Improving reporting standards for polygenic scores in risk prediction studies.

Polygenic risk scores (PRSs), which often aggregate results from genome-wide association studies, can bridge the gap between initial discovery efforts and clinical applications for the estimation of disease risk using genetics. However, there is notable heterogeneity in the application and reporting of these risk scores, which hinders the translation of PRSs into clinical care. Here, in a collaboration between the Clinical Genome Resource (ClinGen) Complex Disease Working Group and the Polygenic Score (PGS) Catalog, we present the Polygenic Risk Score Reporting Standards (PRS-RS), in which we update the Genetic Risk Prediction Studies (GRIPS) Statement to reflect the present state of the field. Drawing on the input of experts in epidemiology, statistics, disease-specific applications, implementation and policy, this comprehensive reporting framework defines the minimal information that is needed to interpret and evaluate PRSs, especially with respect to downstream clinical applications. Items span detailed descriptions of study populations, statistical methods for the development and validation of PRSs and considerations for the potential limitations of these scores. In addition, we emphasize the need for data availability and transparency, and we encourage researchers to deposit and share PRSs through the PGS Catalog to facilitate reproducibility and comparative benchmarking. By providing these criteria in a structured format that builds on existing standards and ontologies, the use of this framework in publishing PRSs will facilitate translation into clinical care and progress towards defining best practice.

A structural variation reference for medical and population genetics.

Structural variants (SVs) rearrange large segments of DNA1 and can have profound consequences in evolution and human disease2,3. As national biobanks, disease-association studies, and clinical genetic testing have grown increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD)4 have become integral in the interpretation of single-nucleotide variants (SNVs)5. However, there are no reference maps of SVs from high-coverage genome sequencing comparable to those for SNVs. Here we present a reference of sequence-resolved SVs constructed from 14,891 genomes across diverse global populations (54% non-European) in gnomAD. We discovered a rich and complex landscape of 433,371 SVs, from which we estimate that SVs are responsible for 25-29% of all rare protein-truncating events per genome. We found strong correlations between natural selection against damaging SNVs and rare SVs that disrupt or duplicate protein-coding sequence, which suggests that genes that are highly intolerant to loss-of-function are also sensitive to increased dosage6. We also uncovered modest selection against noncoding SVs in cis-regulatory elements, although selection against protein-truncating SVs was stronger than all noncoding effects. Finally, we identified very large (over one megabase), rare SVs in 3.9% of samples, and estimate that 0.13% of individuals may carry an SV that meets the existing criteria for clinically important incidental findings7. This SV resource is freely distributed via the gnomAD browser8 and will have broad utility in population genetics, disease-association studies, and diagnostic screening.

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.

[Principles guiding the development of clinical practice guidelines for medical genetics and genomics specialty].

The development of clinical practice guidelines for medical genetics and genomics specialty is a key step in translating basic and clinical genetic research into evidence-based and precision clinical services. This paper briefly expounds the principles of writing high-quality and trustworthy clinical practice guidelines. According to these principles, the management framework, writing process, review and revision procedures, and application monitoring of medical genetic specialty guidelines are described. Systematic review of relevant literature for evidence applicable to the screening, diagnosis, counseling, treatment and prevention of specific genetic diseases is summarized. Specific requirements for writing and reviewing high-quality professional guidelines for medical genetics are introduced. These principles and requirements can ensure that the evidence-based methods and recommendations in the written guidelines conform to current international standards and have specific clinical purposes, scope of practice and time-tracking mechanism. Implementation of such guidelines can promote the translation of basic and clinical genetic research, promote cooperation of medical genetics and other clinical specialties and coordination of interdisciplinary clinical practice guidelines, and provide effective and safe clinical services for patients and their families.

Dwarna: a blockchain solution for dynamic consent in biobanking.

Dynamic consent aims to empower research partners and facilitate active participation in the research process. Used within the context of biobanking, it gives individuals access to information and control to determine how and where their biospecimens and data should be used. We present Dwarna-a web portal for 'dynamic consent' that acts as a hub connecting the different stakeholders of the Malta Biobank: biobank managers, researchers, research partners, and the general public. The portal stores research partners' consent in a blockchain to create an immutable audit trail of research partners' consent changes. Dwarna's structure also presents a solution to the European Union's General Data Protection Regulation's right to erasure-a right that is seemingly incompatible with the blockchain model. Dwarna's transparent structure increases trustworthiness in the biobanking process by giving research partners more control over which research studies they participate in, by facilitating the withdrawal of consent and by making it possible to request that the biospecimen and associated data are destroyed.

Diagnostic gene sequencing panels: from design to report-a technical standard of the American College of Medical Genetics and Genomics (ACMG).

Gene sequencing panels are a powerful diagnostic tool for many clinical presentations associated with genetic disorders. Advances in DNA sequencing technology have made gene panels more economical, flexible, and efficient. Because the genes included on gene panels vary widely between laboratories in gene content (e.g., number, reason for inclusion, evidence level for gene-disease association) and technical completeness (e.g., depth of coverage), standards that address technical and clinical aspects of gene panels are needed. This document serves as a technical standard for laboratories designing, offering, and reporting gene panel testing. Although these principles can apply to multiple indications for genetic testing, the primary focus is on diagnostic gene panels (as opposed to carrier screening or predictive testing) with emphasis on technical considerations for the specific genes being tested. This technical standard specifically addresses the impact of gene panel content on clinical sensitivity, specificity, and validity-in the context of gene evidence for contribution to and strength of evidence for gene-disease association-as well as technical considerations such as sequencing limitations, presence of pseudogenes/gene families, mosaicism, transcript choice, detection of copy-number variants, reporting, and disclosure of assay limitations.

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.

The Responsibility to Recontact Research Participants after Reinterpretation of Genetic and Genomic Research Results.

The evidence base supporting genetic and genomic sequence-variant interpretations is continuously evolving. An inherent consequence is that a variant's clinical significance might be reinterpreted over time as new evidence emerges regarding its pathogenicity or lack thereof. This raises ethical, legal, and financial issues as to whether there is a responsibility to recontact research participants to provide updates on reinterpretations of variants after the initial analysis. There has been discussion concerning the extent of this obligation in the context of both research and clinical care. Although clinical recommendations have begun to emerge, guidance is lacking on the responsibilities of researchers to inform participants of reinterpreted results. To respond, an American Society of Human Genetics (ASHG) workgroup developed this position statement, which was approved by the ASHG Board in November 2018. The workgroup included representatives from the National Society of Genetic Counselors, the Canadian College of Medical Genetics, and the Canadian Association of Genetic Counsellors. The final statement includes twelve position statements that were endorsed or supported by the following organizations: Genetic Alliance, European Society of Human Genetics, Canadian Association of Genetic Counsellors, American Association of Anthropological Genetics, Executive Committee of the American Association of Physical Anthropologists, Canadian College of Medical Genetics, Human Genetics Society of Australasia, and National Society of Genetic Counselors.

Regarding the rights and duties of Clinical Laboratory Geneticists in genetic healthcare systems; results of a survey in over 50 countries.

Specialists of human genetic diagnostics can be divided into four groups: Medical Geneticists (MDG), Genetic Nurses and/or Counsellors (GN/GC), Clinical Laboratory Geneticists (CLG) and Laboratory Genetics Technicians (LGT). While the first two groups are in direct patient contact, the work of the latter two, of equal importance for patient care, are often hidden as they work behind the scenes. Herein the first study on the rights and duties of CLGs is presented. We present the results of a survey performed in 35 European and 18 non-European countries with 100 participating specialists. A national CLG title is available in 60% of European countries, and in 77% of the surveyed European countries a CLG can be the main responsible head of the laboratory performing human genetic tests. However, in only 20% of European countries is a lab-report valid with only a CLGs' signature - even though the report is almost always formulated by the CLG, and an interpretation of the obtained results in a clinical context by the CLG is expected in nearly 90% of European countries. Interestingly, CLGs see patients in 30% of European countries, and are also regularly involved in student education. Overall, the CLG profession includes numerous duties, which are quite similar in all regions of the world. Strikingly, the CLG's rights and responsibilities of leading a lab, or signing a report are regulated differently according to country specific regulations. Overall, the CLG is a well-recognized profession worldwide and often working within a multidisciplinary team of human genetic diagnostics professionals.

Core competencies in genetics for healthcare professionals: results from a literature review and a Delphi method.

BACKGROUND: Advances in genetics and genomics require that healthcare professionals manage and incorporate new technologies into the appropriate clinical practice. The aim of this study was to identify core competencies in genetics for non-geneticists, both physicians and non-physicians. METHODS: We performed a literature review by searching MEDLINE, SCOPUS, and ISI Web of Science databases to identify studies reporting competencies in genetics in terms of knowledge, attitudes and abilities for non-genetic healthcare professionals. Furthermore, we conducted a survey according to a modified Delphi method, involving genetics experts to evaluate the competencies to be included as items of the curricula. RESULTS: Three eligible documents were identified and 3 Delphi rounds were carried out to reach a consensus on the competencies to be incorporated in the curricula. With reference to the curriculum for physicians, 19 items were included in the knowledge domain, 3 in the attitudes and 10 in the abilities domain. We developed two different curricula for non-physicians: one specific for those working in genetic services (20 items in the knowledge domain, 3 in the attitudes and 12 in the abilities) and one for those not working in genetic services (10 items in the knowledge domain, 3 in the attitudes and 2 in the abilities). CONCLUSIONS: We developed 3 curricula in genetics addressed to non-genetic healthcare professionals. They differ in the "knowledge" and "abilities", while the "attitudes" are the same for all the healthcare professionals. Although some concerns about the generalizability of the findings could arise due to the Italian perspective, we envisage the curricula can be used for genetics educational programs in several contexts.

Laboratory analysis of amino acids, 2018 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG).

Amino acid abnormalities are observed in a broad spectrum of inherited metabolic diseases, such as disorders of amino acid metabolism and transport, organic acidemias, and ureagenesis defects. Comprehensive analysis of physiologic amino acids in blood, urine, and cerebrospinal fluid is typically performed in the following clinical settings: evaluation of symptomatic patients in whom a diagnosis is not known; evaluation of previously diagnosed patients to monitor treatment efficacy; evaluation of asymptomatic or presymptomatic (at-risk) relatives of known patients; follow-up testing for an abnormal newborn screen; and assessment of dietary protein adequacy or renal function in general patient populations. Currently, the most common analytical method to quantify amino acids is based on ion exchange chromatography using post-column derivatization with ninhydrin and spectrophotometric detection. Newer methodologies are based on liquid chromatographic separation with detection by mass spectrometry or spectrophotometry. Amino acid analysis by nonseparation methods, such as the flow injection-tandem mass spectrometric (MS/MS) method used for newborn screening, is considered inadequate for the diagnosis of at-risk patients. The purpose of this document is to provide a technical standard for amino acid analysis as applied to the diagnosis and management of inborn errors of metabolism.

Registered access: authorizing data access.

The Global Alliance for Genomics and Health (GA4GH) proposes a data access policy model-"registered access"-to increase and improve access to data requiring an agreement to basic terms and conditions, such as the use of DNA sequence and health data in research. A registered access policy would enable a range of categories of users to gain access, starting with researchers and clinical care professionals. It would also facilitate general use and reuse of data but within the bounds of consent restrictions and other ethical obligations. In piloting registered access with the Scientific Demonstration data sharing projects of GA4GH, we provide additional ethics, policy and technical guidance to facilitate the implementation of this access model in an international setting.

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)

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)