women are offered tests that follow recommended best-practice testing protocols, and screening laboratories should assess whether patient needs are being met.

Three-year experience of a CAP/ACMG methods-based external proficiency testing program for laboratories offering DNA sequencing for rare inherited disorders

Thousands of genetic tests are now offered clinically, but many are for rare disorders that are offered by only a few laboratories. The classic approach to disease-specific external proficiency testing programs is not feasible for such testing, yet calls have been made to provide external oversight. A methods-based Sequencing Educational Challenge Survey was launched in 2010, under joint administration of the College of American Pathologists and the American College of Medical Genetics and Genomics. Three sets of Sanger ABI sequence data were distributed twice per year. Participants were asked to identify, formally name, and interpret the sequence variant(s). Between 2010 and 2012, 117 laboratories participated. Using a proposed assessment scheme (e.g., at least 10 of 12 components correct), 98.3% of the 67 US participants had acceptable performance (235 of 239 challenges; 95% confidence interval: 95.8-99.5%) as compared with 88.9% (136 of 153; 95% confidence interval: 82.8-93.4%) for the 50 international participants. These data provide a high level of confidence that most US laboratories offering rare disease testing are providing consistent and reliable clinical interpretations. Methods-based proficiency testing programs may be one part of the solution to assessing genetic testing based on next-generation sequencing technology.

Standard Reference Material 2366 for Measurement of Human Cytomegalovirus DNA

Human cytomegalovirus (CMV), classified as human herpesvirus 5, is ubiquitous in human populations. Infection generally causes little illness in healthy individuals, but can cause life-threatening disease in those who are immunocompromised or in newborns through complications arising from congenital CMV infection. An important aspect in diagnosis and treatment is to track circulating viral load with molecular methods, particularly with quantitative PCR. Standardization is vital, because of interlaboratory variability (due in part to the variety of assays and calibrants). Toward that end, the U.S. National Institute of Standards and Technology produced a Standard Reference Material 2366 appropriate for establishing metrological traceability of assay calibrants. This standard is composed of CMV DNA (Towne(Δ147) bacterial artificial chromosome DNA). Regions of the CMV DNA that are commonly used as targets for PCR assays were sequenced. Digital PCR was used to quantify the DNA, with concentration expressed as copies per microliter. The materials were tested for homogeneity and stability. An interlaboratory study was conducted by Quality Control for Molecular Diagnostics (Glasgow, UK), in which one component of SRM 2366 was included for analysis by participants in a CMV external quality assessment and proficiency testing program.