Canadian College of Medical Geneticists (CCMG) points to consider: resuming genetic services in a pandemic-a summary.

The COVID-19 pandemic has disrupted the provision of genetic care in Canada. With the public health effort to flatten the curve, many clinics have moved to virtual care for select populations of patients while triaging and postponing others. As genetic services are asked to gradually resume, a roadmap is needed to ensure clinical care decisions for at-risk patients are transparent and equitable, that postponed care is resumed and that patients with or waiting for a genetic diagnosis are not disproportionately affected or abandoned.The purpose of this document is to highlight the guiding ethical principles and stakeholder considerations in resuming genetic services to help guide the competing needs going forward of both limiting exposures while maintaining high-quality care. Considerations highlighted are (1) environment of practice, (2) nature of consult, (3) patient factors, (4) provider factors, and (5) laboratory factors. The intended users are those providing genetic care in a Canadian context with the recognition that there are clinic-specific and regional variations that will influence decision-making. While specific to the Canadian context, the ethical principles used to guide these decisions would be relevant for consideration in other jurisdictions.

Rapid deployment of a telemedicine care model for genetics and metabolism during COVID-19.

The national importance of telemedicine for safe and effective patient care has been highlighted by the current COVID-19 pandemic. Prior to the 2020 pandemic the Division of Genetics and Metabolism piloted a telemedicine program focused on initial and follow-up visits in the patients' home. The goals were to increase access to care, decrease missed work, improve scheduling, and avoid the transport and exposure of medically fragile patients. Visits were conducted by physician medical geneticists, genetic counselors, and biochemical dietitians, together and separately. This allowed the program to develop detailed standard operating procedures. At the onset of the COVID-19 pandemic, this pilot-program was deployed by the full team of 22 providers in one business day. Two physicians remained on-site for patients requiring in-person evaluations. This model optimized patient safety and workforce preservation while providing full access to patients during a pandemic. We provide initial data on visit numbers, types of diagnoses, and no-show rates. Experience in this implementation before and during the pandemic has confirmed the effectiveness and value of telemedicine for a highly complex medical population. This program is a model that can and will be continued well-beyond the current crisis.

Roadmap for Establishing Large-Scale Genomic Medicine Initiatives in Low- and Middle-Income Countries.

In the post-genomic era, genomic medicine interventions as a key component of personalized medicine and tailored-made health care are greatly anticipated following recent scientific and technological advances. Indeed, large-scale sequencing efforts that explore human genomic variation have been initiated in several, mostly developed, countries across the globe, such as the United States, the United Kingdom, and a few others. Here, we highlight the successful implementation of large-scale national genomic initiatives, namely the Genome of Greece (GoGreece) and the DNA do Brasil (DNABr), aiming to emphasize the importance of implementing such initiatives in developing countries. Based on this experience, we also provide a roadmap for replicating these projects in other low-resource settings, thereby bringing genomic medicine in these countries closer to clinical fruition.

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.

Testing single/combined clinical categories on 5110 Italian patients with developmental phenotypes to improve array-based detection rate.

BACKGROUND: Chromosomal microarray analysis (CMA) is nowadays widely used in the diagnostic path of patients with clinical phenotypes. However, there is no ascertained evidence to date on how to assemble single/combined clinical categories of developmental phenotypic findings to improve the array-based detection rate. METHODS: The Italian Society of Human Genetics coordinated a retrospective study which included CMA results of 5,110 Italian patients referred to 17 genetics laboratories for variable combined clinical phenotypes. RESULTS: Non-polymorphic copy number variants (CNVs) were identified in 1512 patients (30%) and 615 (32%) present in 552 patients (11%) were classified as pathogenic. CNVs were analysed according to type, size, inheritance pattern, distribution among chromosomes, and association to known syndromes. In addition, the evaluation of the detection rate of clinical subgroups of patients allowed to associate dysmorphisms and/or congenital malformations combined with any other single clinical sign to an increased detection rate, whereas non-syndromic neurodevelopmental signs and non-syndromic congenital malformations to a decreased detection rate. CONCLUSIONS: Our retrospective study resulted in confirming the high detection rate of CMA and indicated new clinical markers useful to optimize their inclusion in the diagnostic and rehabilitative path of patients with developmental phenotypes.

Genetics and genomic medicine in Iran.

Attention has been focused on the field of genetics and genomics in Iran in recent years and some efforts have been enforced and implemented. However, they are totally not adequate, considering the advances in medical genetics and genomics in the past two decades around the world. Overall, considering the lack of medical genetics residency programs in the Iranian health education system, big demand due to high consanguinity and intraethnic marriages, there is a lag in genetic services and necessity to an immediate response to fill this big gap in Iran. As clarified in the National constitution fundamental law and re-emphasized in the 6th National Development Plan, the Iranian government authority is in charge of providing the standard level of health including genetic services to all Iranian individuals who are in need.

Optimal Integration of Behavioral Medicine into Clinical Genetics and Genomics.

Clinical genetics and genomics will exert their greatest population impact by leveraging the rich knowledge of human behavior that is central to the discipline of behavioral medicine. We contend that more concerted efforts are needed to integrate these fields synergistically, and accordingly, we consider barriers and potential actions to hasten such integration.

An International Summit in Human Genetics and Genomics: Empowering clinical practice and research in developing countries.

To help fill the knowledge gap in human genetics and genomics, an International Summit (IS) in Human Genetics and Genomics was conceived and organized by the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) as a 5-year initiative, from 2016 to 2020. In its first 3 years, 71 professionals from 34 countries received training.

Integrating Genomics into Healthcare: A Global Responsibility.

Genomic sequencing is rapidly transitioning into clinical practice, and implementation into healthcare systems has been supported by substantial government investment, totaling over US$4 billion, in at least 14 countries. These national genomic-medicine initiatives are driving transformative change under real-life conditions while simultaneously addressing barriers to implementation and gathering evidence for wider adoption. We review the diversity of approaches and current progress made by national genomic-medicine initiatives in the UK, France, Australia, and US and provide a roadmap for sharing strategies, standards, and data internationally to accelerate implementation.

Genetics and genomics in Peru: Clinical and research perspective.

Peruvians currently preserve in their DNA the history of 2.5 million years of human evolution and 150,000 years of migration from Africa to Peru or the Americas. The development of Genetics and Genomics in the clinical and academic field is shown in this review.

Cancer genetics program: Follow-up on clinical genetics and genomic medicine in Qatar.

This article presents an overview of the cancer genetics program in Qatar. In addition to summarizing clinical, research, educational, and other aspects, data related to testing outcomes (over the course of approximately 5.5 years) are presented.

The forty years of medical genetics in China.

Medical genetics is the newest cutting-edge discipline that focuses on solving medical problems using genetics knowledge and methods. In China, medical genetics research activities initiated from a poor inner basis but a prosperous outer environment. During the 40 years of reform and opening-up policy, Chinese scientists contributed significantly in the field of medical genetics, garnering considerable attention worldwide. In this review, we highlight the significant findings and/or results discovered by Chinese scientists in monogenic diseases, complex diseases, cancer, genetic diagnosis, as well as gene manipulation and gene therapy. Due to these achievements, China is widely recognized to be at the forefront of medical genetics research and development. However, the significant progress and development that has been achieved could not have been accomplished without sufficient funding and a well-constructed logistics network. The successful implementation of translational and precise medicine sourced from medical genetics will depend on an open ethics policy and intellectual property protection, along with strong support at the national industry level.

Genetic counseling in industry settings: Opportunities in the era of precision health.

The skill sets of genetic counselors are strongly utilized in industry, as evidenced by 20% of genetic counselors reporting employment within industry in 2016. In addition, industry genetic counselors are expanding their roles, taking on new responsibilities, and creating new opportunities. These advances have impacted the profession as a whole including, but not limited to, genetic counseling training curricula, a shift back to genetic counseling directly to patients, and a growing influence of genetic counselors on industry test offerings. Industry genetic counselors and training programs are working together to address the challenges and opportunities presented by workforce changes and novel interpretations of how genetic counselors' core competencies can be utilized. Counseling of patients by industry genetic counselors has become more commonplace and addresses a need for alternate service delivery models. Industry genetic counselors often provide significant contributions to test development, education, marketing, and interpretation. Beyond these broad examples, individual industry genetic counselors have created unique niches for themselves, using their genetic counseling training combined with unique opportunities offered through industry, as illustrated by genetic counselors' various roles and responsibilities highlighted here.

Los servicios de genética médica en Venezuela / Medical genetics services in Venezuela / Serviços de genética médica na Venezuela

RESUMEN Objetivo. Caracterizar los servicios de genética médica de Venezuela con el fin de conocer la distribución de sus recursos, servicios, tecnologías y formación profesional. Métodos. Se realizó una investigación descriptiva, de tipo documental, entre febrero y noviembre de 2016 de los servicios de genética, mediante la revisión de fuentes documentales primarias y el uso de una ficha de recolección de datos en las instituciones de investigación para información referente a disponibilidad de recursos humanos, servicios de atención y diagnóstico, así como formación profesional, y la base de datos de la Sociedad Venezolana de Genética Humana, que permitió identificar los recursos humanos en centros de genética. El criterio de inclusión fue instituciones con recursos humanos formados en genética. Resultados. Los criterios fueron cumplidos por cuatro instituciones de investigación, siete universidades y cuatro hospitales, todos del sector público. En estas instituciones trabajan 124 profesionales, 56 son médicos y 68 se desempeñan en el área de laboratorio. Sesenta y dos por ciento de los profesionales pertenecen a las instituciones de investigación; estas cuentan con servicios de atención clínico, diagnóstico molecular, bioquímico y, con menos frecuencia, los análisis citogenéticos, prenatales y forenses. Cinco regiones del país tienen entre dos y cuatro médicos genetistas por millón de habitantes. El 96% de los profesionales de laboratorio se localizan en dos regiones (Capital y Zuliana), cinco regiones carecen de ellos. Las instituciones de investigación han formado en genética el 40% de los recursos humanos actuales del país. Conclusiones. Los servicios de genética presentan gran variabilidad de opciones diagnósticas, un acceso limitado y grandes aportes en formación profesional; se requieren políticas coordinadas que los integre y disminuya las brechas.

ABSTRACT Objective. To characterize medical genetics services in Venezuela and describe the distribution of their resources, services, technologies, and professional training. Methods. A descriptive, documentary study of genetic services was conducted between February and November 2016, involving a review of primary documentary sources and the use of a data collection form in research institutions to obtain information on the availability of human resources, clinical care, and diagnostic services, as well as professional training. Furthermore, the Venezuelan Society of Human Genetics database was used to identify the human resources available in genetics centers. The criterion for inclusion was being an institution with staff trained in genetics. Results. The inclusion criterion was met by four research institutions, seven universities, and four hospitals, all in the public sector. A total of 124 professionals work in these institutions; 56 of them are physicians and 68 are laboratory staff. Of these professionals, 62% are affiliated with research institutions, which offer patient care services, molecular and biochemical diagnostic services, and, more rarely, cytogenetic, prenatal, and forensic testing. Five regions of the country have between two and four physicians specializing in genetics per million inhabitants. Of the laboratory professionals, 96% are located in two regions (Capital and Zuliana); five regions have none. Research institutions have provided training in genetics to 40% of the country's current human resources. Conclusions. Genetics services show great variability in terms of diagnostic options. They train large numbers of professionals, but access is limited. There is a need for coordinated policies to integrate these services and reduce existing gaps.

RESUMO Objetivo. Caracterizar os serviços de genética médica da Venezuela com a finalidade de conhecer a distribuição dos recursos, prestação de serviços, tecnologias usadas e formação profissional nesta área. Métodos. Uma pesquisa descritiva documental dos serviços de genética médica foi realizada de fevereiro a novembro de 2016. Foi feita uma revisão das fontes documentais primárias nas instituições de pesquisa com o preenchimento de fichas de coleta de dados com informação sobre a disponibilidade de recursos humanos, prestação de serviços de atendimento e diagnóstico e formação profissional. Foi feita também uma revisão do banco de dados da Sociedade Venezuelana de Genética Humana para identificar os recursos humanos nos centros de genética. O critério de inclusão do estudo foi ser uma instituição com recursos humanos formados em genética. Resultados. Os critérios do estudo foram satisfeitos por 4 instituições de pesquisa, 7 universidades e 4 hospitais, todos da rede pública. Foram identificados 124 profissionais trabalhando nestas instituições: 56 médicos e 68 funcionários da área de laboratório. Sessenta e dois por cento dos profissionais pertencem a instituições de pesquisa que prestam serviços de atendimento clínico e diagnóstico molecular e bioquímico e, menos frequentemente, realizam análises citogenéticas, pré-natais e forenses. Cinco regiões do país têm entre 2 e 4 médicos geneticistas por milhão de habitantes. Além disso, 96% dos profissionais de laboratório estão distribuídos em 2 regiões (capital e Zuliana), sendo que não há nenhum profissional em 5 regiões. As instituições de pesquisa formam atualmente 40% dos recursos humanos em genética do país. Conclusões. Os serviços de genética médica são caracterizados por grande variabilidade nas opções diagnósticas, acesso limitado e grande contribuição para a formação profissional. Fazem-se necessárias políticas coordenadas para integrar e reduzir as lacunas.

Clinical implications and considerations for evaluation of in silico algorithms for use with ACMG/AMP clinical variant interpretation guidelines.

Clinical genetics laboratories have recently adopted guidelines for the interpretation of sequence variants set by the American College of Medical Genetics (ACMG) and Association for Molecular Pathology (AMP). The use of in silico algorithms to predict whether amino acid substitutions result in human disease is inconsistent across clinical laboratories. The clinical genetics community must carefully consider how in silico predictions can be incorporated into variant interpretation in clinical practice.Please see related Research article: https://doi.org/10.1186/s13059-017-1353-5.

The role of genetic counsellors in genomic healthcare in the United Kingdom: a statement by the Association of Genetic Nurses and Counsellors.

In the United Kingdom, genetic counsellors work together with clinical geneticists and clinical scientist colleagues within specialist genetics services, but they also often work in multidisciplinary teams (MDTs) outside of such services. There, they contribute genetic knowledge together with expert understanding of how to communicate genetic information effectively. They can offer education and support to the MDT, while providing management advice for both affected patients and the extended at-risk family members. As genomic technologies are implemented across many disciplines within healthcare, genetic counsellors are playing a key role in enabling non-genetic health professionals learn, understand and integrate genomic data into their practice. They are also involved in curriculum development, workforce planning, research, regulation and policy creation - all with the aim of ensuring a robust evidence base from which to practise, together with clear guidelines on what constitutes competence and good practice. The Association of Genetic Nurses and Counsellors (AGNC) in The United Kingdom (UK) and Republic of Ireland is committed to supporting genetic counsellors, across all sectors of healthcare and research, as they help deliver genomic medicine for the patient, family and world-class health services.European Journal of Human Genetics advance online publication, 22 March 2017; doi:10.1038/ejhg.2017.28.