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Maver A, Lohmann K, Borovečki F, Wolstenholme N, Taylor RL, Spielmann M, Haack TB, Gerberding M, Peterlin B, Graessner H. Quality assurance for next-generation sequencing diagnostics of rare neurological diseases in the European Reference Network. Eur J Hum Genet 2024:10.1038/s41431-024-01639-2. [PMID: 38839988 DOI: 10.1038/s41431-024-01639-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/26/2024] [Accepted: 05/14/2024] [Indexed: 06/07/2024] Open
Abstract
In the past decade, next-generation sequencing (NGS) has revolutionised genetic diagnostics for rare neurological disorders (RND). However, the lack of standardised technical, interpretative, and reporting standards poses a challenge for ensuring consistent and high-quality diagnostics globally. To address this, the European Reference Network for Rare Neurological Diseases (ERN-RND) collaborated with the European Molecular Genetics Quality Network (EMQN) to establish an external quality assessment scheme for NGS-based diagnostics in RNDs. The scheme, initiated in 2021 with a pilot involving 29 labs and followed by a second round in 2022 with 42 labs, aimed to evaluate the performance of laboratories in genetic testing for RNDs. Each participating lab analysed genetic data from three hypothetical cases, assessing genotyping, interpretation, and clerical accuracy. Despite a majority of labs using exome or genome sequencing, there was considerable variability in gene content, sequencing quality, adherence to standards, and clinical guidance provision. Results showed that while most labs provided correct molecular diagnoses, there was significant variability in reporting technical quality, adherence to interpretation standards, reporting strategies, and clinical commentary. Notably, some labs returned results with the potential for adverse medical outcomes. This underscores the need for further harmonisation, guideline development, and external quality assessment in the evolving landscape of genomic diagnostics for RNDs. Overall, the experience with the scheme highlighted the generally good quality of participating labs but emphasised the imperative for ongoing improvement in data analysis, interpretation, and reporting to enhance patient safety.
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Affiliation(s)
- Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Katja Lohmann
- Institute of Neurogenetics, University of Luebeck, Luebeck, Germany
| | - Fran Borovečki
- Department of Neurology, University Hospital Centre Zagreb, Zagreb, Croatia
| | | | - Rachel L Taylor
- EMQN CIC, Unit 4 Enterprise Hse, Manchester Science Park, Manchester, UK
| | - Malte Spielmann
- Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Matthias Gerberding
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Holm Graessner
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.
- Centre for Rare Diseases, University of Tübingen, Tübingen, Germany.
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2
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Corominas J, Smeekens SP, Nelen MR, Yntema HG, Kamsteeg EJ, Pfundt R, Gilissen C. Clinical exome sequencing - mistakes and caveats. Hum Mutat 2022; 43:1041-1055. [PMID: 35191116 PMCID: PMC9541396 DOI: 10.1002/humu.24360] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 01/11/2022] [Accepted: 02/18/2022] [Indexed: 11/30/2022]
Abstract
Massive parallel sequencing technology has become the predominant technique for genetic diagnostics and research. Many genetic laboratories have wrestled with the challenges of setting up genetic testing workflows based on a completely new technology. The learning curve we went through as a laboratory was accompanied by growing pains while we gained new knowledge and expertise. Here we discuss some important mistakes that have been made in our laboratory through 10 years of clinical exome sequencing but that have given us important new insights on how to adapt our working methods. We provide these examples and the lessons that we learned to help other laboratories avoid to make the same mistakes.
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Affiliation(s)
- Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sanne P Smeekens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marcel R Nelen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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3
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Krivokuca A, Mihajlovic M, Susnjar S, Spasojevic IB, Minic I, Popovic L, Brankovic-Magic M. Mutational profile of hereditary breast and ovarian cancer - Establishing genetic testing guidelines in a developing country. Curr Probl Cancer 2021; 46:100767. [PMID: 34284872 DOI: 10.1016/j.currproblcancer.2021.100767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 05/16/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022]
Abstract
PURPOSE Because many countries lack the capacity to follow the international guidelines for genetic testing, we suggest the specific approach for establishing local genetic testing guidelines that could be applied in developing countries. We focus on hereditary breast (BC) and ovarian cancer (OC) in Serbia. METHODS From the cohort of 550 persons who were referred for genetic counseling at the Institute for Oncology and Radiology of Serbia, 392 were selected. Personal and family histories were collected and germline DNA was sequenced with NGS in a panel of 20 genes. RESULTS Pathogenic (PV) and likely-pathogenic variants (LPV) were detected in 8 genes with the frequency of 23.7%. The most frequent were in BRCA1(7.6%), BRCA2(4.8%), PALB2(4.1%) and CHEK2(3.8%). They were also detected in ATM(1.8%), NBN(0.8%), TP53(0.5%) and RAD51C(0.3%). Whereas high carrier probability (CP), bilateral BC, BC and OC in the same patient and family history (FH) of BC/OC, were the strongest predictors for BRCA1/2 PV/LPV, lower CP values and early age of BC onset without FH were associated with higher frequency of PALB2 and CHEK2 PV/LPV. CONCLUSIONS Population specific studies to identify specific mutational patterns and predictors of PV/LPV should be conducted in order to make scientifically sound and cost-effective guidelines for genetic testing in developing countries.
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Affiliation(s)
- Ana Krivokuca
- Department for genetic counseling for hereditary cancers, Institute for Oncology and radiology of Serbia, Belgrade.
| | - Milica Mihajlovic
- Department for genetic counseling for hereditary cancers, Institute for Oncology and radiology of Serbia, Belgrade
| | - Snezana Susnjar
- Medical Oncology Department, Institute of Oncology and Radiology of Serbia, Belgrade
| | | | - Ivana Minic
- Medical Oncology Department, Institute of Oncology and Radiology of Serbia, Belgrade
| | - Lazar Popovic
- Medical Oncology Department, Oncology Institute of Vojvodina, Sremska Kamenica, Serbia; Faculty of Medicine, University of Novi Sad, Novi Sad, Serbia
| | - Mirjana Brankovic-Magic
- Department for genetic counseling for hereditary cancers, Institute for Oncology and radiology of Serbia, Belgrade
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4
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Henslee CR, Telgenhoff D. Molecular genetic testing laboratory management: emerging challenges for quality assurance. J Histotechnol 2019; 42:240-244. [PMID: 31913795 DOI: 10.1080/01478885.2019.1630083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
For decades, laboratory managers in the area of molecular genetic testing have struggled to adapt to rapid technological change, growing demand, evolving regulatory frameworks, and frequently changing best practice guidelines. While impressive progress has been made, the scale and scope of these challenges is unlikely to decline in the near future. Instead the challenges are likely to become even more imposing as a result of the emerging new clinical applications, the need for increasingly comprehensive international regulatory and quality assurance frameworks, and the rapidly growing demand for molecular genetic testing in the developing world. All of these challenges can be expected to create new pressures in the areas of cost and efficiency. Efforts to increase the effectiveness and adaptability of quality assurance frameworks should be prioritized with increased attention by scholars, policymakers, and laboratory managers. This review will introduce and familiarize the reader with the basic historical trajectory for the development of quality management frameworks and standardization practices involved in the management of molecular genetic testing laboratories. This review will also identify recurrent dynamics that have posed challenges for quality assurance in the field.
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Affiliation(s)
- Charon R Henslee
- Department of Medical Laboratory Sciences, Tarleton State University, Stephenville, TX, USA
| | - Dale Telgenhoff
- Department of Medical Laboratory Sciences, Tarleton State University, Stephenville, TX, USA
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5
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Zhong Q, Wagner U, Kurt H, Molinari F, Cathomas G, Komminoth P, Barman-Aksözen J, Schneider-Yin X, Rey JP, Vassella E, Rogel U, Diebold J, McKee T, Jochum W, Kashofer K, Hofman P, Zischka M, Moch H, Rechsteiner M, Wild PJ. Multi-laboratory proficiency testing of clinical cancer genomic profiling by next-generation sequencing. Pathol Res Pract 2018; 214:957-963. [PMID: 29807778 DOI: 10.1016/j.prp.2018.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 05/15/2018] [Accepted: 05/19/2018] [Indexed: 01/08/2023]
Abstract
Next-generation sequencing (NGS) enables parallel analysis of multiple genomic targets. The increasing demand for NGS-based multiplexed molecular diagnostics requires standardized protocols and recommendations to ensure reproducibility and accuracy of test results for routine clinical decision making. However, the lack of clinical NGS data from multi-laboratory tests and the absence of inter-laboratory comparisons have hampered the establishment of instructive clinical NGS standards. To fill the gap, we set up Proficiency Testing (PT) for inter-laboratory comparison, in which formalin-fixed paraffin-embedded specimens from eight lung and eight colon cancers were analyzed by 15 European molecular diagnostic laboratories on three different platforms using multiple target enrichment systems. We first performed platform, test, and informatics pipeline validation and conducted sensitivity and specificity analysis by random in silico down-sampling. We then implemented a multi-level filtering strategy based on performance tests of base substitution, replicate runs, and Sanger sequencing verified variants. We finally applied the filter criteria to the NGS data from the respective PT participants and obtained high inter-laboratory agreement. We demonstrated accuracy, scalability, and robustness of NGS by means of PT, serving as a benchmark for detecting clinically actionable molecular alterations in research and diagnostic laboratories. In conclusion, this study strongly highlights the importance of establishing standards for NGS-based testing, particularly when the test results impact on clinical decisions, and systematically provides data sets from multiple different labs to infer such standards.
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Affiliation(s)
- Qing Zhong
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Zurich, Switzerland; Children's Medical Research Institute, University of Sydney, 2145, Westmead, Australia
| | - Ulrich Wagner
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Zurich, Switzerland
| | | | | | - Gieri Cathomas
- Institute of Pathology, Hospital Baselland, 4410, Liestal, Switzerland
| | - Paul Komminoth
- Institute of Pathology, Hospital Triemli, 8063, Zurich, Switzerland
| | | | | | | | - Erik Vassella
- Institute of Pathology, University Bern, 3010, Bern, Switzerland
| | - Uwe Rogel
- Institute of Pathology, Hospital Baden, 5404, Baden, Switzerland
| | - Joachim Diebold
- Institute of Pathology, Hospital Luzern, 6000, Luzern, Switzerland
| | - Thomas McKee
- Institute of Pathology, University Geneva, 1211, Geneva, Switzerland
| | - Wolfram Jochum
- Institute of Pathology, Hospital St. Gallen, 9007, St. Gallen, Switzerland
| | - Karl Kashofer
- Institute of Pathology, Medical University Graz, 8036, Graz, Austria
| | - Paul Hofman
- Institute of Pathology, Hospital Nice, CS, 91179, Nice, France
| | - Melanie Zischka
- Institute of Pathology, Hannover Medical School, 30625, Hannover, Germany
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Zurich, Switzerland
| | - Markus Rechsteiner
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Zurich, Switzerland.
| | - Peter J Wild
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091, Zurich, Switzerland; Senckenberg Institute of Pathology, University Hospital Frankfurt, 60590, Frankfurt, Germany.
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6
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Sánchez-Iglesias S, García-Solaesa V, García-Berrocal B, Sanchez-Martín A, Lorenzo-Romo C, Martín-Pinto T, Gaedigk A, González-Buitrago JM, Isidoro-García M. Role of Pharmacogenetics in Improving the Safety of Psychiatric Care by Predicting the Potential Risks of Mania in CYP2D6 Poor Metabolizers Diagnosed With Bipolar Disorder. Medicine (Baltimore) 2016; 95:e2473. [PMID: 26871771 PMCID: PMC4753865 DOI: 10.1097/md.0000000000002473] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
One of the main concerns in psychiatric care is safety related to drug management. Pharmacogenetics provides an important tool to assess causes that may have contributed the adverse events during psychiatric therapy. This study illustrates the potential of pharmacogenetics to identify those patients for which pharmacogenetic-guided therapy could be appropriate. It aimed to investigate CYP2D6 genotype in our psychiatric population to assess the value of introducing pharmacogenetics as a primary improvement for predicting side effects.A broad series of 224 psychiatric patients comprising psychotic disorders, depressive disturbances, bipolar disorders, and anxiety disorders was included. The patients were genotyped with the AmpliChip CYP450 Test to analyzing 33 allelic variants of the CYP2D6 gene.All bipolar patients with poor metabolizer status showed maniac switching when CYP2D6 substrates such as selective serotonin reuptake inhibitors were prescribed. No specific patterns were identified for adverse events for other disorders.We propose to utilize pharmacogenetic testing as an intervention to aid in the identification of patients who are at risk of developing affective switching in bipolar disorder treated with selective serotonin reuptake inhibitors, CYP2D6 substrates, and inhibitors.
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Affiliation(s)
- Santiago Sánchez-Iglesias
- From the Servicio de Psiquiatría, Hospital Universitario de Salamanca (SS-I, CL-R, TM-P); Instituto Biosanitario de Salamanca, IBSAL (VG-S, BG-B, AS-M, JML-R, MI-G); Servicio de Bioquímica Clínica, Hospital Universitario de Salamanca (BG-B, JMG-B, MI-G); Servicio de Farmacia, Hospital Universitario de Salamanca, Spain (AS-M); Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Hospital (AG); Department of Pediatrics, School of Medicine, University of Missouri-Kansas City, Kansas City, MO, USA (AG); and Departamento de Medicina, Universidad de Salamanca, Spain (MI-G)
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7
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Pacheco-Gonzalez RM, Avila C, Dávila I, García-Sánchez A, Hernández-Hernández L, Benito-Pescador D, Torres R, Prieto-Matos P, Isidoro-Garcia M, Lorente F, Sanz C. Analysis of FOXP3 gene in children with allergy and autoimmune diseases. Allergol Immunopathol (Madr) 2016; 44:32-40. [PMID: 25982578 DOI: 10.1016/j.aller.2015.01.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 01/26/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND Allergy and autoimmunity are important immunological entities underlying chronic diseases in children. In some cases both entities develop simultaneously in the same patient. FOXP3 gene codes for a transcription factor involved in regulation of the immune system. Considering that regulatory T cells are involved in controlling immunological disease development, and the relevant role of FOXP3 in this kind of T cells, the objective of this study was to analyse the FOXP3 gene in the most prevalent autoimmune diseases and/or allergies in childhood in a European population. METHODS A total of 255 Caucasian individuals, 95 controls and 160 patients diagnosed with allergic, autoimmune or both diseases were included in this study. The molecular analysis of FOXP3 was performed by DNA sequencing following the recommendations for quality of the European Molecular Genetics Quality Network. Genomic DNA was extracted from peripheral blood of all participants and was amplified using the polymerase chain reaction. After the visualisation of the amplified fragments by agarose gel-electrophoresis, they were sequenced. RESULTS Thirteen different polymorphisms in FOXP3 gene were found, seven of which had not been previously described. The mutated allele of SNP 7340C>T was observed more frequently in the group of male children suffering from both allergic and autoimmune diseases simultaneously (p=0.004, OR=16.2 [1.34-195.15]). CONCLUSIONS In this study we identified for first time genetic variants of FOXP3 that are significantly more frequent in children who share allergic and autoimmune diseases. These variants mainly affect regulatory sequences that could alter the expression levels of FOXP3 modifying its function including its role in Treg cells.
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Affiliation(s)
| | - C Avila
- Department of Statistics, University of Salamanca, Salamanca, Spain; Biosanitary Institute of Salamanca IBSAL, Salamanca, Spain
| | - I Dávila
- Biosanitary Institute of Salamanca IBSAL, Salamanca, Spain; Department of Allergy, University Hospital of Salamanca, Salamanca, Spain.
| | | | | | | | - R Torres
- Department of Paediatrics, University Hospital of Salamanca, Salamanca, Spain
| | - P Prieto-Matos
- Biosanitary Institute of Salamanca IBSAL, Salamanca, Spain; Department of Paediatrics, University Hospital of Salamanca, Salamanca, Spain
| | - M Isidoro-Garcia
- Biosanitary Institute of Salamanca IBSAL, Salamanca, Spain; Department of Clinical Biochemistry, University Hospital of Salamanca, Salamanca, Spain; Department of Medicine, University of Salamanca, Salamanca, Spain.
| | - F Lorente
- Biosanitary Institute of Salamanca IBSAL, Salamanca, Spain; Department of Paediatrics, University Hospital of Salamanca, Salamanca, Spain
| | - C Sanz
- Biosanitary Institute of Salamanca IBSAL, Salamanca, Spain; Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
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8
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Kalle E, Kubista M, Rensing C. Multi-template polymerase chain reaction. BIOMOLECULAR DETECTION AND QUANTIFICATION 2014; 2:11-29. [PMID: 27896140 PMCID: PMC5121205 DOI: 10.1016/j.bdq.2014.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 12/12/2022]
Abstract
PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.
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Affiliation(s)
- Elena Kalle
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Allmas alle 5, 75007 Uppsala, Sweden
| | - Mikael Kubista
- TATAA Biocenter, Odinsgatan 28, 41103 Göteborg, Sweden; Institute of Biotechnology, Czech Academy of Sciences
| | - Christopher Rensing
- Department of Plant and Environmental Sciences, Faculty of Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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9
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Berwouts S, Fanning K, Morris MA, Barton DE, Dequeker E. Quality assurance practices in Europe: a survey of molecular genetic testing laboratories. Eur J Hum Genet 2012; 20:1118-26. [PMID: 22739339 DOI: 10.1038/ejhg.2012.125] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In the 2000s, a number of initiatives were taken internationally to improve quality in genetic testing services. To contribute to and update the limited literature available related to this topic, we surveyed 910 human molecular genetic testing laboratories, of which 291 (32%) from 29 European countries responded. The majority of laboratories were in the public sector (81%), affiliated with a university hospital (60%). Only a minority of laboratories was accredited (23%), and 26% was certified. A total of 22% of laboratories did not participate in external quality assessment (EQA) and 28% did not use reference materials (RMs). The main motivations given for accreditation were to improve laboratory profile (85%) and national recognition (84%). Nearly all respondents (95%) would prefer working in an accredited laboratory. In accredited laboratories, participation in EQA (P<0.0001), use of RMs (P=0.0014) and availability of continuous education (CE) on medical/scientific subjects (P=0.023), specific tasks (P=0.0018), and quality assurance (P<0.0001) were significantly higher than in non-accredited laboratories. Non-accredited laboratories expect higher restriction of development of new techniques (P=0.023) and improvement of work satisfaction (P=0.0002) than accredited laboratories. By using a quality implementation score (QIS), we showed that accredited laboratories (average score 92) comply better than certified laboratories (average score 69, P<0.001), and certified laboratories better than other laboratories (average score 44, P<0.001), with regard to the implementation of quality indicators. We conclude that quality practices vary widely in European genetic testing laboratories. This leads to a potentially dangerous situation in which the quality of genetic testing is not consistently assured.
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Affiliation(s)
- Sarah Berwouts
- Department of Public Health, Biomedical Quality Assurance Research Unit, KU Leuven, Leuven, Belgium
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10
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Isidoro-García M, Sanz C, García-Solaesa V, Pascual M, Pescador DB, Lorente F, Dávila I. PTGDR gene in asthma: a functional, genetic, and epigenetic study. Allergy 2011; 66:1553-62. [PMID: 21883277 DOI: 10.1111/j.1398-9995.2011.02685.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Asthma affects more than 300 million individuals in the world. Several studies have demonstrated the importance of the genetic component. The aim of this study is to develop a holistic approach, including genetic, epigenetic, and expression analysis to study the Prostaglandin D2 receptor gene (PTGDR) in asthmatic patients. METHODS In this study, 637 Caucasian individuals were included. Genetic variants were characterized by sequencing, and haplotype and diplotype combinations were established. Electrophoretic mobility shift assays (EMSAs) were performed with different promoter variants. An epigenetic analysis of PTGDR was for the first time developed by MassArray assays, and gene expression was determined by real-time polymerase chain reaction. RESULTS The -197T > C (Fisher's P = 0.028) and -613C > T (Fisher's P < 0.001) polymorphisms were found to be significantly associated with allergic asthma and allergy to pollen and mites, respectively. In addition, several haplotype and diplotype combinations were associated with different allergy and asthma phenotypes. The presence of the -613C > T SNP determined variations in the EMSAs. Moreover, consistent differences in the methylation and expression patterns were observed between asthmatic patients and controls determining a 2.34-fold increase of PTGDR gene expression in asthmatic patients. CONCLUSIONS Genetic combinations described have functional implications in the PTGDR promoter activity by changing the transcription factors affinity that will help characterize different risk groups. The differences observed in the transcription factors affinity and in the methylation pattern bring insight into different transcription regulation in these patients. To the best of our knowledge, this is the first work in which the implication of genetic and epigenetic factors of PTGDR has been characterized pointing to putative therapeutic targets.
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Affiliation(s)
- M Isidoro-García
- Department of Clinical Biochemistry, University Hospital of Salamanca, Spain.
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11
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Approaches to quality management and accreditation in a genetic testing laboratory. Eur J Hum Genet 2010; 18 Suppl 1:S1-19. [PMID: 20720559 DOI: 10.1038/ejhg.2010.104] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Medical laboratories, and specifically genetic testing laboratories, provide vital medical services to different clients: clinicians requesting a test, patients from whom the sample was collected, public health and medical-legal instances, referral laboratories and authoritative bodies. All expect results that are accurate and obtained in an efficient and effective manner, within a suitable time frame and at acceptable cost. There are different ways of achieving the end results, but compliance with International Organization for Standardization (ISO) 15189, the international standard for the accreditation of medical laboratories, is becoming progressively accepted as the optimal approach to assuring quality in medical testing. We present recommendations and strategies designed to aid genetic testing laboratories with the implementation of a quality management system, including key aspects such as document control, external quality assessment, internal quality control, internal audit, management review, validation, as well as managing the human side of change. The focus is on pragmatic approaches to attain the levels of quality management and quality assurance required for accreditation according to ISO 15189, within the context of genetic testing. Attention is also given to implementing efficient and effective quality improvement.
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12
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Zhang L, Ni D, Feng Z. External quality assessment of the detection of rickettsioses in China. ASIAN PAC J TROP MED 2010. [DOI: 10.1016/s1995-7645(10)60205-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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13
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Sanz C, Isidoro-García M, Dávila I, de Pedro MP, Méndez SDA, Padrón J, Ruiz-SanFrancisco A, Lorente F. A new PTGDR promoter polymorphism in a population of children with asthma. Pediatr Allergy Immunol 2009; 20:151-6. [PMID: 18811623 DOI: 10.1111/j.1399-3038.2008.00772.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Recently, functional genetic variants of the PTGDR gene have been associated with asthma. The objective of this work was to study polymorphisms of the promoter region of PTGDR and their haplotype and diplotype combinations in a Spanish population of children with asthma. In this study, 200 Caucasian individuals were included. Asthma was specialist-physician diagnosed according to the ATS criteria. The polymorphisms were analyzed by direct sequencing. In the study, the new polymorphism (-613C > T) in the promoter region of PTGDR was analyzed. The CT genotype was more common in controls (17%) than in patients with asthma (1%) (p-value = 0.0003; OR, 0.057; 95% CI, 0.007-0.441). The CCCT CCCC diplotype (promoter positions -613, -549, -441, and -197) was more frequent in the group of patients with asthma [Fisher's p-value = 0.012; OR, 10.24; 95% CI (1.25-83.68)]; this diplotype is unambiguous. To our knowledge, this is the first study of -613C > T PTGDR polymorphism in patients. This analysis provides more complete information on influence of diplotype combinations of PTGDR polymorphisms in asthma.
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Affiliation(s)
- Catalina Sanz
- Department of Allergy, University of Salamanca, Salamanca, Spain
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Berwouts S, Gordon JT, Rundell CA, Barton DE, Dequeker E. Evaluation and use of a synthetic quality control material, included in the European external quality assessment scheme for cystic fibrosis. Hum Mutat 2008; 29:1063-70. [DOI: 10.1002/humu.20764] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Sanz C, Isidoro-García M, Dávila I, Moreno E, Laffond E, Avila C, Lorente F. Promoter genetic variants of prostanoid DP receptor (PTGDR) gene in patients with asthma. Allergy 2006; 61:543-8. [PMID: 16629782 DOI: 10.1111/j.1398-9995.2006.01025.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND PTGDR gene has been identified as an asthma-susceptibility gene. Recently, functional genetic variants have been associated with asthma. The objective of this work was to study -549T>C, -441C>T and -197T>C PTGDR promoter polymorphisms in a Spanish population. METHODS In this study, 197 Caucasian individuals were included. Asthma was specialist-physician diagnosed according to the American Thoracic Society (ATS) criteria and classified following the Global Initiative for Asthma (GINA) guidelines. Skin prick tests were performed in all patients. The polymorphisms were analyzed by direct sequencing. RESULTS -197T>C polymorphism was significantly associated with asthma [Fisher's P-value = 0.007, Monte Carlo P-value (10(4) simulations) = 0.004]. Multivariate analysis adjusted for age and sex confirmed this association with an increased risk of asthma (OR, 3.06; 95% CI, 1.28-7.32; P-value = 0.012). CCT CCC diplotype was associated with asthma (P-value < 0.0001; OR, 1.15; 95% CI, 1.07-1.23), specifically with allergic asthma (P-value < 0.0001). CCT CCC diplotype is unambiguous. All individuals carrying this diplotype had asthma. CONCLUSION We identified a specific promoter variant of PTGDR that could be associated with asthma. This diplotype is a combination of the two highest transcriptional efficiency haplotypes, recently described. Our in vivo results would support for the first time what was demonstrated in vitro about high-transcriptional efficiency PTGDR haplotypes in asthma.
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Affiliation(s)
- C Sanz
- Department of Allergy, University Hospital of Salamanca, Salamanca, Spain
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16
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Ahmad-Nejad P, Dorn-Beineke A, Pfeiffer U, Brade J, Geilenkeuser WJ, Ramsden S, Pazzagli M, Neumaier M. Methodologic European external quality assurance for DNA sequencing: the EQUALseq program. Clin Chem 2006; 52:716-27. [PMID: 16439604 DOI: 10.1373/clinchem.2005.061572] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND DNA sequencing is a key technique in molecular diagnostics, but to date no comprehensive methodologic external quality assessment (EQA) programs have been instituted. Between 2003 and 2005, the European Union funded, as specific support actions, the EQUAL initiative to develop methodologic EQA schemes for genotyping (EQUALqual), quantitative PCR (EQUALquant), and sequencing (EQUALseq). Here we report on the results of the EQUALseq program. METHODS The participating laboratories received a 4-sample set comprising 2 DNA plasmids, a PCR product, and a finished sequencing reaction to be analyzed. Data and information from detailed questionnaires were uploaded online and evaluated by use of a scoring system for technical skills and proficiency of data interpretation. RESULTS Sixty laboratories from 21 European countries registered, and 43 participants (72%) returned data and samples. Capillary electrophoresis was the predominant platform (n = 39; 91%). The median contiguous correct sequence stretch was 527 nucleotides with considerable variation in quality of both primary data and data evaluation. The association between laboratory performance and the number of sequencing assays/year was statistically significant (P <0.05). Interestingly, more than 30% of participants neither added comments to their data nor made efforts to identify the gene sequences or mutational positions. CONCLUSIONS Considerable variations exist even in a highly standardized methodology such as DNA sequencing. Methodologic EQAs are appropriate tools to uncover strengths and weaknesses in both technique and proficiency, and our results emphasize the need for mandatory EQAs. The results of EQUALseq should help improve the overall quality of molecular genetics findings obtained by DNA sequencing.
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Affiliation(s)
- Parviz Ahmad-Nejad
- Institute for Clinical Chemistry and the Department for Statistical Analysis, University Hospital Mannheim of the University of Heidelberg, Mannheim, Germany
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Pompanon F, Bonin A, Bellemain E, Taberlet P. Genotyping errors: causes, consequences and solutions. Nat Rev Genet 2005; 6:847-59. [PMID: 16304600 DOI: 10.1038/nrg1707] [Citation(s) in RCA: 665] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although genotyping errors affect most data and can markedly influence the biological conclusions of a study, they are too often neglected. Errors have various causes, but their occurrence and effect can be limited by considering these causes in the production and analysis of the data. Procedures that have been developed for dealing with errors in linkage studies, forensic analyses and non-invasive genotyping should be applied more broadly to any genetic study. We propose a protocol for estimating error rates and recommend that these measures be systemically reported to attest the reliability of published genotyping studies.
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Affiliation(s)
- François Pompanon
- Laboratoire d'Ecologie Alpine, UMR CNRS 5553, Université Joseph Fourier, B.P. 53, 38041 Grenoble Cedex 9, France.
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Birch L, English CA, Burns M, Keer JT. Generic Scheme for Independent Performance Assessment in the Molecular Biology Laboratory. Clin Chem 2004; 50:1553-9. [PMID: 15231684 DOI: 10.1373/clinchem.2003.029454] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Background: A variety of proficiency testing schemes are available for specific molecular analyses, but there is an acute need for more widely accessible schemes to assess and demonstrate general competence in DNA analysis.
Methods: Fifteen laboratories, including academic, clinical, and commercial organizations, were recruited into the prototype assessment exercise. A range of test samples were provided, and participants were required to extract DNA from simple matrices, perform PCR amplification, and score the samples as positive or negative by electrophoretic analysis of the amplification products. Results were requested as both gel images and a completed results table, and the performance of each laboratory was then scored on the submitted analytical results.
Results: Overall, laboratories performed the analysis successfully, with participants scoring a high proportion of the samples correctly in the two rounds of the scheme. However, not all of the laboratories were able to achieve amplification for all samples, and the performance of some laboratories was not consistent in the two rounds. In addition, several analytical problems were encountered at all stages of the process, including DNA extraction, PCR amplification, and correct recording of results.
Conclusions: The generic approach described here has enabled effective cross-sectoral benchmarking of laboratories from a variety of analytical sectors. The problems encountered by some participating laboratories highlight the need for quality control and checks at all stages of the process to ensure accuracy of results. A statistical analysis of the results (ANOVA) allowed meaningful comparison of the consistency and sensitivity achieved by laboratories, demonstrating that an effective balance was achieved between the level of data obtained from laboratories and the time expenditure required from participants.
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Affiliation(s)
- Lyndsey Birch
- BioAnalytical Innovation Team, LGC Ltd, Queens Road, Teddington, Middlesex TW11 0LY, UK
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Thunnissen FBJM, Tilanus MGJ, Ligtenberg MJL, Nederlof PM, Dinjens WNM, Meulemans E, Van den Brule AJC, van Noesel CJM, de Leeuw WJF, Schuuring E. Quality control in diagnostic molecular pathology in the Netherlands; proficiency testing for patient identification in tissue samples. J Clin Pathol 2004; 57:717-20. [PMID: 15220364 PMCID: PMC1770359 DOI: 10.1136/jcp.2003.011973] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
AIMS To describe the evolution of proficiency testing for molecular diagnostic pathology with respect to determining unambiguously the patient identity of tissue samples by microsatellite analysis. METHOD Four rounds of quality control exchanges of samples from different patients were sent with the purpose of identifying the correct origin of these samples. The samples were either paraffin wax embedded sections on glass, sections in tubes, or isolated DNA. Blinded samples were distributed to all participating laboratories. No restrictions to the method and short tandem repeat markers used for identification were imposed. RESULTS In four subsequent rounds the number of participating laboratories increased from three to 10. The numbers of samples tested increased in time from five to 12. The microsatellite markers used by the different laboratories showed little overlap. In the first three rounds, in which isolated DNA was provided, all samples were accurately classified irrespective of the microsatellite markers used. In the last round, which also included paraffin wax embedded sections, a small number of laboratories experienced problems, either with amplification or incorrect classification of a few samples. CONCLUSION Proficiency testing was useful, and showed country wide high quality and correct identification of (patient) samples with molecular techniques for diagnostic purposes.
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Affiliation(s)
- F B J M Thunnissen
- Department of Pathology, Canisius Wilhelmina Hospital, 6532 SZ Nijmegen, The Netherlands.
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Affiliation(s)
- Suzanne M Cox
- Association of Schools of Public Health, Washington DC, USA
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Raggi CC, Pinzani P, Paradiso A, Pazzagli M, Orlando C. External quality assurance program for PCR amplification of genomic DNA: an Italian experience. Clin Chem 2003; 49:782-91. [PMID: 12709370 DOI: 10.1373/49.5.782] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND External quality assurance (EQA) programs for diagnostic tests based on nucleic acid amplification have not been widely implemented in clinical laboratories and remain limited to few tests. Development of specific EQA programs based on application-based proficiency testing for any diagnostic molecular target is challenging. Development of EQA trials based on methodologic proficiency testing and directed to the evaluation of analytical aspects common to the majority of PCR-based tests may be valuable. METHODS We developed an EQA program for evaluation of DNA extraction and amplification and analysis of products after PCR. Participants received a package containing primers and reference materials to evaluate three specific controls for, respectively, DNA extraction (quality and quantity), PCR performance (specificity and efficiency), and interpretation of results after electrophoresis. Each participant was asked to return to the organizers a form with their numerical results and an aliquot of all amplified samples for joint evaluation. RESULTS Results varied in all phases of the experimental procedure: preamplification, amplification, and post-PCR interpretation. To give a general estimation on the quality of performances for each laboratory, we designed a score scheme in which the results of any specific action were evaluated on the basis of the distribution around the median consensus values. The maximum possible score was 84. On the basis of total score obtained by each laboratory, we created a qualitative ranking list that provided the final interpretation of results as excellent (>63 points; n = 4 laboratories), good (53-63 points; n = 13), sufficient (42-52 points; n = 15), poor (31-41 points; n = 3), and not acceptable (<31 points; n = 4). CONCLUSIONS This survey demonstrates the importance of EQA trials based on methodologic proficiency testing directed to evaluation of analytical aspects common to the majority of PCR-based tests.
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Affiliation(s)
- Claudia Casini Raggi
- Department of Clinical Physiopathology, University of Florence, viale Pieraccini 6, 50139 Florence, Italy
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