1
|
Chen Y, Zhao R, Huang Z, Chu C, Xiao Y, Hu X, Wang X. A small-scale external quality assessment for PCR detection of group B streptococcus in China. Clin Chim Acta 2024; 553:117733. [PMID: 38128816 DOI: 10.1016/j.cca.2023.117733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Group B streptococcus (GBS) is considered a leading cause of maternal and infant morbidity and mortality. Molecular diagnosis is a routinely used approach for GBS screening to protect pregnant women and prevent early-onset GBS neonatal disease. The objective of this study was to identify issues and guarantee the dependability of GBS molecular diagnosis by an external quality assessment (EQA) scheme. METHODS The EQA panel comprised eight samples spiked with 10-fold dilutions of GBS suspension (20-2,000,000 copies/mL), and 2 negative control samples. The panels were coded randomly and distributed to participating laboratories for GBS detection. RESULTS In total, 44 participating laboratories submitted results with eight commercial GBS PCR assays and one in-house assay. Among them, 36 obtained an acceptable or higher performance score, while 8 required improvement. Among the 440 results returned, 62 (14.1 %) were incorrect, including 5 false positives and 57 false negatives. CONCLUSIONS Our small-scale EQA showed that most participating laboratories have reliable diagnostic capacities for GBS PCR detection. Nonetheless, further improvements in the detection performance of some laboratories are required, particularly with low-concentration samples. Our survey also reinforces the use of EQA as an essential tool to evaluate the overall proficiency of clinical laboratories.
Collapse
Affiliation(s)
- Yingwei Chen
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Ran Zhao
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Zhongqiang Huang
- Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Chengxiang Chu
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Yanqun Xiao
- Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, China
| | - Xiaobo Hu
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, China; Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, China.
| | - Xueliang Wang
- Department of Quality Control Material R&D, Shanghai Center for Clinical Laboratory, Shanghai, China; Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, China.
| |
Collapse
|
2
|
Fan X, Bai Q, Shi C, Xiao Y, Wang X. External quality assessment for the molecular detection of microsatellite instability in China, 2021-2022. Expert Rev Mol Diagn 2023; 23:1037-1043. [PMID: 37682059 DOI: 10.1080/14737159.2023.2257133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/14/2023] [Accepted: 08/27/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND Microsatellite instability (MSI) analysis of tumors informs Lynch syndrome testing, therapeutic choice, and prognosis. The status of MSI is mainly detected by polymerase chain reaction coupled with capillary electrophoresis. However, there are various assays with different detection loci and the obtained results may vary. The objective of this study was to evaluate the concordance among different assays and the performance among different laboratories. METHODS External quality assessment (EQA) for the detection of MSI was performed in 2021 and 2022. Each sample panel consisted of five samples, including microsatellite-stable and MSI tumor tissues. The sample panels were coded at random, and the returned results were compared and scored. RESULTS The fully validated sample panels showed appropriate applicability with commercially available assays. There were eight false-negative results in 2021 and five false results (two false-positives and three false-negatives) in 2022. Among the participating laboratories, in 2021, 20 (74.07%) provided completely correct results; in 2022, 38 (92.68%) obtained an optimal score. CONCLUSION The molecular detection of MSI in China exhibited an improvement in a 2-year EQA study. Participation in EQA program is an efficient way of assessing the performance of laboratories and improving their ability.
Collapse
Affiliation(s)
- Xiaoyu Fan
- Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, P.R. China
| | - Qianming Bai
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, P.R. China
| | - Chunli Shi
- Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, P.R. China
| | - Yanqun Xiao
- Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, P.R. China
| | - Xueliang Wang
- Department of Molecular Biology, Shanghai Center for Clinical Laboratory, Shanghai, P.R. China
- Department of Molecular Diagnostic Innovation Technology, Shanghai Academy of Experimental Medicine, Shanghai, P.R. China
| |
Collapse
|
3
|
Verderio P, Ciniselli CM, Gaignaux A, Pastori M, Saracino S, Kofanova O, Betsou F. External Quality Assurance programs for processing methods provide evidence on impact of preanalytical variables. N Biotechnol 2022; 72:29-37. [PMID: 36049650 DOI: 10.1016/j.nbt.2022.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/09/2022] [Accepted: 08/28/2022] [Indexed: 12/14/2022]
Abstract
An annual External Quality Assurance (EQA) program has been provided to processing laboratories over the last ten years, allowing them to assess the performance of their processing methods, such as nucleic acid extractions or peripheral blood mononuclear cell (PBMC) isolation and cryopreservation. The objective of this study was to perform a global analysis on almost 1000 EQA scheme/participant data in order to assess (i) the impact of critical preanalytical factors on quantitative or qualitative attributes of different types of specimens and (ii) laboratory performance pattern over time. Statistical analysis was performed within each EQA scheme based on categorized preanalytical data provided by the participants and on centralized measurements of relevant quality attributes of the produced specimens (z-scores): DNA, cell-free (cf)DNA or RNA extraction from blood, DNA or RNA extraction from formalin fixed tissue, DNA or RNA extraction from frozen tissue, DNA extraction from saliva or stool, viable PBMC isolation and cryopreservation. The most critical preanalytical factors in nucleic acid extraction schemes were the nucleic acid extraction method and kit, the elution buffer, the enzymes used during extraction, the input material quantity and the storage temperature. Several indications of laboratory performance improvement over time could be seen. The conclusions are that EQA for processing methods provides unique evidence-based insights into the impact of preanalytical factors and the comparative performance of different processing methods and kits, while supporting laboratories in validating their processing methods.
Collapse
Affiliation(s)
- Paolo Verderio
- Unit of Bioinformatics and Biostatistics, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy
| | - Chiara Maura Ciniselli
- Unit of Bioinformatics and Biostatistics, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy
| | - Amélie Gaignaux
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, 1 rue Louis Rech, 3555, Luxembourg
| | - Marta Pastori
- Unit of Bioinformatics and Biostatistics, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy
| | - Sabrina Saracino
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, 1 rue Louis Rech, 3555, Luxembourg
| | - Olga Kofanova
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, 1 rue Louis Rech, 3555, Luxembourg.
| | - Fay Betsou
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, 1 rue Louis Rech, 3555, Luxembourg; Institut Pasteur, Université Paris Cité, CRBIP, F-75015 Paris, France
| |
Collapse
|
4
|
Wang D, Zhang Y, li R, Li J, Zhang R. Consistency and reproducibility of large panel next-generation sequencing: Multi-laboratory assessment of somatic mutation detection on reference materials with mismatch repair and proofreading deficiency. J Adv Res 2022; 44:161-172. [PMID: 36725187 PMCID: PMC9937796 DOI: 10.1016/j.jare.2022.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/16/2022] [Accepted: 03/27/2022] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION Clinical precision oncology increasingly relies on accurate genome-wide profiling using large panel next generation sequencing; however, difficulties in accurate and consistent detection of somatic mutation from individual platforms and pipelines remain an open question. OBJECTIVES To obtain paired tumor-normal reference materials that can be effectively constructed and interchangeable with clinical samples, and evaluate the performance of 56 panels under routine testing conditions based on the reference samples. METHODS Genes involved in mismatch repair and DNA proofreading were knocked down using the CRISPR-Cas9 technology to accumulate somatic mutations in a defined GM12878 cell line. They were used as reference materials to comprehensively evaluate the reproducibility and accuracy of detection results of oncopanels and explore the potential influencing factors. RESULTS In total, 14 paired tumor-normal reference DNA samples from engineered cell lines were prepared, and a reference dataset comprising 168 somatic mutations in a high-confidence region of 1.8 Mb were generated. For mutations with an allele frequency (AF) of more than 5% in reference samples, 56 panels collectively reported 1306 errors, including 729 false negatives (FNs), 179 false positives (FPs) and 398 reproducibility errors. The performance metric varied among panels with precision and recall ranging from 0.773 to 1 and 0.683 to 1, respectively. Incorrect and inadequate filtering accounted for a large proportion of false discovery (including FNs and FPs), while low-quality detection, cross-contamination and other sequencing errors during the wet bench process were other sources of FNs and FPs. In addition, low AF (<5%) considerably influenced the reproducibility and comparability among panels. CONCLUSIONS This study provided an integrated practice for developing reference standard to assess oncopanels in detecting somatic mutations and quantitatively revealed the source of detection errors. It will promote optimization, validation, and quality control among laboratories with potential applicability in clinical use.
Collapse
Affiliation(s)
- Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Yuanfeng Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Rui li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
| |
Collapse
|
5
|
Pancrazzi A, Ognibene A, Moncada A, Torre V. Experience of Uncommon EGFR Mutation in Lung Scheme Quality Program: Discussing Risks and Opportunities for the Improvement of Laboratory Response. Glob Med Genet 2021; 8:171-175. [PMID: 34877575 PMCID: PMC8635828 DOI: 10.1055/s-0041-1732481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/15/2021] [Indexed: 11/09/2022] Open
Abstract
Background
The quality programs can be considered to be a valuable tool for global and individual growth. Each result, obtained by a single laboratory, contributes to define the standardization of the response. In the case of the uncommon epidermal growth factor receptor (EGFR) mutations, the molecular result is sometimes difficult to interpret in terms of biological significance and therapy choosing. The standardization effort in the diagnostic lung setting also consists of active quality program participation.
Materials and Methods
The quality control analysis, which is defined as a clinical case, was performed by the extraction of DNA from FFPE sections and by RT-PCR on the EGFR (exons 19, 20, 21), BRAF, and KRAS genes. The laboratory performed a validation sequencing of EGFR exon 20 with the help of the Sanger method.
Results
The laboratory reported positivity for EGFR exon 20 insertions and negative results for BRAF and KRAS. The quality test finished with the redaction of a report containing the recommendation to consider the efficacy of therapy with tyrosine kinase inhibitors (TKI). This specific interpretation has determined poor performance judgment by the quality provider, which explained why most of these mutations are TKI-resistant.
Conclusions
This experience provides an opportunity to reflect on the critical aspects of this diagnostic setting. The detection of some uncommon EGFR mutations should entail the mutation characterization, especially for the rare exon 20 insertions, of which are not classifiable as “resistant.” Moreover, this experience allows reflecting on the quality program design, mandatory actions for the laboratory, and routine activity in the oncologic multidisciplinary team.
Collapse
Affiliation(s)
- Alessandro Pancrazzi
- Department of Laboratory Medicine, Clinical and Molecular Pathology Unit, San Donato Hospital, Arezzo, Italy
| | - Agostino Ognibene
- Department of Laboratory Medicine, Clinical and Molecular Pathology Unit, San Donato Hospital, Arezzo, Italy
| | - Alice Moncada
- Department of Laboratory Medicine, Clinical and Molecular Pathology Unit, San Donato Hospital, Arezzo, Italy
| | - Valerio Torre
- Department of Oncology, Pathological Anatomy Laboratory, San Donato Hospital, Arezzo, Italy
| |
Collapse
|
6
|
Hofman P. EGFR Status Assessment for Better Care of Early Stage Non-Small Cell Lung Carcinoma: What Is Changing in the Daily Practice of Pathologists? Cells 2021; 10:2157. [PMID: 34440926 PMCID: PMC8392580 DOI: 10.3390/cells10082157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 02/08/2023] Open
Abstract
The recent emergence of novel neoadjuvant and/or adjuvant therapies for early stage (I-IIIA) non-small cell lung carcinoma (NSCLC), mainly tyrosine kinase inhibitors (TKIs) targeting EGFR mutations and immunotherapy or chemo-immunotherapy, has suddenly required the evaluation of biomarkers predictive of the efficacy of different treatments in these patients. Currently, the choice of one or another of these treatments mainly depends on the results of immunohistochemistry for PD-L1 and of the status of EGFR and ALK. This new development has led to the setup of different analyses for clinical and molecular pathology laboratories, which have had to rapidly integrate a number of new challenges into daily practice and to establish new organization for decision making. This review outlines the impact of the management of biological samples in laboratories and discusses perspectives for pathologists within the framework of EGFR TKIs in early stage NSCLC.
Collapse
Affiliation(s)
- Paul Hofman
- Laboratory of Clinical and Experimental Pathology, CHU Nice, FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06108 Nice, France; ; Tel.: +33-492-038-855; Fax: +33-492-8850
- CHU Nice, FHU OncoAge, Hospital-Integrated Biobank BB-0033-00025, Université Côte d’Azur, 06000 Nice, France
| |
Collapse
|
7
|
The evolving landscape of biomarker testing for non-small cell lung cancer in Europe. Lung Cancer 2021; 154:161-175. [PMID: 33690091 DOI: 10.1016/j.lungcan.2021.02.026] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/18/2021] [Accepted: 02/21/2021] [Indexed: 12/31/2022]
Abstract
The discovery of oncogenic driver mutations rendering non-small cell lung cancer (NSCLC) targetable by small-molecule inhibitors, and the development of immunotherapies, have revolutionised NSCLC treatment. Today, instead of non-selective chemotherapies, all patients with advanced NSCLC eligible for treatment (and increasing numbers with earlier, less extensive disease) require fast and comprehensive screening of biomarkers for first-line patient selection for targeted therapy, chemotherapy, or immunotherapy (with or without chemotherapy). To avoid unnecessary re-biopsies, biomarker screening before first-line treatment should also include markers that are actionable from second-line onwards; PD-L1 expression testing is also mandatory before initiating treatment. Population differences exist in the frequency of oncogenic driver mutations: EGFR mutations are more frequent in Asia than Europe, whereas the converse is true for KRAS mutations. In addition to approved first-line therapies, a number of emerging therapies are being investigated in clinical trials. Guidelines for biomarker testing vary by country, with the number of actionable targets and the requirement for extensive molecular screening strategies expected to increase. To meet diagnostic demands, rapid screening technologies for single-driver mutations have been implemented. Improvements in DNA- and RNA-based next-generation sequencing technologies enable analysis of a group of genes in one assay; however, turnaround times remain relatively long. Consequently, rapid screening technologies are being implemented alongside next-generation sequencing. Further challenges in the evolving landscape of biomarker testing in NSCLC are actionable primary and secondary resistance mechanisms to targeted therapies. Therefore, comprehensive testing on re-biopsies, collected at the time of disease progression, in combination with testing of circulating tumour DNA may provide important information to guide second- or third-line therapies. Furthermore, longitudinal biomarker testing can provide insights into tumour evolution and heterogeneity during the course of the disease. We summarise best practice strategies for Europe in the changing landscape of biomarker testing at diagnosis and during treatment.
Collapse
|
8
|
Abstract
Response evaluation for cancer treatment consists primarily of clinical and radiological assessments. In addition, a limited number of serum biomarkers that assess treatment response are available for a small subset of malignancies. Through recent technological innovations, new methods for measuring tumor burden and treatment response are becoming available. By utilization of highly sensitive techniques, tumor-specific mutations in circulating DNA can be detected and circulating tumor DNA (ctDNA) can be quantified. These so-called liquid biopsies provide both molecular information about the genomic composition of the tumor and opportunities to evaluate tumor response during therapy. Quantification of tumor-specific mutations in plasma correlates well with tumor burden. Moreover, with liquid biopsies, it is also possible to detect mutations causing secondary resistance during treatment. This review focuses on the clinical utility of ctDNA as a response and follow-up marker in patients with non-small cell lung cancer, melanoma, colorectal cancer, and breast cancer. Relevant studies were retrieved from a literature search using PubMed database. An overview of the available literature is provided and the relevance of ctDNA as a response marker in anti-cancer therapy for clinical practice is discussed. We conclude that the use of plasma-derived ctDNA is a promising tool for treatment decision-making based on predictive testing, detection of resistance mechanisms, and monitoring tumor response. Necessary steps for translation to daily practice and future perspectives are discussed.
Collapse
|
9
|
Causes behind error rates for predictive biomarker testing: the utility of sending post-EQA surveys. Virchows Arch 2020; 478:995-1006. [PMID: 33225398 PMCID: PMC8099794 DOI: 10.1007/s00428-020-02966-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/14/2022]
Abstract
External quality assessment (EQA) schemes assess the performance of predictive biomarker testing in lung and colorectal cancer and have previously demonstrated variable error rates. No information is currently available on the underlying causes of incorrect EQA results in the laboratories. Participants in EQA schemes by the European Society of Pathology between 2014 and 2018 for lung and colorectal cancer were contacted to complete a survey if they had at least one analysis error or test failure in the provided cases. Of the 791 surveys that were sent, 325 were completed including data from 185 unique laboratories on 514 incorrectly analyzed or failed cases. For the digital cases and immunohistochemistry, the majority of errors were interpretation-related. For fluorescence in situ hybridization, problems with the EQA materials were reported frequently. For variant analysis, the causes were mainly methodological for lung cancer but variable for colorectal cancer. Post-analytical (clerical and interpretation) errors were more likely detected after release of the EQA results compared to pre-analytical and analytical issues. Accredited laboratories encountered fewer reagent problems and more often responded to the survey. A recent change in test methodology resulted in method-related problems. Testing more samples annually introduced personnel errors and lead to a lower performance in future schemes. Participation to quality improvement projects is important to reduce deviating test results in laboratories, as the different error causes differently affect the test performance. EQA providers could benefit from requesting root cause analyses behind errors to offer even more tailored feedback, subschemes, and cases.
Collapse
|
10
|
Keppens C, Schuuring E, Dequeker EMC. Managing Deviating EQA Results: A Survey to Assess the Corrective and Preventive Actions of Medical Laboratories Testing for Oncological Biomarkers. Diagnostics (Basel) 2020; 10:E837. [PMID: 33080995 PMCID: PMC7603102 DOI: 10.3390/diagnostics10100837] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 12/24/2022] Open
Abstract
Laboratories testing predictive biomarkers in lung and colorectal cancer are advised to participate in external quality assessment (EQA) schemes. This study aimed to investigate which corrective actions were taken by laboratories if predetermined performance criteria were not met, to ultimately improve current test practices. EQA participants from the European Society of Pathology between 2014 and 2018 for lung and colorectal cancer were contacted, if they had at least one analysis error or test failure in the provided cases, to complete a survey. For 72.4% of 514 deviating EQA results, an appropriate action was performed, most often including staff training (15.2%) and protocol revisions (14.6%). Main assigned persons were the molecular biologist (40.0%) and pathologist (46.5%). A change in test method or the use of complex techniques, such as next-generation sequencing, required more training and the involvement of dedicated personnel to reduce future test failures. The majority of participants adhered to ISO 15189 and implemented suitable actions by designated staff, not limited to accredited laboratories. However, for 27.6% of cases (by 20 laboratories) no corrective action was taken, especially for pre-analytic problems and complex techniques. The surveys were feasible to request information on results follow-up and further recommendations were provided.
Collapse
Affiliation(s)
- Cleo Keppens
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, University of Leuven, Kapucijnenvoer 35d, 3000 Leuven, Belgium;
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen (UMCG), University of Groningen, Hanzeplein 1, 9700 RB Groningen, The Netherlands;
| | - Elisabeth MC Dequeker
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, University of Leuven, Kapucijnenvoer 35d, 3000 Leuven, Belgium;
| |
Collapse
|
11
|
Thunnissen E, Weynand B, Udovicic-Gagula D, Brcic L, Szolkowska M, Hofman P, Smojver-Ježek S, Anttila S, Calabrese F, Kern I, Skov B, Perner S, Dale VG, Eri Z, Haragan A, Leonte D, Carvallo L, Prince SS, Nicholson S, Sansano I, Ryska A. Lung cancer biomarker testing: perspective from Europe. Transl Lung Cancer Res 2020; 9:887-897. [PMID: 32676354 PMCID: PMC7354119 DOI: 10.21037/tlcr.2020.04.07] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A questionnaire on biomarker testing previously used in central European countries was extended and distributed in Western and Central European countries to the pathologists participating at the Pulmonary Pathology Society meeting 26-28 June 2019 in Dubrovnik, Croatia. Each country was represented by one responder. For recent biomarkers the availability and reimbursement of diagnoses of molecular alterations in non-small cell lung carcinoma varies widely between different, also western European, countries. Reimbursement of such assessments varies widely between unavailability and payments by the health care system or even pharmaceutical companies. The support for testing from alternative sources, such as the pharmaceutical industry, is no doubt partly compensating for the lack of public health system support, but it is not a viable or long-term solution. Ideally, a structured access to testing and reimbursement should be the aim in order to provide patients with appropriate therapeutic options. As biomarker enabled therapies deliver a 50% better probability of outcome success, improved and unbiased reimbursement remains a major challenge for the future.
Collapse
Affiliation(s)
- Erik Thunnissen
- Department of Pathology, AmsterdamUMC, Location VU Medical Center, Amsterdam, The Netherlands
| | | | - Dalma Udovicic-Gagula
- Clinical Center University of Sarajevo, Department of Pathology and Cytology, Sarajevo, Bosnia and Herzegovina
| | - Luka Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Malgorzata Szolkowska
- National Tuberculosis and Lung Diseases Research Institute, Department of Pathology, Warsaw, Poland
| | - Paul Hofman
- Nice University Hospital, FHU OncoAge, Laboratory of Clinical and Experimental Pathology, Nice, France
| | - Silvana Smojver-Ježek
- Clinical Unit for Pulmonary Cytology, Department of Pathology and Cytology, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Sisko Anttila
- Department of Pathology, HUSLAB, Helsinki and Uusimaa Health Care District, Helsinki, Finland
| | - Fiorella Calabrese
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | - Izidor Kern
- Laboratory for cytology and pathology, University Clinic Golnik, Golnik, Slovenia
| | - Birgit Skov
- Department of Pathology, University Hospital, Copenhagen Ø, Denmark
| | - Sven Perner
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany;,Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Vibeke G. Dale
- Department of Pathology, St. Olavs Hospital, Trondheim, Norway
| | - Zivka Eri
- Institute for pulmonary diseases of Vojvodina, Department for Pathology, put dr Goldmana 4, Sremska Kamenica, Serbia
| | - Alex Haragan
- Department of Pathology, Royal Liverpool University Hospital, Liverpool, England
| | - Diana Leonte
- National Institute of Pneumology, Pathology Department, Bucharest, Romania
| | - Lina Carvallo
- Institute of Anatomical and Molecular Pathology, Faculty of Medicine – University of Coimbra, Coimbra, Portugal
| | - Spasenja Savic Prince
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Siobhan Nicholson
- Department of Histopathology, St. James’s Hospital, Dublin 8, Ireland
| | - Irene Sansano
- Pathology Department, Passeig de la Vall d’Hebron 119-129, Barcelona, Spain
| | - Ales Ryska
- The Fingerland Department of Pathology, Charles University Medical Faculty and University Hospital, Hradec Kralove, Czech Republic
| |
Collapse
|
12
|
Keppens C, Dequeker EMC, Rouleau E, 't Hart N, Bubendorf L, Dufraing K, Garrec C, Guéguen P, Lamy A, Marchetti A, Pauwels P, Ryska A, Tack V, Tornillo L, Van Casteren K, von der Thüsen JH, Zwaenepoel K, Lissenberg-Witte B, Thunnissen E, Schuuring E. Sensitive detection methods are key to identify secondary EGFR c.2369C>T p.(Thr790Met) in non-small cell lung cancer tissue samples. BMC Cancer 2020; 20:366. [PMID: 32357863 PMCID: PMC7193365 DOI: 10.1186/s12885-020-06831-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/06/2020] [Indexed: 01/15/2023] Open
Abstract
Background Correct identification of the EGFR c.2369C>T p.(Thr790Met) variant is key to decide on a targeted therapeutic strategy for patients with acquired EGFR TKI resistance in non-small cell lung cancer. The aim of this study was to evaluate the correct detection of this variant in 12 tumor tissue specimens tested by 324 laboratories participating in External Quality Assessment (EQA) schemes. Methods Data from EQA schemes were evaluated between 2013 and 2018 from cell lines (6) and resections (6) containing the EGFR c.2369C>T p.(Thr790Met) mutation. Adequate performance was defined as the percentage of tests for which an outcome was available and correct. Additional data on the used test method were collected from the participants. Chi-squared tests on contingency tables and a biserial rank correlation were applied by IBM SPSS Statistics version 25 (IBM, Armonk, NY, USA). Results In 26 of the 1190 tests (2.2%) a technical failure occurred. For the remaining 1164 results, 1008 (86.6%) were correct, 151 (12.9%) were false-negative and 5 (0.4%) included incorrect mutations. Correct p.(Thr790Met) detection improved over time and for repeated scheme participations. In-house non-next-generation sequencing (NGS) techniques performed worse (81.1%, n = 293) compared to non-NGS commercial kits (85.2%, n = 656) and NGS (97.0%, n = 239). Over time there was an increase in the users of NGS. Resection specimens performed worse (82.6%, n = 610 tests) compared to cell line material (90.9%, n = 578 tests), except for NGS (96.3%, n = 344 for resections and 98.6%, n = 312 for cell lines). Samples with multiple mutations were more difficult compared to samples with the single p.(Thr790Met) variant. A change of the test method was shown beneficial to reduce errors but introduced additional analysis failures. Conclusions A significant number of laboratories that offer p.(Thr790Met) testing did not detect this relevant mutation compared to the other EQA participants. However, correct identification of this variant is improving over time and was higher for NGS users. Revising the methodology might be useful to resolve errors, especially for resection specimens with low frequency or multiple variants. EQA providers should include challenging resections in the scheme.
Collapse
Affiliation(s)
- Cleo Keppens
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, University of Leuven, Leuven, Belgium
| | - Elisabeth M C Dequeker
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, University of Leuven, Leuven, Belgium
| | - Etienne Rouleau
- Service de Génétique des Tumeurs, Gustave Roussy, Villejuif Cedex, France
| | - Nils 't Hart
- Department of Pathology, University of Groningen, University Medical Center Groningen (UMCG), Hanzeplein 1, PO Box 30001, 9700, RB, Groningen, the Netherlands.,Department of Pathology, Isala, Zwolle, The Netherlands
| | - Lukas Bubendorf
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Kelly Dufraing
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, University of Leuven, Leuven, Belgium
| | - Céline Garrec
- Institut de Biologie, CHU Hôtel Dieu, Laboratoire de Génétique Moléculaire, Nantes Cedex 1, France
| | - Paul Guéguen
- CHRU Brest/Hôpital Morvan, Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Brest, France
| | - Aude Lamy
- CHU de Rouen / Hôpital Charles Nicolle, laboratoire de génétique somatique des tumeurs, Rouen Cedex, France
| | - Antonio Marchetti
- Laboratory of Molecular Diagnostics, Center for Advanced Studies and Technology, University of Chieti, 66100, Chieti, Italy
| | - Patrick Pauwels
- Department of Pathology, University Hospital Antwerp, Edegem, Belgium.,Centre for Oncological Research (CORE), University of Antwerp, Edegem, Belgium
| | - Ales Ryska
- Department of Pathology, Charles University Medical Faculty Hospital, Hradec Kralove, Czech Republic
| | - Véronique Tack
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, University of Leuven, Leuven, Belgium
| | - Luigi Tornillo
- Institute of Pathology, University Hospital Basel, Basel, Switzerland.,GILAB, Allschwil, AG, Switzerland
| | - Kaat Van Casteren
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, University of Leuven, Leuven, Belgium.,Department of Pathology, University Hospital Antwerp, Edegem, Belgium.,Centre for Oncological Research (CORE), University of Antwerp, Edegem, Belgium
| | - Jan H von der Thüsen
- Department of pathology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Karen Zwaenepoel
- Department of Pathology, University Hospital Antwerp, Edegem, Belgium.,Centre for Oncological Research (CORE), University of Antwerp, Edegem, Belgium
| | - Birgit Lissenberg-Witte
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Epidemiology and Biostatistics, Amsterdam, The Netherlands
| | - Erik Thunnissen
- Department of pathology, VU University Medical Center (VUMC) Amsterdam, Amsterdam, the Netherlands
| | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen (UMCG), Hanzeplein 1, PO Box 30001, 9700, RB, Groningen, the Netherlands.
| |
Collapse
|
13
|
Wang QL, Zhou CL, Yin YF, Xiao L, Wang Y, Li K. An enzymatic on/off switch-mediated assay for KRAS hotspot point mutation detection of circulating tumor DNA. J Clin Lab Anal 2020; 34:e23305. [PMID: 32207862 PMCID: PMC7439329 DOI: 10.1002/jcla.23305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/10/2019] [Accepted: 01/07/2020] [Indexed: 12/13/2022] Open
Abstract
Background To detect the mutations of KRAS gene in colorectal cancer patients and other cancer patients, it is of value to develop non‐invasive, sensitive, specific, easy, and low‐cost assays. Methods Templates harboring hotspot mutations of the KRAS gene were constructed, and primers were designed for evaluation of the specificity, and sensitivity of detection system consisted of exonuclease polymerase‐mediated on/off switch; then, gel electrophoresis and real‐time PCR were performed for verification. The assay was verified by testing the DNA pool of normal controls and circulating DNA (ctDNA) samples from 14 tumor patients, as compared to Sanger sequencing. Results A specific and sensitive assay consisted of exonuclease polymerase‐mediated on/off switch, and multiplex real‐time PCR method has been established. This assay could detect <100 copies of KRAS mutation in more than 10 million copies of wild‐type KRAS gene fragments. This assay was applied to test KRAS gene mutations in three cases of fourteen ctDNA samples, and the results were consistent with Sanger sequencing. However, this PCR‐based assay was more sensitive and easier to be interpreted. Conclusion This assay can detect the presence of KRAS hotspot mutations in clinical circulating tumor DNA samples. The assay has a potential to be used in early diagnosis of colorectal cancer as well as other types of cancer.
Collapse
Affiliation(s)
- Qing-Lin Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Cui-Lan Zhou
- Department of Human Anatomy, University of South China, Hengyang, China
| | - Yu-Fang Yin
- Department of Pharmacology and Neuroscience, SIU Medical School, Springfield, IL, USA
| | - Li Xiao
- Laboratory of Molecular Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuan Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Kai Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China.,GeneTalks Biotechnology Inc., Changsha, China
| |
Collapse
|
14
|
van den Broek D, Hiltermann TJN, Biesma B, Dinjens WNM, 't Hart NA, Hinrichs JWJ, Leers MPG, Monkhorst K, van Oosterhout M, Scharnhorst V, Schuuring E, Speel EJM, van den Heuvel MM, van Schaik RHN, von der Thüsen J, Willems SM, de Visser L, Ligtenberg MJL. Implementation of Novel Molecular Biomarkers for Non-small Cell Lung Cancer in the Netherlands: How to Deal With Increasing Complexity. Front Oncol 2020; 9:1521. [PMID: 32039011 PMCID: PMC6987414 DOI: 10.3389/fonc.2019.01521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/17/2019] [Indexed: 12/30/2022] Open
Abstract
The diagnostic landscape of non-small cell lung cancer (NSCLC) is changing rapidly with the availability of novel treatments. Despite high-level healthcare in the Netherlands, not all patients with NSCLC are tested with the currently relevant predictive tumor markers that are necessary for optimal decision-making for today's available targeted or immunotherapy. An expert workshop on the molecular diagnosis of NSCLC involving pulmonary oncologists, clinical chemists, pathologists, and clinical scientists in molecular pathology was held in the Netherlands on December 10, 2018. The aims of the workshop were to facilitate cross-disciplinary discussions regarding standards of practice, and address recent developments and associated challenges that impact future practice. This paper presents a summary of the discussions and consensus opinions of the workshop participants on the initial challenges of harmonization of the detection and clinical use of predictive markers of NSCLC. A key theme identified was the need for broader and active participation of all stakeholders involved in molecular diagnostic services for NSCLC, including healthcare professionals across all disciplines, the hospitals and clinics involved in service delivery, healthcare insurers, and industry groups involved in diagnostic and treatment innovations. Such collaboration is essential to integrate different technologies into molecular diagnostics practice, to increase nationwide patient access to novel technologies, and to ensure consensus-preferred biomarkers are tested.
Collapse
Affiliation(s)
- Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - T. Jeroen N. Hiltermann
- Department of Pulmonary Diseases, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Bonne Biesma
- Department of Pulmonary Diseases, Jeroen Bosch Hospital, 's-Hertogenbosch, Netherlands
| | - Winand N. M. Dinjens
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Nils A. 't Hart
- Department of Pathology, Isala Klinieken, Zwolle, Netherlands
| | - John W. J. Hinrichs
- Symbiant Pathology Expert Centre, Alkmaar, Netherlands
- Department of Pathology, University Medical Center, Utrecht, Netherlands
| | - Mathie P. G. Leers
- Department of Clinical Chemistry, Zuyderland Medical Center, Sittard-Geleen, Netherlands
| | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | | | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Ernst-Jan M. Speel
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, Netherlands
| | | | - Ron H. N. van Schaik
- Department of Clinical Chemistry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jan von der Thüsen
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Stefan M. Willems
- Department of Pathology, University Medical Center, Utrecht, Netherlands
| | | | - Marjolijn J. L. Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
- Department of Pathology, Radboud University Medical Center, Nijmegen, Netherlands
| |
Collapse
|
15
|
Ntzifa A, Kroupis C, Haliassos A, Lianidou E. A pilot plasma-ctDNA ring trial for the Cobas® EGFR Mutation Test in clinical diagnostic laboratories. Clin Chem Lab Med 2019; 57:e97-e101. [PMID: 30267626 DOI: 10.1515/cclm-2018-0676] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 08/20/2018] [Indexed: 11/15/2022]
Affiliation(s)
- Aliki Ntzifa
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Christos Kroupis
- Department of Clinical Biochemistry and Molecular Diagnostics, Attikon University General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Evi Lianidou
- Analysis of Circulating Tumor Cells, Lab of Analytical Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens 15771, Greece
| |
Collapse
|
16
|
Multicenter Evaluation of the Fully Automated PCR-Based Idylla EGFR Mutation Assay on Formalin-Fixed, Paraffin-Embedded Tissue of Human Lung Cancer. J Mol Diagn 2019; 21:1010-1024. [DOI: 10.1016/j.jmoldx.2019.06.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 05/14/2019] [Accepted: 06/13/2019] [Indexed: 01/19/2023] Open
|
17
|
One byte at a time: evidencing the quality of clinical service next-generation sequencing for germline and somatic variants. Eur J Hum Genet 2019; 28:202-212. [PMID: 31570784 PMCID: PMC6974611 DOI: 10.1038/s41431-019-0515-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/03/2019] [Accepted: 08/29/2019] [Indexed: 12/16/2022] Open
Abstract
Next-generation sequencing (NGS) is replacing other molecular techniques to become the de facto gene diagnostics approach, transforming the speed of diagnosis for patients and expanding opportunities for precision medicine. Consequently, for accredited laboratories as well as those seeking accreditation, both objective measures of quality and external review of laboratory processes are required. External quality assessment (EQA), or Proficiency Testing (PT), can assess a laboratory’s service through an independent external agency, the EQA provider. The analysis of a growing number of genes and whole exome and genomes is now routine; therefore, an EQA must be delivered to enable all testing laboratories to participate. In this paper, we describe the development of a unique platform and gene target independent EQA scheme for NGS, designed to scale from current to future requirements of clinical diagnostic laboratories testing for germline and somatic variants. The EQA results from three annual rounds indicate that clinical diagnostic laboratories are providing an increasingly high-quality NGS service and variant calling abilities are improving. From an EQA provider perspective, challenges remain regarding delivery and performance criteria, as well as in analysing similar NGS approaches between cohorts with meaningful metrics, sample sourcing and data formats.
Collapse
|
18
|
Jing R, Wang H, Ju S, Cui M. Reference materials for molecular diagnostics: Current achievements and future strategies. Clin Biochem 2018; 56:11-17. [DOI: 10.1016/j.clinbiochem.2018.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 04/08/2018] [Accepted: 04/17/2018] [Indexed: 02/06/2023]
|
19
|
Horan MP, Chai SY, Munusamy N, Tay KH, Wienholt L, Tye-Din JA, Daveson J, Varney M, Badrick T. High rates of variation in HLA-DQ2/DQ8 testing for coeliac disease: results from an RCPAQAP pilot program. J Clin Pathol 2018; 71:900-905. [PMID: 29764931 DOI: 10.1136/jclinpath-2018-205209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 04/29/2018] [Accepted: 04/30/2018] [Indexed: 12/27/2022]
Abstract
AIM Coeliac disease(CD) is a highly prevalent, gluten-dependent, autoimmune enteropathy. While the diagnosis is based on serological and histological criteria, genotyping of the human leucocyte antigens (HLA) DQ2 and DQ8 has been shown to have substantial clinical utility, especially in excluding the diagnosis in patients who do not carry either antigen. As a result, HLA genotyping is now being performed by more laboratories and has recently become one of the most frequently requested genetic tests in Australia. To date, there has been little scrutiny on the accuracy and reporting of results by laboratories new to HLA typing. In response to clinician feedback that identified potentially clinically significant discrepancies in HLA typing results, the Royal College of Pathologists of Australasia Quality Assurance Programs (RCPAQAP) undertook a pilot study to assess laboratory performance in the detection of HLA-DQ2/DQ8 and their associated HLA-DQA1 and HLA-DQB1 alleles. METHODS DNA was extracted from 5 patients and sent to 10 laboratories for external quality assurance (EQA) testing. Laboratories were assessed for reporting in genotyping, interpretation and methodology. RESULTS Our findings showed that at least 80% of laboratories underperform with respect to recommended guidelines for HLA typing and reporting for CD, with 40% of laboratories failing to provide any clinical interpretation or full genotyping data. This suboptimal level of reporting may lead to ambiguities for downstream clinical interpretation that may compromise patient management. CONCLUSIONS These findings highlight the importance of adherence to standardised guidelines for optimal performance and reporting of HLA results and substantiate the need for EQA and proficiency testing for laboratories providing this service.
Collapse
Affiliation(s)
| | - Sze Yee Chai
- RCPAQAP Molecular Genetics, St. Leonard's, Sydney, New South Wales, Australia
| | - Nalishia Munusamy
- RCPAQAP Molecular Genetics, St. Leonard's, Sydney, New South Wales, Australia
| | - Kwang Hong Tay
- RCPAQAP Molecular Genetics, St. Leonard's, Sydney, New South Wales, Australia
| | - Louise Wienholt
- RCPAQAP Molecular Genetics, St. Leonard's, Sydney, New South Wales, Australia
| | - Jason A Tye-Din
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Gastroenterology Department, The Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - James Daveson
- University of Queensland, Brisbane, Queensland, Australia.,Wesley Medical Research, Brisbane, Queensland, Australia.,St Andrew's War Memorial Hospital, Brisbane, Queensland, Australia
| | - Michael Varney
- Victorian Transplantation and Immunogenetics Service, Australian Red Cross Blood Service, Melbourne, Victoria, Australia
| | - Tony Badrick
- RCPAQAP Molecular Genetics, St. Leonard's, Sydney, New South Wales, Australia
| |
Collapse
|
20
|
Keppens C, Tack V, Hart N', Tembuyser L, Ryska A, Pauwels P, Zwaenepoel K, Schuuring E, Cabillic F, Tornillo L, Warth A, Weichert W, Dequeker E. A stitch in time saves nine: external quality assessment rounds demonstrate improved quality of biomarker analysis in lung cancer. Oncotarget 2018; 9:20524-20538. [PMID: 29755669 PMCID: PMC5945546 DOI: 10.18632/oncotarget.24980] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/26/2018] [Indexed: 12/23/2022] Open
Abstract
Biomarker analysis has become routine practice in the treatment of non-small cell lung cancer (NSCLC). To ensure high quality testing, participation to external quality assessment (EQA) schemes is essential. This article provides a longitudinal overview of the EQA performance for EGFR, ALK, and ROS1 analyses in NSCLC between 2012 and 2015. The four scheme years were organized by the European Society of Pathology according to the ISO 17043 standard. Participants were asked to analyze the provided tissue using their routine procedures. Analysis scores improved for individual laboratories upon participation to more EQA schemes, except for ROS1 immunohistochemistry (IHC). For EGFR analysis, scheme error rates were 18.8%, 14.1% and 7.5% in 2013, 2014 and 2015 respectively. For ALK testing, error rates decreased between 2012 and 2015 by 5.2%, 3.2% and 11.8% for the fluorescence in situ hybridization (FISH), FISH digital, and IHC subschemes, respectively. In contrast, for ROS1 error rates increased between 2014 and 2015 for FISH and IHC by 3.2% and 9.3%. Technical failures decreased over the years for all three markers. Results show that EQA contributes to an ameliorated performance for most predictive biomarkers in NSCLC. Room for improvement is still present, especially for ROS1 analysis.
Collapse
Affiliation(s)
- Cleo Keppens
- University of Leuven, Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, Leuven, Belgium
| | - Véronique Tack
- University of Leuven, Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, Leuven, Belgium
| | - Nils 't Hart
- University Medical Center Groningen, Department of Pathology, Groningen, The Netherlands
| | - Lien Tembuyser
- University of Leuven, Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, Leuven, Belgium
| | - Ales Ryska
- Charles University Medical Faculty and University Hospital, Department of Pathology, Hradec Kralove, Czech Republic
| | - Patrick Pauwels
- Center for Oncologic Research (CORE), University of Antwerp, Antwerp, Belgium
| | - Karen Zwaenepoel
- University Hospital Antwerp, Department of Pathology, Edegem, Belgium
| | - Ed Schuuring
- University Medical Center Groningen, Department of Pathology, Groningen, The Netherlands
| | - Florian Cabillic
- Cytogenetics and Cellular Biology Department, CHU de Rennes, Rennes, France.,INSERM, INRA, Université Rennes 1, Université Bretagne Loire, Nutrition Metabolisms and Cancer, Rennes, France
| | - Luigi Tornillo
- University of Basel, Basel, Switzerland.,GILAB AG, Allschwil, Switzerland
| | - Arne Warth
- University Hospital Heidelberg, Heidelberg, Germany
| | | | - Elisabeth Dequeker
- University of Leuven, Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit, Leuven, Belgium
| | | |
Collapse
|
21
|
Ryska A, Berzinec P, Brcic L, Cufer T, Dziadziuszko R, Gottfried M, Kovalszky I, Olszewski W, Oz B, Plank L, Timar J. NSCLC molecular testing in Central and Eastern European countries. BMC Cancer 2018. [PMID: 29523116 PMCID: PMC5845184 DOI: 10.1186/s12885-018-4023-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Background The introduction of targeted treatments for subsets of non-small cell lung cancer (NSCLC) has highlighted the importance of accurate molecular diagnosis to determine if an actionable genetic alteration is present. Few data are available for Central and Eastern Europe (CEE) on mutation rates, testing rates, and compliance with testing guidelines. Methods A questionnaire about molecular testing and NSCLC management was distributed to relevant specialists in nine CEE countries, and pathologists were asked to provide the results of EGFR and ALK testing over a 1-year period. Results A very high proportion of lung cancer cases are confirmed histologically/cytologically (75–100%), and molecular testing of NSCLC samples has been established in all evaluated CEE countries in 2014. Most countries follow national or international guidelines on which patients to test for EGFR mutations and ALK rearrangements. In most centers at that time, testing was undertaken on request of the clinician rather than on the preferred reflex basis. Immunohistochemistry, followed by fluorescent in situ hybridization confirmation of positive cases, has been widely adopted for ALK testing in the region. Limited reimbursement is a significant barrier to molecular testing in the region and a disincentive to reflex testing. Multidisciplinary tumor boards are established in most of the countries and centers, with 75–100% of cases being discussed at a multidisciplinary tumor board at specialized centers. Conclusions Molecular testing is established throughout the CEE region, but improved and unbiased reimbursement remains a major challenge for the future. Increasing the number of patients reviewed by multidisciplinary boards outside of major centers and access to targeted therapy based on the result of molecular testing are other major challenges. Electronic supplementary material The online version of this article (10.1186/s12885-018-4023-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ales Ryska
- The Fingerland Department of Pathology, Charles University Faculty of Medicine and University Hospital, Hradec Králové, Czech Republic.
| | - Peter Berzinec
- Department of Oncology, Specialised Hospital of St Zoerardus Zobor, Nitra, Slovakia
| | - Luka Brcic
- Institute of Pathology, Medical University of Graz, Graz, Austria.,Institute of Pathology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Tanja Cufer
- Medical Faculty Ljubljana, University Clinic Golnik, Golnik, Slovenia
| | | | | | - Ilona Kovalszky
- 1st Institute of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | | | - Buge Oz
- Cerrahpasa Medical Faculty, Istanbul, Turkey
| | - Lukas Plank
- Department of Pathology, Comenius University, Jessenius Medical Faculty and University Hospital, Martin, Slovakia
| | - Jozsef Timar
- 1st Institute of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| |
Collapse
|
22
|
Ellison G, Wallace A, Kohlmann A, Patton S. A comparative study of germline BRCA1 and BRCA2 mutation screening methods in use in 20 European clinical diagnostic laboratories. Br J Cancer 2017; 117:710-716. [PMID: 28751759 PMCID: PMC5572178 DOI: 10.1038/bjc.2017.223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/24/2017] [Accepted: 06/21/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Thousands of clinically relevant variations in BRCA1 and BRCA2 have been discovered and this poses a significant challenge with respect to the accurate detection, analysis turn-around time, characterisation and interpretation of these sequence variants. METHODS We evaluated the performance of different BRCA1/2 gene testing practices in routine diagnostic use in 20 European laboratories, with a focus on next-generation sequencing-based strategies as this is the technical approach implemented by or under adoption by most European clinical laboratories. Participant laboratories, selected on expertise and diagnostic service quality, tested 10 identical DNA samples containing a range of challenging pathogenic variants. RESULTS A small number of errors in the detection of pathogenic and significant variants were identified (2.6% diagnostic error rate). There was a high degree of concordance (>97%) across all laboratories for all variants detected. No systematic technical flaw was identified in the strategies employed across the participating laboratories. CONCLUSIONS The discrepancies identified are most likely due to human error or the way the methodology has been implemented locally, for example, next-generation sequencing bioinformatics pipelines, rather than technical limitations of the methods. The choice of BRCA1/2 testing method will therefore depend on multiple factors including required throughput and turn-around times, access to equipment, expertise and budget.
Collapse
Affiliation(s)
- Gillian Ellison
- AstraZeneca, Personalised Healthcare and Biomarkers, Alderley Park, Macclesfield SK10 4TG, UK
| | - Andrew Wallace
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester M13 9WL, UK
| | - Alexander Kohlmann
- AstraZeneca, Personalised Healthcare and Biomarkers, Alderley Park, Macclesfield SK10 4TG, UK
| | - Simon Patton
- European Molecular Genetics Quality Network, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester M13 9WL, UK
| |
Collapse
|
23
|
Malapelle U, Mayo-de-Las-Casas C, Molina-Vila MA, Rosell R, Savic S, Bihl M, Bubendorf L, Salto-Tellez M, de Biase D, Tallini G, Hwang DH, Sholl LM, Luthra R, Weynand B, Vander Borght S, Missiaglia E, Bongiovanni M, Stieber D, Vielh P, Schmitt F, Rappa A, Barberis M, Pepe F, Pisapia P, Serra N, Vigliar E, Bellevicine C, Fassan M, Rugge M, de Andrea CE, Lozano MD, Basolo F, Fontanini G, Nikiforov YE, Kamel-Reid S, da Cunha Santos G, Nikiforova MN, Roy-Chowdhuri S, Troncone G. Consistency and reproducibility of next-generation sequencing and other multigene mutational assays: A worldwide ring trial study on quantitative cytological molecular reference specimens. Cancer Cytopathol 2017; 125:615-626. [PMID: 28475299 DOI: 10.1002/cncy.21868] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/23/2017] [Accepted: 03/10/2017] [Indexed: 02/05/2023]
Abstract
BACKGROUND Molecular testing of cytological lung cancer specimens includes, beyond epidermal growth factor receptor (EGFR), emerging predictive/prognostic genomic biomarkers such as Kirsten rat sarcoma viral oncogene homolog (KRAS), neuroblastoma RAS viral [v-ras] oncogene homolog (NRAS), B-Raf proto-oncogene, serine/threonine kinase (BRAF), and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA). Next-generation sequencing (NGS) and other multigene mutational assays are suitable for cytological specimens, including smears. However, the current literature reflects single-institution studies rather than multicenter experiences. METHODS Quantitative cytological molecular reference slides were produced with cell lines designed to harbor concurrent mutations in the EGFR, KRAS, NRAS, BRAF, and PIK3CA genes at various allelic ratios, including low allele frequencies (AFs; 1%). This interlaboratory ring trial study included 14 institutions across the world that performed multigene mutational assays, from tissue extraction to data analysis, on these reference slides, with each laboratory using its own mutation analysis platform and methodology. RESULTS All laboratories using NGS (n = 11) successfully detected the study's set of mutations with minimal variations in the means and standard errors of variant fractions at dilution points of 10% (P = .171) and 5% (P = .063) despite the use of different sequencing platforms (Illumina, Ion Torrent/Proton, and Roche). However, when mutations at a low AF of 1% were analyzed, the concordance of the NGS results was low, and this reflected the use of different thresholds for variant calling among the institutions. In contrast, laboratories using matrix-assisted laser desorption/ionization-time of flight (n = 2) showed lower concordance in terms of mutation detection and mutant AF quantification. CONCLUSIONS Quantitative molecular reference slides are a useful tool for monitoring the performance of different multigene mutational assays, and this could lead to better standardization of molecular cytopathology procedures. Cancer Cytopathol 2017;125:615-26. © 2017 American Cancer Society.
Collapse
Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | | | - Rafael Rosell
- Catalan Institute of Oncology, Badalona, Spain
- Instituto Oncológico Dr Rosell (IOR), Quirón-Dexeus University Institute, Barcelona, Spain
| | - Spasenija Savic
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Michel Bihl
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Manuel Salto-Tellez
- Molecular Pathology Programme, Centre for Cancer Research and Cell Biology Queen's University Belfast, Belfast, United Kingdom
| | - Dario de Biase
- Department of Pharmacy and Biotechnology - University of Bologna, Bologna, Italy
| | | | - David H Hwang
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Rajyalakshmi Luthra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Birgit Weynand
- Department of Pathology, Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Sara Vander Borght
- Department of Pathology, Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Edoardo Missiaglia
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Massimo Bongiovanni
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | | | | | | | - Alessandra Rappa
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Massimo Barberis
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Nicola Serra
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit University of Padua, Padua, Italy
| | - Massimo Rugge
- Department of Medicine (DIMED), Surgical Pathology Unit University of Padua, Padua, Italy
| | | | - Maria D Lozano
- Department of Pathology, University Clinic of Navarra, Pamplona, Spain
| | - Fulvio Basolo
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Yuri E Nikiforov
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Suzanne Kamel-Reid
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
| | - Gilda da Cunha Santos
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
| | - Marina N Nikiforova
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | |
Collapse
|
24
|
Bernabé R, Hickson N, Wallace A, Blackhall FH. What do we need to make circulating tumour DNA (ctDNA) a routine diagnostic test in lung cancer? Eur J Cancer 2017; 81:66-73. [PMID: 28609695 DOI: 10.1016/j.ejca.2017.04.022] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/31/2017] [Accepted: 04/27/2017] [Indexed: 12/09/2022]
Abstract
The gold standard test for detection of epidermal growth factor receptor (EGFR) mutation is to genotype somatic DNA extracted from a tissue biopsy or cytology specimen. Yet, in at least 20% of patients this is not possible for various reasons including insufficient availability of neoplastic tissue, lack of fitness of the available tissue for a biopsy or that a biopsy is not technically feasible. Consequently, there has been intense investigation of circulating tumour DNA (ctDNA), released into the plasma fraction of blood from cancer cells during apoptosis/necrosis, as a minimally invasive 'liquid biopsy' and surrogate for cancer tissue. In 2014, the license for the EGFR tyrosine kinase inhibitor (EGFR-TKI), gefitinib, was updated to allow the use of plasma to determine EGFR mutation status in patients where tissue was not available. Then in 2016 the United States Food and Drug Administration (US FDA) approved the first companion diagnostic plasma EGFR test. Herein, we review the evidence for ctDNA as a diagnostic in patients with non-small cell lung cancer (NSCLC) and describe steps needed to incorporate such 'liquid biopsies' into everyday routine practice.
Collapse
Affiliation(s)
- Reyes Bernabé
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK; Medical Oncology Department, Hospital Virgen Del Rocio, Seville, Spain
| | - Nicholas Hickson
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester, UK
| | - Andrew Wallace
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester, UK
| | - Fiona Helen Blackhall
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, UK; Division of Molecular and Clinical Cancer Sciences, University of Manchester, Manchester, UK.
| |
Collapse
|
25
|
Lin G, Zhang K, Han Y, Li J. Quality control materials for pharmacogenomic testing in the clinic. Clin Chem Lab Med 2017; 55:926-933. [PMID: 27845879 DOI: 10.1515/cclm-2016-0755] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/05/2016] [Indexed: 12/27/2022]
Abstract
Pharmacogenomics has significantly added to our understanding of drug responses in clinical pharmacology, changing the paradigm of treatment decisions. Interrogations of both inherited and somatic variations for therapeutic purposes are increasingly being adopted in clinics, where quality control (QC) materials are required. However, for many pharmacogenomic tests, the acquisition of well-characterized QC materials is often difficult or impossible. In this review, several sources of appropriate QC materials for therapy-associated genetic testing are discussed. Among them, the novel methods for producing renewable controls that resemble patient samples are highlighted. Owing to technological complexity, more efforts are needed to develop proper controls for next-generation sequencing-based assay.
Collapse
|
26
|
Han Y, Zhang R, Lin G, Zhang K, Xie J, Li J. Quality Assessment of Reporting Performance for EGFR Molecular Diagnosis in Non-Small Cell Lung Cancer. Oncologist 2017; 22:1325-1332. [PMID: 28701573 DOI: 10.1634/theoncologist.2017-0042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/08/2017] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Reports serve as a bridge between laboratories and clinicians, help synthesize an overwhelming amount of raw data into evidence-based medicine, and play a significant role in designing clinical treatments. In an effort to guarantee high-quality epidermal growth factor receptor (EGFR) gene mutation testing and reporting performance, the National Center for Clinical Laboratories launched a proficiency testing (PT) scheme reflecting clinical practices in China since 2014. This study focuses on the quality assessment of gene mutation reports. MATERIALS AND METHODS Fifty-three laboratories that submitted reports in both 2014 and 2016 EGFR gene mutation PT schemes were selected for report analysis and comparison according to predefined evaluation criteria. RESULTS The average score for reports from 2014 was 14 out of 30 points. The overall scores for reports from 2016 improved substantially, yielding an average score of 20 out of 30 points. Among the evaluation criteria, general items were well documented in the reports. However, items specific to molecular diagnosis were far from satisfactory, and some items were even missing. CONCLUSION The quality assessment of clinical written reports from 2014 and 2016 demonstrates that substantial improvements have been made in overall reporting performance. However, not all statements pertaining to important elements met expectations. To continue education, repeated PT schemes need to be executed in a timely fashion to expose and address existing shortcomings in clinical reports. There remains ample room for improvement towards generating concise, comprehensive, and readable reports. IMPLICATIONS FOR PRACTICE This article compares the quality of clinical gene mutation reports submitted in 2014 to those submitted in 2016 epidermal growth factor receptor proficiency testing schemes, exposes the existing shortcomings, and discusses ways to communicate results more effectively in the future. The findings demonstrate that notable progress was observed in the overall reporting performance. However, key points specific to molecular diagnosis were far from expectation, and some items were even missing. Standardization needs to be emphasized to improve the report format and content. This article provides a reference that laboratories can use to write concise, comprehensive, and readily accessible clinical reports.
Collapse
Affiliation(s)
- Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| |
Collapse
|
27
|
Cheng MM, Palma JF, Scudder S, Poulios N, Liesenfeld O. The Clinical and Economic Impact of Inaccurate EGFR Mutation Tests in the Treatment of Metastatic Non-Small Cell Lung Cancer. J Pers Med 2017; 7:jpm7030005. [PMID: 28657610 PMCID: PMC5618152 DOI: 10.3390/jpm7030005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/26/2017] [Indexed: 01/17/2023] Open
Abstract
Advances in personalized medicine are supported by companion diagnostic molecular tests. Testing accuracy is critical for selecting patients for optimal therapy and reducing treatment-related toxicity. We assessed the clinical and economic impact of inaccurate test results between laboratory developed tests (LDTs) and a US Food and Drug Administration (FDA)-approved test for detection of epidermal growth factor receptor (EGFR) mutations. Using a hypothetical US cohort of newly diagnosed metastatic non-small cell lung cancer (NSCLC) patients and EURTAC (erlotinib versus standard chemotherapy as first-line treatment for European patients with advanced EGFR mutation-positive non-small-cell lung cancer) clinical trial data, we developed a decision analytic model to estimate the probability of misclassification with LDTs compared to a FDA-approved test. We estimated the clinical and economic impact of inaccurate test results by quantifying progression-free and quality-adjusted progression-free life years (PFLYs, QAPFLYs) lost, and costs due to incorrect treatment. The base-case analysis estimated 2.3% (n = 1422) of 60,502 newly diagnosed metastatic NSCLC patients would be misclassified with LDTs compared to 1% (n = 577) with a FDA-approved test. An average of 477 and 194 PFLYs were lost among the misclassified patients tested with LDTs compared to the FDA-approved test, respectively. Aggregate treatment costs for patients tested with LDTs were approximately $7.3 million more than with the FDA-approved test, due to higher drug and adverse event costs among patients incorrectly treated with targeted therapy or chemotherapy, respectively. Invalid tests contributed to greater probability of patient misclassification and incorrect therapy. In conclusion, risks associated with inaccurate EGFR mutation tests pose marked clinical and economic consequences to society. Utilization of molecular diagnostic tests with demonstrated accuracy could help to maximize the potential of personalized medicine.
Collapse
Affiliation(s)
- Mindy M Cheng
- Roche Molecular Systems, Inc., 4300 Hacienda Dr., Pleasanton, CA 94588, USA.
| | - John F Palma
- Roche Sequencing Solutions, 4300 Hacienda Dr., Pleasanton, CA 94588, USA.
| | - Sidney Scudder
- Roche Molecular Systems, Inc., 4300 Hacienda Dr., Pleasanton, CA 94588, USA.
| | - Nick Poulios
- Roche Molecular Systems, Inc., 4300 Hacienda Dr., Pleasanton, CA 94588, USA.
| | - Oliver Liesenfeld
- Roche Molecular Systems, Inc., 4300 Hacienda Dr., Pleasanton, CA 94588, USA.
| |
Collapse
|
28
|
Tack V, Dufraing K, Deans ZC, van Krieken HJ, Dequeker EMC. The ins and outs of molecular pathology reporting. Virchows Arch 2017; 471:199-207. [PMID: 28343306 DOI: 10.1007/s00428-017-2108-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/07/2017] [Accepted: 03/12/2017] [Indexed: 01/15/2023]
Abstract
The raid evolution in molecular pathology resulting in an increasing complexity requires careful reporting. The need for standardisation is clearer than ever. While synoptic reporting was first used for reporting hereditary genetic diseases, it is becoming more frequent in pathology, especially molecular pathology reports too. The narrative approach is no longer feasible with the growing amount of essential data present on the report, although narrative components are still necessary for interpretation in molecular pathology. On the way towards standardisation of reports, guidelines can be a helpful tool. There are several guidelines that focus on reporting in the field of hereditary diseases, but it is not always feasible to extrapolate these to the reporting of somatic variants in molecular pathology. The rise of multi-gene testing causes challenges for the laboratories. In order to provide a continuous optimisation of the laboratory testing process, including reporting, external quality assessment is essential and has already proven to improve the quality of reports. In general, a clear and concise report for molecular pathology can be created by including elements deemed important by different guidelines, adapting the report to the process flows of the laboratory and integrating the report with the laboratory information management system and the patient record.
Collapse
Affiliation(s)
- Véronique Tack
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Kapucijnenvoer 35 Blok D, 3000, Leuven, Belgium
| | - Kelly Dufraing
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Kapucijnenvoer 35 Blok D, 3000, Leuven, Belgium
| | - Zandra C Deans
- Department of Laboratory Medicine, UK NEQAS for Molecular Genetics, UK NEQAS Edinburgh, The Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Han J van Krieken
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elisabeth M C Dequeker
- Biomedical Quality Assurance Research Unit, Department of Public Health and Primary Care, KU Leuven, Kapucijnenvoer 35 Blok D, 3000, Leuven, Belgium.
| |
Collapse
|
29
|
Fiorentino M, Scarpelli M, Lopez-Beltran A, Cheng L, Montironi R. Considerations for standardizing predictive molecular pathology for cancer prognosis. Expert Rev Mol Diagn 2016; 17:47-55. [PMID: 27897454 DOI: 10.1080/14737159.2017.1266258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Molecular tests that were once ancillary to the core business of cyto-histopathology are becoming the most relevant workload in pathology departments after histopathology/cytopathology and before autopsies. This has resulted from innovations in molecular biology techniques, which have developed at an incredibly fast pace. Areas covered: Most of the current widely used techniques in molecular pathology such as FISH, direct sequencing, pyrosequencing, and allele-specific PCR will be replaced by massive parallel sequencing that will not be considered next generation, but rather, will be considered to be current generation sequencing. The pre-analytical steps of molecular techniques such as DNA extraction or sample preparation will be largely automated. Moreover, all the molecular pathology instruments will be part of an integrated workflow that traces the sample from extraction to the analytical steps until the results are reported; these steps will be guided by expert laboratory information systems. In situ hybridization and immunohistochemistry for quantification will be largely digitalized as much as histology will be mostly digitalized rather than viewed using microscopy. Expert commentary: This review summarizes the technical and regulatory issues concerning the standardization of molecular tests in pathology. A vision of the future perspectives of technological changes is also provided.
Collapse
Affiliation(s)
- Michelangelo Fiorentino
- a Pathology Service , Addarii Institute of Oncology, S. Orsola-Malpighi Hospital , Bologna , Italy
| | - Marina Scarpelli
- b Section of Pathological Anatomy , Marche Polytechnic University, School of Medicine, United Hospitals , Ancona , Italy
| | | | - Liang Cheng
- d Department of Pathology and Laboratory Medicine , Indiana University School of Medicine , Indianapolis , IN , USA
| | - Rodolfo Montironi
- a Pathology Service , Addarii Institute of Oncology, S. Orsola-Malpighi Hospital , Bologna , Italy
| |
Collapse
|
30
|
ctDNA Determination of EGFR Mutation Status in European and Japanese Patients with Advanced NSCLC: The ASSESS Study. J Thorac Oncol 2016; 11:1682-9. [DOI: 10.1016/j.jtho.2016.05.036] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/26/2016] [Accepted: 05/26/2016] [Indexed: 01/20/2023]
|
31
|
Overview of Thoracic Oncology Trials in Cooperative Groups Around the Globe. Clin Lung Cancer 2016; 18:5-12. [PMID: 27473736 DOI: 10.1016/j.cllc.2016.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 06/01/2016] [Accepted: 06/13/2016] [Indexed: 11/20/2022]
Abstract
Survival rates of patients with either early and advanced stage non-small-cell lung cancer (NSCLC) have improved with newer systemic therapy and radiation techniques, including combination regimens, targeted therapies, and immunotherapies. The cancer cooperative groups have historically played a critical role in the advancement of NSCLC therapy. Annually, representatives from cooperative groups worldwide convene at the International Lung Cancer Congress (ILCC). In summer 2015, the ILCC reached its 16th anniversary. This article highlights the NSCLC studies presented by participating groups in 2015.
Collapse
|
32
|
Tack V, Deans ZC, Wolstenholme N, Patton S, Dequeker EMC. What's in a Name? A Coordinated Approach toward the Correct Use of a Uniform Nomenclature to Improve Patient Reports and Databases. Hum Mutat 2016; 37:570-5. [DOI: 10.1002/humu.22975] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/04/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Véronique Tack
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit; KU Leuven; Leuven Belgium
| | - Zandra C. Deans
- Department of Laboratory Medicine, UK NEQAS for Molecular Genetics, UK NEQAS Edinburgh; The Royal Infirmary of Edinburgh; Edinburgh UK
| | - Nicola Wolstenholme
- EMQN, Manchester Centre for Genomic Medicine; St Mary's Hospital; Manchester M13 9WL UK
| | - Simon Patton
- EMQN, Manchester Centre for Genomic Medicine; St Mary's Hospital; Manchester M13 9WL UK
| | - Elisabeth M. C. Dequeker
- Department of Public Health and Primary Care, Biomedical Quality Assurance Research Unit; KU Leuven; Leuven Belgium
| |
Collapse
|
33
|
Dequeker EM, Keppens C, Egele C, Delen S, Lamy A, Lemoine A, Sabourin JC, Andrieu C, Ligtenberg M, Fetique D, Tops B, Descarpentries C, Blons H, Denoux Y, Aube C, Penault-Llorca F, Hofman P, Leroy K, Le Marechal C, Doucet L, Duranton-Tanneur V, Pedeutour F, Soubeyran I, Côté JF, Emile JF, Vignaud JM, Monhoven N, Haddad V, Laurent-Puig P, van Krieken H, Nowak F, Lonchamp E, Bellocq JP, Rouleau E. Three Rounds of External Quality Assessment in France to Evaluate the Performance of 28 Platforms for Multiparametric Molecular Testing in Metastatic Colorectal and Non-Small Cell Lung Cancer. J Mol Diagn 2016; 18:205-14. [DOI: 10.1016/j.jmoldx.2015.09.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/29/2015] [Accepted: 09/23/2015] [Indexed: 12/31/2022] Open
|
34
|
Gautschi O, Stadelmann C, Aebersold-Keller F, König K, Büttner R, Heukamp LC, Betticher D, Baumann C, Buser K, Calderoni A, Casty A, DʼAddario G, Irlé C, Mamot C, Morant R, Trojan A, Pellicioli E, Jehle-Schwertfeger S, Aebi S, Diebold J. Mutation Profiling of Lung Cancers with Long-Term Response to Gefitinib Therapy. Oncol Res Treat 2015; 38:560-9. [DOI: 10.1159/000441367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/01/2015] [Indexed: 11/19/2022]
|
35
|
Normanno N, Pinto C, Castiglione F, Fenizia F, Barberis M, Marchetti A, Fontanini G, De Rosa G, Taddei GL. The Italian external quality assessment for RAS testing in colorectal carcinoma identifies methods-related inter-laboratory differences. J Transl Med 2015; 13:287. [PMID: 26335936 PMCID: PMC4557483 DOI: 10.1186/s12967-015-0655-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/27/2015] [Indexed: 12/22/2022] Open
Abstract
Background In 2014 the European Medicines Agency included exon 2, 3 and 4 KRAS and NRAS testing for the selection of metastatic colorectal cancer (mCRC) patients eligible for the therapy with anti-EGFR monoclonal antibodies. The Italian Association of Medical Oncology (AIOM) and the Italian Society of Pathology and Cytology (SIAPEC) organized an external quality assessment (EQA) scheme for CRC to evaluate inter-laboratory consistency and to ensure standardization of the results in the transition from KRAS to all-RAS testing. Methods Ten formalin fixed paraffin embedded specimens including KRAS/NRAS (exons 2, 3, 4) and BRAF (codon 600) mutations were validated by three referral laboratories and sent to 88 participant centers. Molecular pathology sample reports were also requested to each laboratory. A board of assessors from AIOM and SIAPEC evaluated the results according to a predefined scoring system. The scheme was composed of two rounds. Results In the first round 36 % of the 88 participants failed, with 23 centers having at least one false positive or false negative while 9 centers did not meet the deadline. The genotyping error rate was higher when Sanger sequencing was employed for testing as compared with pyrosequencing (3 vs 1.3 %; p = 0.01; Pearson Chi Square test). In the second round, the laboratories improved their performance, with 23/32 laboratories passing the round. Overall, 79/88 participants passed the RAS EQA scheme. Standardized Human Genome Variation Society nomenclature was incorrectly used to describe the mutations identified and relevant variations were noticed in the genotype specification. Conclusion The results of the Italian RAS EQA scheme indicate that the mutational analyses are performed with good quality in many Italian centers, although significant differences in the methods used were highlighted. The relatively high number of centers failing the first round underlines the fundamental role in continued education covered by EQA schemes.
Collapse
Affiliation(s)
- Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori "Fondazione Giovanni Pascale"-IRCCS, Via M. Semmola, 80131, Naples, Italy. .,Laboratory of Pharmacogenomics, Centro di Ricerche Oncologiche di Mercogliano (CROM), Istituto Nazionale Tumori "Fondazione Giovanni Pascale" IRCCS, Naples, Italy.
| | - Carmine Pinto
- Medical Oncology, S. Maria Hospital - IRCCS, Reggio Emilia, Italy.
| | - Francesca Castiglione
- Department of Human Pathology and Oncology, University of Florence, Florence, Italy.
| | - Francesca Fenizia
- Laboratory of Pharmacogenomics, Centro di Ricerche Oncologiche di Mercogliano (CROM), Istituto Nazionale Tumori "Fondazione Giovanni Pascale" IRCCS, Naples, Italy.
| | - Massimo Barberis
- Department of Pathology and Laboratory Medicine, European Institute of Oncology, Milan, Italy.
| | - Antonio Marchetti
- Center of Predictive Molecular Medicine, University-Foundation, CeSI Biotech, Chieti, Italy.
| | - Gabriella Fontanini
- Division of Pathological Anatomy, Department of Surgical, Medical, Molecular Pathology and Critical Care, University of Pisa, Pisa, Italy.
| | - Gaetano De Rosa
- Pathology Section, Department of Advanced Biomedical Sciences, University of Naples Federico II, Naples, Italy.
| | - Gian Luigi Taddei
- Department of Human Pathology and Oncology, University of Florence, Florence, Italy.
| |
Collapse
|
36
|
Berg J, Fjellbirkeland L, Suhrke P, Jebsen P, Lund-Iversen M, Kleinberg L, Helgeland L, Brustugun OT, Helland Å. EGFR mutation testing of lung cancer patients - Experiences from Vestfold Hospital Trust. Acta Oncol 2015; 55:149-55. [PMID: 26313507 DOI: 10.3109/0284186x.2015.1062537] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Patients with advanced stage lung cancer and somatic mutations in the epithelial growth factor receptor (EGFR) gene are currently treated with tyrosine-kinase inhibitors. The Norwegian Lung Cancer Group (NLCG) recommended EGFR testing of all patients with non-small cell lung carcinoma (NSCLC) from June 2010. From March 2013, testing of squamous cell carcinomas was terminated. We have analysed how these recommendation were followed at a medium-sized Norwegian hospital and we present data on mutation frequency, retesting and possible explanations for missing test results. MATERIAL AND METHODS All pathology reports for patients diagnosed with NSCLC at Vestfold Hospital Trust were examined for the period June 2010 to December 2013. Mutation analyses were done at the Department of Pathology, Oslo University Hospital. RESULTS Material was sent for EGFR analysis for 256 of the 304 eligible patients diagnosed in the period. Material from 48 patients was never sent for EGFR testing, of which five samples consisted of too few tumour cells. For the rest, no obvious reason for omitting EGFR mutation analyses was identified. During the first six months of our study period, material from 25 of 66 NSCLC patients (38%) was not tested, whereas only six of the 118 patients (5%) in 2013 were not tested. For 34 patients, the first tissue specimen contained too few tumour cells and a new sample was sent for EGFR analyses for 11 of these. EGFR mutation was detected in 7.1% of the analysed NSCLC and in 9.4% of adenocarcinomas. DISCUSSION Especially for patients with advanced stages of NSCLC, EGFR mutation status is necessary for treatment stratification. Our results show that the guidelines were followed increasingly over time for patients diagnosed with NSCLC at the Vestfold Hospital Trust. The establishment of interdisciplinary meetings has improved the diagnostic routines.
Collapse
Affiliation(s)
- Janna Berg
- a Department of Medicine , Vestfold Hospital Trust , Tønsberg , Norway
| | - Lars Fjellbirkeland
- b Department of Pulmonology , Oslo University Hospital Rikshospitalet , Oslo , Norway
| | - Pål Suhrke
- c Department of Pathology , Vestfold Hospital Trust , Tønsberg , Norway
| | - Peter Jebsen
- d Department of Pathology , Oslo University Hospital , Oslo , Norway
| | | | - Lilach Kleinberg
- d Department of Pathology , Oslo University Hospital , Oslo , Norway
| | - Lars Helgeland
- e Department of Pathology , Haukeland Universitetssykehus , Haukeland , Norway
| | - Odd Terje Brustugun
- f Department of Genetics/Oncology , Oslo University Hospital , Oslo , Norway
| | - Åslaug Helland
- f Department of Genetics/Oncology , Oslo University Hospital , Oslo , Norway
| |
Collapse
|
37
|
Endorsing good quality assurance practices in molecular pathology: risks and recommendations for diagnostic laboratories and external quality assessment providers. Virchows Arch 2015; 468:31-41. [PMID: 26306715 DOI: 10.1007/s00428-015-1839-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/06/2015] [Accepted: 08/17/2015] [Indexed: 12/13/2022]
Abstract
Quality assurance is an indispensable element in a molecular diagnostic laboratory. The ultimate goal is to warrant patient safety. Several risks that can compromise high quality procedures are at stake, from sample collection to the test performed by the laboratory, the reporting of test results to clinicians, and the organization of effective external quality assessment schemes. Quality assurance should therefore be safeguarded at each level and should imply a holistic multidisciplinary approach. This review aims to provide an overview of good quality assurance practices and discusses certain risks and recommendations to promote and improve quality assurance for both diagnostic laboratories and for external quality assessment providers. The number of molecular targets is continuously rising, and new technologies are evolving. As this poses challenges for clinical implementation and increases the demand for external quality assessment, the formation of an international association for improving quality assurance in molecular pathology is called for.
Collapse
|
38
|
Roemen GM, zur Hausen A, Speel EJM. Adequate tissue for adequate diagnosis: what do we really need? Lung Cancer 2015. [DOI: 10.1183/2312508x.10010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
39
|
Abstract
Cancer is a disease of the genome with diverse aetiologies including the accumulation of acquired mutations throughout the genome. There has been a flood of knowledge improving our understanding of the biology and molecular genetics of melanoma, lung and colorectal cancer since the genomics era started. Translation of this knowledge into a better understanding of cell proliferation, survival and apoptosis has produced a paradigm shift in medical oncology enabling gene-based cancer treatment (called personalised or precision medicine). Somatic mutation analysis is crucial for a genomics approach since it can identify driver mutations-the "Achilles' heel" of cancer, and support clinical decision-making through targeted therapy. Nevertheless, the applications of somatic DNA testing in cancer face many challenges such as obtaining comprehensive coverage of the cancer genome with limited DNA being available, and delivering an accurate report in a timely fashion without false-negative and false-positive results. Further advances in DNA technologies and bioinformatics will overcome these issues and maximise opportunities for targeted therapy. Somatic mutation analysis will then become an integral part of cancer management for all malignancies.
Collapse
Affiliation(s)
- Bing Yu
- 1 Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia ; 2 Sydney Medical School (Central), the University of Sydney, NSW 2006, Australia ; 3 Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Sandra A O'Toole
- 1 Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia ; 2 Sydney Medical School (Central), the University of Sydney, NSW 2006, Australia ; 3 Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| | - Ronald J Trent
- 1 Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia ; 2 Sydney Medical School (Central), the University of Sydney, NSW 2006, Australia ; 3 Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
| |
Collapse
|
40
|
Kapp JR, Diss T, Spicer J, Gandy M, Schrijver I, Jennings LJ, Li MM, Tsongalis GJ, de Castro DG, Bridge JA, Wallace A, Deignan JL, Hing S, Butler R, Verghese E, Latham GJ, Hamoudi RA. Variation in pre-PCR processing of FFPE samples leads to discrepancies in BRAF and EGFR mutation detection: a diagnostic RING trial. J Clin Pathol 2014; 68:111-8. [PMID: 25430497 PMCID: PMC4316935 DOI: 10.1136/jclinpath-2014-202644] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Aims Mutation detection accuracy has been described extensively; however, it is surprising that pre-PCR processing of formalin-fixed paraffin-embedded (FFPE) samples has not been systematically assessed in clinical context. We designed a RING trial to (i) investigate pre-PCR variability, (ii) correlate pre-PCR variation with EGFR/BRAF mutation testing accuracy and (iii) investigate causes for observed variation. Methods 13 molecular pathology laboratories were recruited. 104 blinded FFPE curls including engineered FFPE curls, cell-negative FFPE curls and control FFPE tissue samples were distributed to participants for pre-PCR processing and mutation detection. Follow-up analysis was performed to assess sample purity, DNA integrity and DNA quantitation. Results Rate of mutation detection failure was 11.9%. Of these failures, 80% were attributed to pre-PCR error. Significant differences in DNA yields across all samples were seen using analysis of variance (p<0.0001), and yield variation from engineered samples was not significant (p=0.3782). Two laboratories failed DNA extraction from samples that may be attributed to operator error. DNA extraction protocols themselves were not found to contribute significant variation. 10/13 labs reported yields averaging 235.8 ng (95% CI 90.7 to 380.9) from cell-negative samples, which was attributed to issues with spectrophotometry. DNA measurements using Qubit Fluorometry demonstrated a median fivefold overestimation of DNA quantity by Nanodrop Spectrophotometry. DNA integrity and PCR inhibition were factors not found to contribute significant variation. Conclusions In this study, we provide evidence demonstrating that variation in pre-PCR steps is prevalent and may detrimentally affect the patient's ability to receive critical therapy. We provide recommendations for preanalytical workflow optimisation that may reduce errors in down-stream sequencing and for next-generation sequencing library generation.
Collapse
Affiliation(s)
- Joshua R Kapp
- Division of Surgery and Interventional Sciences, University College London, London, UK
| | - Tim Diss
- University College London Advanced Diagnostics, University College London, London, UK
| | - James Spicer
- Division of Research Oncology, Guy's and St. Thomas' Hospital NHS Trust, London, UK
| | - Michael Gandy
- University College London Advanced Diagnostics, University College London, London, UK
| | - Iris Schrijver
- Department of Pathology, Stanford University Medical Center, Stanford, USA
| | - Lawrence J Jennings
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Marilyn M Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, USA
| | | | | | - Julia A Bridge
- Department of Pathology, University of Nebraska Medical Center, Omaha, USA
| | - Andrew Wallace
- Regional Genetics Laboratory, Central Manchester University Hospital NHS Trust, Manchester, UK
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, UCLA School of Medicine, Los Angeles, USA
| | - Sandra Hing
- Paediatric Malignancy Department, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Rachel Butler
- All Wales Genetics Laboratory, Cardiff and Vale NHS Trust, Cardiff, UK
| | - Eldo Verghese
- Pathology and Tumour biology, University of Leeds, Leeds, UK
| | | | - Rifat A Hamoudi
- Division of Surgery and Interventional Sciences, University College London, London, UK
| |
Collapse
|