Cleo Keppens

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

Personalized medicine has gained increasing importance in clinical oncology, and several clinically important biomarkers are implemented in routine practice. In an effort to guarantee high quality of molecular testing in France, three subsequent external quality assessment rounds were organized at the initiative of the National Cancer Institute between 2012 and 2014. The schemes included clinically relevant biomarkers for metastatic colorectal (KRAS, NRAS, BRAF, PIK3CA, microsatellite instability) and non-small cell lung cancer (EGFR, KRAS, BRAF, PIK3CA, ERBB2), and they represent the first multigene/multicancer studies throughout Europe. In total, 56 laboratories coordinated by 28 regional molecular centers participated in the schemes. Laboratories received formalin-fixed, paraffin-embedded samples and were asked to use routine methods for molecular testing to predict patient response to targeted therapies. They were encouraged to return results within 14 calendar days after sample receipt. Both genotyping and reporting were evaluated separately. During the three external quality assessment rounds, mean genotype scores were all above the preset standard of 90% for all biomarkers. Participants were mainly challenged in case of rare insertions or deletions. Assessment of the written reports showed substantial progress between the external quality assessment schemes on multiple criteria. Several essential elements such as the clinical interpretation of test results and the reason for testing still require improvement by continued external quality assessment education.

Review of the implementation of plasma ctDNA testing on behalf of IQN Path ASBL: a perspective from an EQA providers’ survey

Molecular biomarker analysis for the personalised treatment of non-small cell lung cancer (NSCLC) and colorectal cancer (CRC) is becoming more common, due to the number and availability of molecular targets for predictive biomarker testing increasing [1]. Clinical laboratories must implement accurate test procedures and provide timely and reliable test results, to ensure that appropriate therapies are administered to patients [2]. The challenge for laboratories is to keep pace with molecular biomarker developments while maintaining excellence in service standards. Plasma circulating tumour DNA (ctDNA) may be found in the blood of cancer patients, alongside a larger fraction of circulating free DNA (cfDNA). Plasma ctDNA testing is becoming more common in the management of cancer patients [3]. It has several advantages: in the absence of suitable or sufficient tissue biopsy, it yields material for molecular analysis, can demonstrate molecular resistance to targeted treatment and is an alternative to invasive tissue sampling [4]. Plasma ctDNA analysis may also prove useful in cases of intra- and inter-tumour heterogeneity [5]. With formal approval from the European Medicine Agency (EMA), several clinical applications for plasma ctDNA testing are now being considered, including the detection of Epidermal Growth Factor Receptor (EGFR) mutations in the plasma of patients with advanced NSCLC [6]. The implementation of new methods such as plasma ctDNA testing can be challenging for diagnostic laboratories. Indeed, it has been shown that inexperience in specialised and complex techniques can compromise the result quality [2, 7]. To address these issues, four EQA providers came together under the umbrella organisation the International Quality Network for Pathology IQN Path (IQN Path): Association Italiana di Oncologia Medica (AIOM), European Molecular Genetics Quality Network (EMQN), European Society of Pathology (ESP) EQA and the United Kingdom National External Quality Assessment Service (UK NEQAS) for Molecular Genetics. Their aim was to survey testing methods currently in use and to pilot an EQA which assessed the standards of plasma ctDNA testing. This article summarises the results of the survey, which evaluated current laboratory practices in this field and which will subsequently inform the design of a pilot EQA scheme for plasma ctDNA testing.

A stitch in time saves nine: external quality assessment rounds demonstrate improved quality of biomarker analysis in lung cancer

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.

Describing the Reportable Range Is Important for Reliable Treatment Decisions: A Multiple Laboratory Study for Molecular Tumor Profiling Using Next-Generation Sequencing

Because interpretation of next-generation sequencing (NGS) data remains challenging, optimization of the NGS process is needed to obtain correct sequencing results. Therefore, extensive validation and continuous monitoring of the quality is essential. NGS performance was compared with traditional detection methods and technical quality of nine NGS technologies was assessed. First, nine formalin-fixed, paraffin-embedded patient samples were analyzed by 114 laboratories by using different detection methods. No significant differences in performance were observed between analyses with NGS and traditional techniques. Second, two DNA control samples were analyzed for a selected number of variants by 26 participants with the use of nine different NGS technologies. Quality control metrics were analyzed from raw data files and a survey about routine procedures. Results showed large differences in coverages, but observed variant allele frequencies in raw data files were in line with predefined variant allele frequencies. Many false negative results were found because of low-quality regions, which were not reported as such. It is recommended to disclose the reportable range, the fraction of targeted genomic regions for which calls of acceptable quality can be generated, to avoid any errors in therapy decisions. NGS can be a reliable technique, only if essential quality control during analysis is applied and reported.

Accreditation, setting and experience as indicators to assure quality in oncology biomarker testing laboratories

BackgroundPredictive biomarkers allow clinicians to optimise cancer treatment decisions. Therefore, molecular biomarker test results need to be accurate and swiftly available. To ensure quality of oncology biomarker testing, external quality assessments (EQA) for somatic variant analyses were organised. This study hypothesised whether laboratory characteristics influence the performance of laboratories and whether these can be imposed before authorisation of biomarker testing.MethodsLongitudinal EQA data from the European Society of Pathology were available over six (metastatic colorectal cancer) and four years (non-small cell lung cancer), including the percentage of analysis errors and technical failures, and information on laboratory characteristics (accreditation status, laboratory setting, number of samples analysed and detection method). Statistical models for repeated measurements were used to analyse the association between the EQA results and the laboratory characteristics.ResultsLaboratory accreditation was associated with fewer analysis errors in early stages of biomarker introduction into the laboratory. Analysing more samples, or university and research laboratories showed better performance. Changing the detection method did not have an effect.ConclusionThe indicators support the clinicians in choosing molecular pathology laboratories by improving quality assurance and guaranteeing patient safety. Accreditation of laboratories, centralisation of biomarker testing or a university and research setting should be stimulated.