Els Dequeker

Consensus on the use and interpretation of cystic fibrosis mutation analysis in clinical practice

It is often challenging for the clinician interested in cystic fibrosis (CF) to interpret molecular genetic results, and to integrate them in the diagnostic process. The limitations of genotyping technology, the choice of mutations to be tested, and the clinical context in which the test is administered can all influence how genetic information is interpreted. This paper describes the conclusions of a consensus conference to address the use and interpretation of CF mutation analysis in clinical settings. Although the diagnosis of CF is usually straightforward, care needs to be exercised in the use and interpretation of genetic tests: genotype information is not the final arbiter of a clinical diagnosis of CF or CF transmembrane conductance regulator (CFTR) protein related disorders. The diagnosis of these conditions is primarily based on the clinical presentation, and is supported by evaluation of CFTR function (sweat testing, nasal potential difference) and genetic analysis. None of these features are sufficient on their own to make a diagnosis of CF or CFTR-related disorders. Broad genotype/phenotype associations are useful in epidemiological studies, but CFTR genotype does not accurately predict individual outcome. The use of CFTR genotype for prediction of prognosis in people with CF at the time of their diagnosis is not recommended. The importance of communication between clinicians and medical genetic laboratories is emphasized. The results of testing and their implications should be reported in a manner understandable to the clinicians caring for CF patients.

Recommendations for reporting results of diagnostic genetic testing (biochemical, cytogenetic and molecular genetic).

Genetic test results can have considerable importance for patients, their parents and more remote family members. Clinical therapy and surveillance, reproductive decisions and genetic diagnostics in family members, including prenatal diagnosis, are based on these results. The genetic test report should therefore provide a clear, concise, accurate, fully interpretative and authoritative answer to the clinical question. The need for harmonizing reporting practice of genetic tests has been recognised by the External Quality Assessment (EQA), providers and laboratories. The ESHG Genetic Services Quality Committee has produced reporting guidelines for the genetic disciplines (biochemical, cytogenetic and molecular genetic). These guidelines give assistance on report content, including the interpretation of results. Selected examples of genetic test reports for all three disciplines are provided in an annexe.

Integration of next-generation sequencing in clinical diagnostic molecular pathology laboratories for analysis of solid tumours; an expert opinion on behalf of IQN Path ASBL

The clinical demand for mutation detection within multiple genes from a single tumour sample requires molecular diagnostic laboratories to develop rapid, high-throughput, highly sensitive, accurate and parallel testing within tight budget constraints. To meet this demand, many laboratories employ next-generation sequencing (NGS) based on small amplicons. Building on existing publications and general guidance for the clinical use of NGS and learnings from germline testing, the following guidelines establish consensus standards for somatic diagnostic testing, specifically for identifying and reporting mutations in solid tumours. These guidelines cover the testing strategy, implementation of testing within clinical service, sample requirements, data analysis and reporting of results. In conjunction with appropriate staff training and international standards for laboratory testing, these consensus standards for the use of NGS in molecular pathology of solid tumours will assist laboratories in implementing NGS in clinical services.

European workshop on genetic testing offer in Europe

The workshop was designed with the aim of bringing together experts and stakeholders in the field of genetic testing to discuss the (future) organization of genetic testing in Europe. Obviously since it is not be possible to adequately deal with all aspects of genetic testing within the framework of one workshop, a limited number of issues have been selected. The selection was based on the importance and urgency of the matter and the need and opportunity for action at the European level, and the likelihood for successful intervention. Primary deliverables of this workshop have been planned as to be able to define a vision on the use, value and integration of genomic medicine into clinical practice and to prepare a briefing note to highlight the specific points that deserve the Commission’s interest. Quality of genetic testing and organization of genetic testing services were the two main themes of the scope of the workshop. To warrant the quality of the genetic diagnostic laboratories the way forward is to make accreditation the norm, i.e. the diagnostic laboratories in Europe should be accredited. To further guarantee equity, the regulation should include the requirement for all tests to be within the scope accreditation. The embedding of genetic testing in a healthcare setting can ensure a context where due emphasis is being provided on the individualized medical supervision of patients, the presence of pre-test and post-test counseling, psychological follow-up if appropriate and quality assurance of the tests performed. In light of growing number of companies selling and advertising genetic tests, it is crucial that information is available for healthcare professionals and the general public that gives background on genetic testing and describes the provision of genetic testing services.

Genetic testing in Europe: transborder testing is a necessity

Genetic tests are now offered internationally, through both public and private sector genetic testing services. Physicians prescribing these tests and biologists receiving the samples need to know which tests are available, where they are performed and whether the identified laboratories meet quality standards. To fulfil this need, http://www.orpha.net was launched thirteen years ago to set up a database of clinical laboratories in the field of rare diseases. Data was collected in 1 country in 1997, 15 in 2003, 26 in 2006 and 38 in 2010. This major effort was made possible thanks to resources from the EC DG for Public Health. In collaboration with the EuroGentest Network of Excellence, information on quality management has been added to the Orphanet database over the past four years. To obtain information on genetic testing in Orphanet, it is possible to search by disease name or by gene (symbol or name in English) in addition to the traditional search by name of laboratory or professional. The information provided on laboratories includes data on quality management. Currently, 956 laboratories offering tests for 1,559 genes are registered in the Orphanet database. The test offer differs greatly from one large country to another: Germany (1,141 genes), France (874 genes), Italy (625 genes), Spain (582 genes), UK (414 genes). Medium and small-sized countries have a test offer ranging from 1 to 233 genes. This situation explains the large cross-border flow of specimens and underlines the need to provide access to services in other countries when necessary, especially for very rare diseases. Testing for Cystic fibrosis is the only service which is provided by every country. The distribution of this test offer will be presented.

Reply to Sajantila and Budowle

We thank Drs Sajantila and Budowle1 for raising this interesting and important topic. They correctly point out that our Recommendations for reporting results of diagnostic genetic testing2 do not cover the special circumstances surrounding the reporting of post-mortem genetic testing. We did not consider this issue while preparing our recommendations, focusing instead on reporting of routine genetic testing (biochemical, cytogenetic and molecular genetic). Although some of our recommendations will apply to all reports of genetic testing, there may be important exceptions when post-mortem results are being reported.

Reply: Postmortem medicolegal genetic diagnostics also require reporting guidance : Reply to Sajantila and Budowle

We thank Drs Sajantila and Budowle1 for raising this interesting and important topic. They correctly point out that our Recommendations for reporting results of diagnostic genetic testing2 do not cover the special circumstances surrounding the reporting of post-mortem genetic testing. We did not consider this issue while preparing our recommendations, focusing instead on reporting of routine genetic testing (biochemical, cytogenetic and molecular genetic). Although some of our recommendations will apply to all reports of genetic testing, there may be important exceptions when post-mortem results are being reported.

Postmortem medicolegal genetic diagnostics also require reporting guidance Reply

We thank Drs Sajantila and Budowle1 for raising this interesting and important topic. They correctly point out that our Recommendations for reporting results of diagnostic genetic testing2 do not cover the special circumstances surrounding the reporting of post-mortem genetic testing. We did not consider this issue while preparing our recommendations, focusing instead on reporting of routine genetic testing (biochemical, cytogenetic and molecular genetic). Although some of our recommendations will apply to all reports of genetic testing, there may be important exceptions when post-mortem results are being reported.

137INIMPORTANCE OF EXTERNAL QUALITY ASSESSEMENT IN IMMUNO-ONCOLOGY

ABSTRACT The important role of immunohistochemistry (IHC) is well known. IHC will recognize antigens and, consequently, identify and classify specific cells within a cell population whose morphology is heterogenous or apparently homogenous. Since many years external quality assessment (EQA) schemes for IHC are organized by NORDIQC and UK NEAQS. Since some years, IHC can be used for treatment selection in advanced NSCLC. In 2012, the European Society of Pathology (ESP) proposed an EQA scheme to promote high quality biomarker testing in NSCLC for EGFR mutation analysis and ALK rearrangement detection (IHC, FISH). From 2014 on, ROS1 testing is also included. The scheme aims to assess and improve the current status of testing in NSCLC, to provide education and remedial measures, to permit inter-laboratory comparison and to allow validation of test methods by distributing validated material harboring well-defined aberrations. In total, 173 different laboratories participated in the pilot rounds. In the first round, 29 laboratories submitted results for ALK IHC. In the second round, 58 laboratories submitted results for ALK IHC. If carefully clinically validated according to ISO 15189, ALK IHC may be considered as a screening method to select specimens for ALK FISH testing. In the context that at the time of the pilot studies no interlaboratory comparison validation studies were available, ALK IHC performance from our study shows that IHC testing is well implemented. Not surprisingly however, the error rates for IHC were greater than for FISH. Our study demonstrates improvement of ALK testing after only two rounds. It is expected that larger datasets, spanning a larger number of EQA participations will demonstrate a statistically significant improvement in performance. On scheme level, the decreased error rates in the second round demonstrated improvement for both ALK FISH and ALK IHC. Error rates for ALK FISH TMA and ALK IHC were still high (>5%), which stresses the need for continued education through EQA. Based on the results from this study, recommendations for the methodology, analysis, interpretation and result reporting were issued. External quality assessment is a crucial element to improve the quality of molecular testing. Disclosure: All authors have declared no conflicts of interest.