Problems in variation interpretation guidelines and in their implementation in computational tools.

BACKGROUND: ACMG/AMP and AMP/ASCO/CAP have released guidelines for variation interpretation, and ESHG for diagnostic sequencing. These guidelines contain recommendations including the use of computational prediction methods. The guidelines per se and the way they are implemented cause some problems. METHODS: Logical reasoning based on domain knowledge. RESULTS: According to the guidelines, several methods have to be used and they have to agree. This means that the methods with the poorest performance overrule the better ones. The choice of the prediction method(s) should be made by experts  based on systematic benchmarking studies reporting all the relevant performance measures. Currently variation interpretation methods have been applied mainly to amino acid substitutions and splice site variants; however, predictors for some other types of variations are available and there will be tools for new application areas in the near future. Common problems in prediction method usage are discussed. The number of features used for method training or the number of variation types predicted by a tool are not indicators of method performance. Many published gene, protein or disease-specific benchmark studies suffer from too small dataset rendering the results useless. In the case of binary predictors, equal number of positive and negative cases is beneficial for training, the imbalance has to be corrected for performance assessment. Predictors cannot be better than the data they are based on and used for training and testing. Minor allele frequency (MAF) can help to detect likely benign cases, but the recommended MAF threshold is apparently too high. The fact that many rare variants are disease-causing or -related does not mean that rare variants in general would be harmful. How large a portion of the tested variants a tool can predict (coverage) is not a quality measure. CONCLUSION: Methods used for variation interpretation have to be carefully selected. It should be possible to use only one predictor, with proven good performance or a limited number of complementary predictors with state-of-the-art performance. Bear in mind that diseases and pathogenicity have a continuum and variants are not dichotomic i.e. either pathogenic or benign, either.

CCMG practice guideline: laboratory guidelines for next-generation sequencing.

PurposeThe purpose of this document is to provide guidance for the use of next-generation sequencing (NGS, also known as massively parallel sequencing or MPS) in Canadian clinical genetic laboratories for detection of genetic variants in genomic DNA and mitochondrial DNA for inherited disorders, as well as somatic variants in tumour DNA for acquired cancers. They are intended for Canadian clinical laboratories engaged in developing, validating and using NGS methods. METHODS OF STATEMENT DEVELOPMENT: The document was drafted by the Canadian College of Medical Geneticists (CCMG) Ad Hoc Working Group on NGS Guidelines to make recommendations relevant to NGS. The statement was circulated for comment to the CCMG Laboratory Practice and Clinical Practice committees, and to the CCMG membership. Following incorporation of feedback, the document was approved by the CCMG Board of Directors. DISCLAIMER: The CCMG is a Canadian organisation responsible for certifying medical geneticists and clinical laboratory geneticists, and for establishing professional and ethical standards for clinical genetics services in Canada. The current CCMG Practice Guidelines were developed as a resource for clinical laboratories in Canada and should not be considered to be inclusive of all information laboratories should consider in the validation and use of NGS for a clinical laboratory service.

Normas éticas para la realización de pruebas predictivas en los servicios de genética médica de Cuba / Ethical norms for the execution of predictive tests in the medical genetics´ services in Cuba

Introducción: Las nuevas tecnologías disponibles en el campo de la genética humana y médica pueden ser utilizadas, cada vez más, con fines médicos preventivos. Existe también el riesgo de su uso indebido que favorezca la discriminación y la eutanasia selectiva y minimice el papel de los condicionantes sociales en la salud de las poblaciones. Objetivo: Establecer normas éticas para garantizar que las pruebas presintomáticas en Cuba se realicen conforme a los principios éticos de respeto a la autonomía, justicia, beneficencia y no maleficencia. Métodos: Estas normas se elaboraron a partir de una propuesta discutida y consensuada en talleres nacionales con la participación de genetistas clínicos de todo el país y aprobadas por el Comité de Ética del Centro Nacional de Genética Médica y el Ministerio de Salud Pública. Resultados: Las normas aprobadas consideraron aspectos esenciales como el conocimiento sobre el alcance de la información que la prueba revelará y sus implicaciones a nivel personal y familiar, el consentimiento informado para su realización, las condiciones en que se realiza y la seguridad de sus resultados, las obligaciones médicas antes, durante y después de la realización de la prueba y lo concerniente a la privacidad y confidencialidad de la información. Conclusiones: La generalización y cumplimiento de las normas aprobadas asegura la protección a individuos y familias vulnerables, contribuye a mejorar su atención médica y a aminorar el impacto que sobre su salud, su reproducción y su vida en general, tienen las severas enfermedades para las que están en riesgo o padecen(AU)

Introduction: New technologies available in the field of human and medical genetics can increasingly be used for preventive medical purposes. There is also the risk of misuse that favors discrimination and selective euthanasia, and that minimizes the role of social determinants in the health of the populations. Objectives: To establish ethical norms to ensure that presymptomatic tests in Cuba are carried out in accordance with the principles of respect for autonomy, justice, beneficence and non-malice. Methods: These norms were elaborated from a proposal discussed and agreed upon in national workshops with the participation of clinical geneticists from all over the country and approved by the Ethics Committee of the National Center of Medical Genetics and the Ministry of Public Health. Results: The approved norms considered essential aspects such as: the knowledge about the scope of information that the test will reveal and its implications on a personal and family level, informed consent for its implementation, the conditions under which it is performed, and the safety of its results; medical obligations before, during and after the performance of the test; and all concerning to the privacy and confidentiality of the information. Conclusions: The generalization and compliance of these ethical norms ensure the protection of vulnerable individuals and families, contributes to improving their medical care and to reducing the impact on their health, their reproduction and life in general terms of the severe diseases they are at risk or suffering from(AU)

European registration process for Clinical Laboratory Geneticists in genetic healthcare.

Tremendous progress in genetics and genomics led to a wide range of healthcare providers, genetic tests, and more patients who can benefit from these developments. To guarantee and improve the quality of genetic testing, a unified European-based registration for individuals qualified in biomedicine was realized. Therefore a Europe-wide recognition of the profession 'European registered Clinical Laboratory Geneticist (ErCLG)' based on a syllabus of core competences was established which allows for harmonization in professional education. The 'European Board of Medical Genetics division - Clinical Laboratory Geneticist' provides now since 3 years the possibility to register as an ErCLG. Applicants may be from all European countries and since this year also from outside of Europe. Five subtitles reflect the exact specialty of each ErCLG, who can reregister every 5 years. A previously not possible statistics based on ~300 individuals from 19 countries as holders of an ErCLG title provides interesting insights into the professionals working in human genetics. It could be substantiated that there are around twice as many females than males and that a PhD title was achieved by 80% of registered ErCLGs. Also most ErCLGs are still trained as generalists (66%), followed by such ErCLGs with focus on molecular genetics (23%); the remaining are concentrated either on clinical (6%), tumor (4%) or biochemical genetics (1%). In conclusion, besides MDs and genetic counselors/nurses an EU-wide recognition system for Clinical Laboratory Geneticist has been established, which strengthens the status of specialists working in human genetic diagnostics in Europe and worldwide.

Manual de normas y procedimientos servicios de genética médica en Cuba 2017

El manual de normas y procedimientos. Servicios médica en Cuba, tiene el propósito de constituirse en el documento metodológico rector para la organización y funcionalmente de lo servicios de genética médica en el país. Es una herramienta en el trabajo diario de los profesionales y técnicos que laboran en función de la promoción-prevención de las enfermedades genéticas y los defectos congénitos como parte del Sistema Nacional de Salud.

Conflicting Interpretation of Genetic Variants and Cancer Risk by Commercial Laboratories as Assessed by the Prospective Registry of Multiplex Testing.

Purpose Massively parallel sequencing allows simultaneous testing of multiple genes associated with cancer susceptibility. Guidelines are available for variant classification; however, interpretation of these guidelines by laboratories and providers may differ and lead to conflicting reporting and, potentially, to inappropriate medical management. We describe conflicting variant interpretations between Clinical Laboratory Improvement Amendments-approved commercial clinical laboratories, as reported to the Prospective Registry of Multiplex Testing (PROMPT), an online genetic registry. Methods Clinical data and genetic testing results were gathered from 1,191 individuals tested for inherited cancer susceptibility and self-enrolled in PROMPT between September 2014 and October 2015. Overall, 518 participants (603 genetic variants) had a result interpreted by more than one laboratory, including at least one submitted to ClinVar, and these were used as the final cohort for the current analysis. Results Of the 603 variants, 221 (37%) were classified as a variant of uncertain significance (VUS), 191 (32%) as pathogenic, and 34 (6%) as benign. The interpretation differed among reporting laboratories for 155 (26%). Conflicting interpretations were most frequently reported for CHEK2 and ATM, followed by RAD51C, PALB2, BARD1, NBN, and BRIP1. Among all participants, 56 of 518 (11%) had a variant with conflicting interpretations ranging from pathogenic/likely pathogenic to VUS, a discrepancy that may alter medical management. Conclusions Conflicting interpretation of genetic findings from multiplex panel testing used in clinical practice is frequent and may have implications for medical management decisions.

Medical implications of technical accuracy in genome sequencing.

BACKGROUND: As whole exome sequencing (WES) and whole genome sequencing (WGS) transition from research tools to clinical diagnostic tests, it is increasingly critical for sequencing methods and analysis pipelines to be technically accurate. The Genome in a Bottle Consortium has recently published a set of benchmark SNV, indel, and homozygous reference genotypes for the pilot whole genome NIST Reference Material based on the NA12878 genome. METHODS: We examine the relationship between human genome complexity and genes/variants reported to be associated with human disease. Specifically, we map regions of medical relevance to benchmark regions of high or low confidence. We use benchmark data to assess the sensitivity and positive predictive value of two representative sequencing pipelines for specific classes of variation. RESULTS: We observe that the accuracy of a variant call depends on the genomic region, variant type, and read depth, and varies by analytical pipeline. We find that most false negative WGS calls result from filtering while most false negative WES variants relate to poor coverage. We find that only 74.6% of the exonic bases in ClinVar and OMIM genes and 82.1% of the exonic bases in ACMG-reportable genes are found in high-confidence regions. Only 990 genes in the genome are found entirely within high-confidence regions while 593 of 3,300 ClinVar/OMIM genes have less than 50% of their total exonic base pairs in high-confidence regions. We find greater than 77 % of the pathogenic or likely pathogenic SNVs currently in ClinVar fall within high-confidence regions. We identify sites that are prone to sequencing errors, including thousands present in publicly available variant databases. Finally, we examine the clinical impact of mandatory reporting of secondary findings, highlighting a false positive variant found in BRCA2. CONCLUSIONS: Together, these data illustrate the importance of appropriate use and continued improvement of technical benchmarks to ensure accurate and judicious interpretation of next-generation DNA sequencing results in the clinical setting.

[Regional molecular genetics centers in thoracic oncology: what and who should be tested?]. / Plateformes de biologie moléculaire en oncologie thoracique: quelles recherches, pour qui?

Management of NSCLC patients is more and more individualized especially on the base of bioguided treatments. In order to guarantee an access for all the patients too this type of strategy, the French NCI supports since 2006 a nationwide network of 28 regional genetics center. The financial support is based on public funds. The French NCI recommends today the assessment of seven biomarkers for all stage IV non squamous NSCLC patients. Due to financial and technical reasons, this recommendation must be followed. However, the molecular profiling of lung cancer patients would ideally be extended across all stages and all histological types of the disease in order to improve our knowledge in this field and provides the patient with an opportunity to access a bioguided treatment as frequently as possible.

Return of individual research results and incidental findings in the clinical trials cooperative group setting.

The National Cancer Institute (NCI)-funded cooperative group cancer clinical trial system develops experimental therapies and often collects samples from patients for correlative research. The cooperative group bank (CGB) system maintains biobanks with a current policy not to return research results to individuals. An online survey was created, and 10 directors of CGBs completed the surveys asking about understanding and attitudes in changing policies to consider return of incidental findings (IFs) and individual research results (IRRs) of health significance. The potential impact of the 10 consensus recommendations of Wolf et al. presented in this issue are examined. Reidentification of samples is often not problematic; however, changes to the current banking and clinical trial systems would require significant effort to fulfill an obligation of recontact of subjects. Additional resources, as well as a national advisory board would be required to standardize implementation.

The development and implementation of an in-service exam for medical genetics residency programs.

PURPOSE: In-service exams are a commonly used educational tool in postgraduate medical education. Although most specialties utilize such an exam, medical genetics did not. It was decided in the spring of 2009 at the inaugural Medical Genetics Residency Program Directors (PDs) Group meeting to develop and implement such a test. METHODS: Using questions sent in from PDs, a 125-question exam was created, with 125 multiple-choice questions according to the format of the National Board of Medical Examiners. The exam covered genetics in the following areas: basic/molecular (~45 questions), cancer and adult (20), prenatal (20), biochemical (20), pediatric/dysmorphology (20). The exam was administered for the first time in February 2010, and again with modifications in 2011. RESULTS: In total, 174 trainees from 35 programs completed the exam in 2010; in 2011 the number increased to 214, representing 39 US programs, and 4 Canadian programs. For both years, most participants were medical genetics residents (106 in 2010; 127 in 2011), but a substantial number of clinical laboratory fellows also participated (68 in 2010; 85 in 2011). CONCLUSION: The development and implementation of this test were an overall success, in that in two years we were able to secure almost 100% participation from medical genetics residency programs, and that we created an infrastructure to develop and implement this exam on a yearly basis. There is need for improvement, notably in the relatively low mean score and relatively narrow spread of scores. However, we believe that, with efforts under way to improve the quality of the questions, the in-service exam will become a fundamental tool in medical genetics residency education.

Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results.

Genetic testing of cancer susceptibility genes is now widely applied in clinical practice to predict risk of developing cancer. In general, sequence-based testing of germline DNA is used to determine whether an individual carries a change that is clearly likely to disrupt normal gene function. Genetic testing may detect changes that are clearly pathogenic, clearly neutral, or variants of unclear clinical significance. Such variants present a considerable challenge to the diagnostic laboratory and the receiving clinician in terms of interpretation and clear presentation of the implications of the result to the patient. There does not appear to be a consistent approach to interpreting and reporting the clinical significance of variants either among genes or among laboratories. The potential for confusion among clinicians and patients is considerable and misinterpretation may lead to inappropriate clinical consequences. In this article we review the current state of sequence-based genetic testing, describe other standardized reporting systems used in oncology, and propose a standardized classification system for application to sequence-based results for cancer predisposition genes. We suggest a system of five classes of variants based on the degree of likelihood of pathogenicity. Each class is associated with specific recommendations for clinical management of at-risk relatives that will depend on the syndrome. We propose that panels of experts on each cancer predisposition syndrome facilitate the classification scheme and designate appropriate surveillance and cancer management guidelines. The international adoption of a standardized reporting system should improve the clinical utility of sequence-based genetic tests to predict cancer risk.

Competences, education and support for new roles in cancer genetics services: outcomes from the cancer genetics pilot projects.

In 2004 the Department of Health in collaboration with Macmillan Cancer Support set up service development projects to pilot the integration of genetics in mainstream medicine in the area of cancer genetics.In developing these services, new roles and responsibilities were devised that required supporting programmes of education and training. The NHS National Genetics Education and Development Centre has worked with the projects to draw together their experience in these aspects. New roles include the Cancer Family Nurse Specialist, in which a nurse working in a cancer setting was trained to identify and manage genetic or family history concerns, and the Genetic Risk Assessment Practitioner--a small team of practitioners working within a secondary care setting to deliver a standardised risk assessment pathway. Existing roles were also adapted for a different setting, in particular the use of genetic counsellors working in a community ethnic minority setting. These practitioners undertook a range of clinical activities that can be mapped directly to the 'UK National Workforce Competences for Genetics in Clinical Practice for Non-genetics Healthcare Staff' framework developed by Skills for Health and the NHS National Genetics Education and Development Centre (2007; draft competence framework). The main differences between the various roles were in the ordering of genetic tests and the provision of advice on invasive preventive options such as mastectomy. Those involved in service development also needed to develop competences in project management, business skills, audit and evaluation, working with users, general management (personnel, multi-agency work and marketing), educational supervision, IT, public and professional outreach, and research. Important resources to support the development of new roles and competences included pathways and guidelines, a formal statement of competences, a recognised syllabus, appropriate and timely courses, the availability of a mentor, supervision and opportunities to discuss cases, a formal assessment of learning and continuing support from specialist genetics services. This represents a current resource gap that will be of concern to cancer networks and a challenge to providers of educational resources and regional genetics services.

Medical genetics in Zulia, a State of Venezuela.

Zulia is a state located in the northwest of Venezuela. Congenital malformations, deformities and chromosomal anomalies are the second cause of infant and neonatal mortality. There are seven public and private groups providing genetic services, the most important of which, the Medical Genetic Unit at the Zulia University was created in 1973. So far, this unit has provided genetic services to 12,000 families, and has been responsible for undergraduate and postgraduate education in human and medical genetics. Prenatal diagnosis is performed at the Unit and a private practice group, the most frequent referral reason being advanced maternal age. The most frequent genetic diseases in the state are Huntington's disease, sickle cell anemia, neural tube defects and Down's syndrome. Research in genetics includes the clinical, epidemiological and molecular characterization of hereditary diseases, cancer, reproductive problems and genetic diversity. Other public groups are conducting research on dementias, including Alzheimer's disease, and on the genotoxic effects of environmental pollutants.