Whole-genome sequencing in health care: recommendations of the European Society of Human Genetics. Eur J Hum Genet. 2013;21:580-584. [PMID: 23676617 DOI: 10.1038/ejhg.2013.46]

Compare and contrast: a cross-national study across UK, USA and Greek experts regarding return of incidental findings from clinical sequencing

Return of incidental findings (IFs) from clinical sequencing has become a hotly debated topic over the past year. Efforts are being made by several bodies to provide guidance at both national and international levels; however, no studies comparing attitudes of experts across different countries have been published so far. Our goal was to investigate attitudes towards return of IFs from clinical sequencing across UK, USA and Greek experts. Thirty in-depth interviews were conducted with genetics and genomic experts with different backgrounds. Our study revealed more differences when experts were compared according to their professional background than their country. General principles guiding the decision-making and the feedback process were common across all experts but the details of integrating these tests might vary as different professionals reported different needs and attitudes.

Genomics in the clinic: ethical and policy challenges in clinical next-generation sequencing programs at early adopter USA institutions

Next-generation sequencing (NGS) technologies are poised to revolutionize clinical diagnosis and treatment, but raise significant ethical and policy challenges. This review examines NGS program challenges through a synthesis of published literature, website and conference presentation content, and interviews at early-adopting institutions in the USA. Institutions are proactively addressing policy challenges related to the management and technical aspects of program development. However, ethical challenges related to patient-related aspects have not been fully addressed. These complex challenges present opportunities to develop comprehensive and standardized regulations across programs. Understanding the strengths, weaknesses and current practices of evolving NGS program approaches are important considerations for institutions developing NGS services, policymakers regulating or funding NGS programs and physicians and patients considering NGS services.

Whole-exome sequencing as a diagnostic tool: current challenges and future opportunities

Whole-exome sequencing (WES) represents a significant breakthrough in the field of human genetics. This technology has largely contributed to the identification of new disease-causing genes and is now entering clinical laboratories. WES represents a powerful tool for diagnosis and could reduce the 'diagnostic odyssey' for many patients. In this review, we present a technical overview of WES analysis, variants annotation and interpretation in a clinical setting. We evaluate the usefulness of clinical WES in different clinical indications, such as rare diseases, cancer and complex diseases. Finally, we discuss the efficacy of WES as a diagnostic tool and the impact on patient management.

The clinical application of genome-wide sequencing for monogenic diseases in Canada: Position Statement of the Canadian College of Medical Geneticists

Purpose and scope

The aim of this Position Statement is to provide recommendations for Canadian medical geneticists, clinical laboratory geneticists, genetic counsellors and other physicians regarding the use of genome-wide sequencing of germline DNA in the context of clinical genetic diagnosis. This statement has been developed to facilitate the clinical translation and development of best practices for clinical genome-wide sequencing for genetic diagnosis of monogenic diseases in Canada; it does not address the clinical application of this technology in other fields such as molecular investigation of cancer or for population screening of healthy individuals.

Methods of statement development

Two multidisciplinary groups consisting of medical geneticists, clinical laboratory geneticists, genetic counsellors, ethicists, lawyers and genetic researchers were assembled to review existing literature and guidelines on genome-wide sequencing for clinical genetic diagnosis in the context of monogenic diseases, and to make recommendations relevant to the Canadian context. The statement was circulated for comment to the Canadian College of Medical Geneticists (CCMG) membership-at-large and, following incorporation of feedback, approved by the CCMG Board of Directors. 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.

Results and conclusions

Recommendations include (1) clinical genome-wide sequencing is an appropriate approach in the diagnostic assessment of a patient for whom there is suspicion of a significant monogenic disease that is associated with a high degree of genetic heterogeneity, or where specific genetic tests have failed to provide a diagnosis; (2) until the benefits of reporting incidental findings are established, we do not endorse the intentional clinical analysis of disease-associated genes other than those linked to the primary indication; and (3) clinicians should provide genetic counselling and obtain informed consent prior to undertaking clinical genome-wide sequencing. Counselling should include discussion of the limitations of testing, likelihood and implications of diagnosis and incidental findings, and the potential need for further analysis to facilitate clinical interpretation, including studies performed in a research setting. These recommendations will be routinely re-evaluated as knowledge of diagnostic and clinical utility of clinical genome-wide sequencing improves. While the document was developed to direct practice in Canada, the applicability of the statement is broader and will be of interest to clinicians and health jurisdictions internationally.

Attitudes of nearly 7000 health professionals, genomic researchers and publics toward the return of incidental results from sequencing research

Genome-wide sequencing in a research setting has the potential to reveal health-related information of personal or clinical utility for the study participant. There is increasing pressure to return research findings to participants that may not be related to the project aims, particularly when these could be used to prevent disease. Such secondary, unsolicited or 'incidental findings' (IFs) may be discovered unintentionally when interpreting sequence data, or as the result of a deliberate opportunistic screen. This cross-sectional, web-based survey investigated attitudes of 6944 individuals from 75 countries towards returning IFs from genome research. Participants included four relevant stakeholder groups: 4961 members of the public, 533 genetic health professionals, 843 non-genetic health professionals and 607 genomic researchers who were invited via traditional media, social media and professional e-mail list-serve. Treatability and perceived utility of incidental results were deemed important with 98% of stakeholders personally interested in learning about preventable life-threatening conditions. Although there was a generic interest in receiving genomic information, stakeholders did not expect researchers to opportunistically screen for IFs in a research setting. On many items, genetic health professionals had significantly more conservative views compared with other stakeholders. This finding demonstrates a disconnect between the views of those handling the findings of research and those participating in research. Exploring, evaluating and ultimately addressing this disconnect should form a priority for researchers and clinicians alike. This social sciences study offers the largest dataset, published to date, of attitudes towards issues surrounding the return of IFs from sequencing research.

Multiple system atrophy: the application of genetics in understanding etiology

Classically defined phenotypically by a triad of cerebellar ataxia, parkinsonism, and autonomic dysfunction in conjunction with pyramidal signs, multiple system atrophy (MSA) is a rare and progressive neurodegenerative disease affecting an estimated 3-4 per every 100,000 individuals among adults 50-99 years of age. With a pathological hallmark of alpha-synuclein-immunoreactive glial cytoplasmic inclusions (GCIs; Papp-Lantos inclusions), MSA patients exhibit marked neurodegenerative changes in the striatonigral and/or olivopontocerebellar structures of the brain. As a member of the alpha-synucleinopathy family, which is defined by its well-demarcated alpha-synuclein-immunoreactive inclusions and aggregation, MSA's clinical presentation exhibits several overlapping features with other members including Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Given the extensive fund of knowledge regarding the genetic etiology of PD revealed within the past several years, a genetic investigation of MSA is warranted. While a current genome-wide association study is underway for MSA to further clarify the role of associated genetic loci and single-nucleotide polymorphisms, several cases have presented solid preliminary evidence of a genetic etiology. Naturally, genes and variants manifesting known associations with PD (and other phenotypically similar neurodegenerative disorders), including SNCA and MAPT, have been comprehensively investigated in MSA patient cohorts. More recently variants in COQ2 have been linked to MSA in the Japanese population although this finding awaits replication. Nonetheless, significant positive associations with subsequent independent replication studies have been scarce. With very limited information regarding genetic mutations or alterations in gene dosage as a cause of MSA, the search for novel risk genes, which may be in the form of common variants or rare variants, is the logical nexus for MSA research. We believe that the application of next generation genetic methods to MSA will provide valuable insight into the underlying causes of this disease, and will be central to the identification of etiologic-based therapies.

Governing the research-care divide in clinical biobanking: Dutch perspectives

Biobanking, the large-scale, systematic collection of data and tissue for open-ended research purposes, is on the rise, particularly in clinical research. The infrastructures for the systematic procurement, management and eventual use of human tissue and data are positioned between healthcare and research. However, the positioning of biobanking infrastructures and transfer of tissue and data between research and care is not an innocuous go-between. Instead, it involves changes in both domains and raises issues about how distinctions between research and care are drawn and policed. Based on an analysis of the emergence and development of clinical biobanking in the Netherlands, this article explores how processes of bio-objectification associated with biobanking arise, redefining the ways in which distinctions between research and clinical care are governed.

Analyzing communication in genetic consultations--a systematic review

OBJECTIVE

To systematically review studies that have analyzed communication within medical consultations involving genetic specialists and report on their findings and design.

METHODS

Drawing from PRISMA and appropriate guidelines for reviewing qualitative research, a systematic search of seven databases was conducted, followed by selection of studies for inclusion based on a set of criteria. Three authors conducted data extraction and narrative synthesis.

RESULTS

Twenty-two studies were identified and were heterogeneous in setting, design, and methods, with many including limited descriptions of health professionals involved. Despite this variability, studies generally pursued the following three main objectives: searching for structural patterns within consultations, investigating communication and genetic counseling concepts, and linking process with input- and outcome-measures. Structural patterns identified included clinician dialog dominating consultations, and talk being mostly biomedical. Counseling and communication concepts investigated were: risk communication, the negotiation of power and knowledge, and adherence to genetic counseling ideals. Attempts to link consultation data to input- or outcome-measures were often unsuccessful.

CONCLUSION

More interdisciplinary research, grounded in appropriate theoretical frameworks, is needed to explore inherent complexities in this setting.

PRACTICE IMPLICATIONS

Findings from this review can be used to guide the design of future research into the process of genetic consultations.

An implementation framework for the feedback of individual research results and incidental findings in research

BACKGROUND

This article outlines procedures for the feedback of individual research data to participants. This feedback framework was developed in the context of a personalized medicine research project in Canada. Researchers in this domain have an ethical obligation to return individual research results and/or material incidental findings that are clinically significant, valid and actionable to participants. Communication of individual research data must proceed in an ethical and efficient manner. Feedback involves three procedural steps: assessing the health relevance of a finding, re-identifying the affected participant, and communicating the finding. Re-identification requires researchers to break the code in place to protect participant identities. Coding systems replace personal identifiers with a numerical code. Double coding systems provide added privacy protection by separating research data from personal identifying data with a third "linkage" database. A trusted and independent intermediary, the "keyholder", controls access to this linkage database.

DISCUSSION

Procedural guidelines for the return of individual research results and incidental findings are lacking. This article outlines a procedural framework for the three steps of feedback: assessment, re-identification, and communication. This framework clarifies the roles of the researcher, Research Ethics Board, and keyholder in the process. The framework also addresses challenges posed by coding systems. Breaking the code involves privacy risks and should only be carried out in clearly defined circumstances. Where a double coding system is used, the keyholder plays an important role in balancing the benefits of individual feedback with the privacy risks of re-identification. Feedback policies should explicitly outline procedures for the assessment of findings, and the re-identification and contact of participants. The responsibilities of researchers, the Research Ethics Board, and the keyholder must be clearly defined. We provide general guidelines for keyholders involved in feedback. We also recommend that Research Ethics Boards should not be directly involved in the assessment of individual findings. Hospitals should instead establish formal, interdisciplinary clinical advisory committees to help researchers determine whether or not an uncertain finding should be returned.

Rapid pulsed whole genome sequencing for comprehensive acute diagnostics of inborn errors of metabolism

Background

Massively parallel DNA sequencing (MPS) has the potential to revolutionize diagnostics, in particular for monogenic disorders. Inborn errors of metabolism (IEM) constitute a large group of monogenic disorders with highly variable clinical presentation, often with acute, nonspecific initial symptoms. In many cases irreversible damage can be reduced by initiation of specific treatment, provided that a correct molecular diagnosis can be rapidly obtained. MPS thus has the potential to significantly improve both diagnostics and outcome for affected patients in this highly specialized area of medicine.

Results

We have developed a conceptually novel approach for acute MPS, by analysing pulsed whole genome sequence data in real time, using automated analysis combined with data reduction and parallelization. We applied this novel methodology to an in-house developed customized work flow enabling clinical-grade analysis of all IEM with a known genetic basis, represented by a database containing 474 disease genes which is continuously updated. As proof-of-concept, two patients were retrospectively analysed in whom diagnostics had previously been performed by conventional methods. The correct disease-causing mutations were identified and presented to the clinical team after 15 and 18 hours from start of sequencing, respectively. With this information available, correct treatment would have been possible significantly sooner, likely improving outcome.

Conclusions

We have adapted MPS to fit into the dynamic, multidisciplinary work-flow of acute metabolic medicine. As the extent of irreversible damage in patients with IEM often correlates with timing and accuracy of management in early, critical disease stages, our novel methodology is predicted to improve patient outcome. All procedures have been designed such that they can be implemented in any technical setting and to any genetic disease area. The strategy conforms to international guidelines for clinical MPS, as only validated disease genes are investigated and as clinical specialists take responsibility for translation of results. As follow-up in patients without any known IEM, filters can be lifted and the full genome investigated, after genetic counselling and informed consent.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1090) contains supplementary material, which is available to authorized users.

Is there a duty to recontact in light of new genetic technologies? A systematic review of the literature

PURPOSE

With rapid advances in genetic technologies, new genetic information becomes available much faster today than just a few years ago. This has raised questions about whether clinicians have a duty to recontact eligible patients when new genetic information becomes available and, if such duties exist, how they might be implemented in practice.

METHODS

We report the results of a systematic literature search on the ethical, legal, social (including psychological), and practical issues involved in recontacting former patients who received genetic services. We identified 1,428 articles, of which 61 are covered in this review.

RESULTS

The empirical evidence available indicates that most but not all patients value being recontacted. A minority of (older) articles conclude that recontacting should be a legal duty. Most authors consider recontacting to be ethically desirable but practically unfeasible. Various solutions to overcome these practical barriers have been proposed, involving efforts of laboratories, clinicians, and patients.

CONCLUSION

To advance the discussion on implementing recontacting in clinical genetics, we suggest focusing on the question of in what situations recontacting might be regarded as good standard of care. To this end, reaching a professional consensus, obtaining more extensive empirical evidence, and developing professional guidelines are important.

[Concepts for the return of secondary genetic findings in medical diagnostics and research]

High-throughput sequencing of whole genomes is technically already at a high level and is being discussed as a cost-effective alternative to other targeted, analytical procedures for clinical diagnosis of heritable disorders. On the other hand, with whole genome and whole exome sequencing, there is a high likelihood of uncovering secondary findings not associated with the primary aim of the investigation. This article tries to outline the current scientific and technical status of whole genome and whole exome sequencing and of the national and international recommendations concerning the handling of secondary genetic findings which are already available, above all in the research-related context and less so in the clinical context.

Präkonzeptionelle und vorgeburtliche klinische Genomsequenzierung

Hintergrund

Innerhalb kürzester Zeit haben Hochdurchsatzanalysen von Exomen und Genomen Eingang in die postnatale klinisch-diagnostische Anwendung gefunden. Bei hoher technischer Analysezuverlässigkeit, sinkenden Kosten und kurzen Analysezeiten ist das Potenzial, welches sich für diese Anwendung auch für das präkonzeptionelle Screening und die Pränataldiagnostik ergeben könnte, offensichtlich. Insbesondere diese beiden Anwendungsgebiete erfordern eine sehr hohe Sicherheit in der klinischen Befundinterpretation. Eine weitere Herausforderung gegenüber der postnatalen diagnostischen Anwendung wird die Beurteilung des klinischen Manifestationsspektrums präklinisch oder pränatal erhobener genomischer Sequenzdaten sein.

Material und Methoden

Abgeleitet von den Erfahrungen mit NGS-Analysen im postnatalen diagnostischen Ansatz erfolgen eine Übertragung und ein Ausblick auf die Anwendung der Methode im Kontext der Familienplanung.

Diskussion und Ergebnisse

Der Beitrag beschränkt sich auf die technische und klinische Anwendbarkeit. Diskutiert werden der Einsatz von NGS als umfassende Screeningmethode von Populationen, Niedrigrisikokollektiven und die Beschränkung auf ausgewählte, dem individuellen Risikoprofil angepasste Analysen. Letztere könnten kurz- bis mittelfristig Eingang in die präkonzeptionelle und auch vorgeburtliche Diagnostik finden.

Delivery of a clinical genomics service

Over the past five years, next generation sequencing has revolutionised the discovery of genes responsible for rare inherited diseases previously resistant to traditional discovery techniques. This review considers how this new technology is being introduced into clinical practice to aid diagnosis and improve the clinical management of individuals and families affected by rare diseases where access to genetic testing was previously limited. We compare and contrast the different approaches that have been adopted including panel based tests, exome and genome sequencing. We provide insights from our own clinical practice demonstrating the challenges and benefits of this new technology.

Public views on participating in newborn screening using genome sequencing

Growing discussion on the use of whole-genome or exome sequencing (WG/ES) in newborn screening (NBS) has raised concerns regarding the generation of incidental information on millions of infants annually. It is unknown whether integrating WG/ES would alter public expectations regarding participation in universal NBS. We assessed public willingness to participate in NBS using WG/ES compared with current NBS. Our secondary objective was to assess the public's beliefs regarding a parental responsibility to participate in WG/ES-based NBS compared with current NBS. We examined self-reported attitudes regarding willingness to participate in NBS using a cross-sectional national survey of Canadian residents recruited through an internet panel, reflective of the Canadian population by age, gender and region. Our results showed that fewer respondents would be willing to participate in NBS using WG/ES compared with NBS using current technologies (80 vs 94%, P<0.001), or perceived a parental responsibility to participate in WG/ES-based NBS vs current NBS (30 vs 48%, P<0.001). Our findings suggest that integrating WG/ES into NBS might reduce participation, and challenge the moral authority that NBS programmes rely upon to ensure population benefits. These findings point to the need for caution in the untargeted use of WG/ES in public health contexts.

The best interests of the child and the return of results in genetic research: international comparative perspectives

BACKGROUND

Paediatric genomic research raises particularly challenging questions on whether and under what circumstances to return research results. In the paediatric context, decision-making is guided by the best interests of the child framework, as enshrined in the 1989 international Convention on the Rights of the Child. According to this Convention, rights and responsibilities are shared between children, parents, researchers, and the state. These "relational" obligations are further complicated in the context of genetic research.

DISCUSSION

A comparative review of international, regional and national documents on the return of research results reveals that there is a dearth of normative documents in the paediatric context. The best interests of the child framework is increasingly complicated by a growing appreciation of pediatric autonomy and the development thereof; parental rights (particularly when parents are affected by the genomic information of their children); and the right not to know.

SUMMARY

This comparative analysis reveals that policy-makers and legislators have responded to the above challenges in different ways. Nevertheless, in Europe as well as in Canada, there is an emerging trend towards making the return of certain results mandatory in the paediatric context, should this course of action prove to be in the best interests of the child.

Availability of treatment drives decisions of genetic health professionals about disclosure of incidental findings

Contrasting opinions exist regarding the disclosure of incidental findings detected through clinical genomic testing. This study used a discrete choice experiment to investigate genetic health professionals' preferences for the disclosure of incidental findings in an Australian paediatric setting. Four attributes of conditions relating to incidental findings were investigated: availability of prevention and treatment, chance of symptoms ever developing, age of onset and severity. Questionnaires from 59 Australian genetic health professionals were analysed. Results show that when evaluating incidental findings for disclosure, these professionals value the availability of prevention and treatment for the condition above all other characteristics included in the study. The framework of this discrete choice experiment can be used to investigate the preferences of other stakeholders such as paediatricians and parents about disclosure of incidental findings. The results of this study may be considered when assessing which categories of incidental findings are most suitable for disclosure in clinical practice.

Informed consent for exome sequencing research in families with genetic disease: the emerging issue of incidental findings

Genomic sequencing technology is increasingly used in genetic research. Studies of informed consent for exome and genome sequencing (ES/GS) research have largely involved hypothetical scenarios or healthy individuals enrolling in population-based studies. Studies have yet to explore the consent experiences of adults with inherited disease. We conducted a qualitative interview study of 15 adults recently enrolled in a large-scale ES/GS study (11 affected adults, four parents of affected children). Our study had two goals: (1) to explore three theoretical barriers to consent for ES/GS research (interpretive/technical complexity, possibility of incidental findings, and risks of loss of privacy); and (2) to explore how interviewees experienced the consent process. Interviewees could articulate study goals and processes, describe incidental findings, discuss risks of privacy loss, and reflect on their consent experience. Few expected the study would identify the genetic cause of their condition. All elected to receive incidental findings. Interviewees acknowledged paying little attention to potential implications of incidental findings in light of more pressing goals of supporting research regarding their own medical conditions. Interviewees suggested that experience living with a genetic condition prepared them to adjust to incidental findings. Interviewees also expressed little concern about loss of confidentiality of study data. Some experienced the consent process as very long. None desired reconsent prior to return of study results. Families with inherited disease likely would benefit from a consent process in which study risks and benefits were discussed in the context of prior experiences with genetic research and genetic disease.

Use of an electronic medical record to create the marshfield clinic twin/multiple birth cohort

Population-based genetic analyses, such as the Genome-Wide Association Study (GWAS), have proven powerful for describing the genetic complexities of common disease in epidemiologic research. However, the significant challenges faced by population-based study designs have resulted in revitalization of family-based approaches, including twin studies. Twin studies are unique in their ability to ascertain both heritable and environmental contributions to human disease. Several regional and national twin registries have been constructed using a variety of methods to identify potential twins. A significant challenge in constructing these large twin registries includes the substantial resources required to recruit participants, collect phenotypic data, and update the registries as time progresses. Here we describe the use of the Marshfield Clinic electronic medical record (EMR) to identify a cohort of 19,226 patients enriched for twins or multiples. This cohort defines the Marshfield Clinic Twin/Multiple Birth Cohort (MCTC). An EMR system provides both a mechanism to identify potential twins and a source of detailed phenotypic data in near real time without the need for patient contact outside standard medical care. To demonstrate that the MCTC can be used for genetic-based epidemiologic research, concordance rates for muscular dystrophy (MD) and fragile-X syndrome-two highly heritable diseases-were assessed. Observations indicate that both MD and fragile-X syndrome are highly correlated among affected twins in the MCTC (P ≅ 3.7 × 10(-6) and 1.1 × 10(-4) , respectively). These findings suggest that EMR systems may not only be an effective resource for predicting families of twins, but can also be rapidly applied to epidemiologic research.

Review of current methods, applications, and data management for the bioinformatics analysis of whole exome sequencing

The advent of next-generation sequencing technologies has greatly promoted advances in the study of human diseases at the genomic, transcriptomic, and epigenetic levels. Exome sequencing, where the coding region of the genome is captured and sequenced at a deep level, has proven to be a cost-effective method to detect disease-causing variants and discover gene targets. In this review, we outline the general framework of whole exome sequence data analysis. We focus on established bioinformatics tools and applications that support five analytical steps: raw data quality assessment, pre-processing, alignment, post-processing, and variant analysis (detection, annotation, and prioritization). We evaluate the performance of open-source alignment programs and variant calling tools using simulated and benchmark datasets, and highlight the challenges posed by the lack of concordance among variant detection tools. Based on these results, we recommend adopting multiple tools and resources to reduce false positives and increase the sensitivity of variant calling. In addition, we briefly discuss the current status and solutions for big data management, analysis, and summarization in the field of bioinformatics.

Defining and managing incidental findings in genetic and genomic practice

The rapidly declining costs and increasing speeds of whole-genome analysis mean that genetic testing is undergoing a shift from targeted approaches to broader ones that look at the entire genome. As whole-genome technologies gain widespread use, questions about the management of so-called incidental findings-those unrelated to the question being asked-need urgent consideration. In this review, we bring together current understanding and arguments about (1) appropriate terminology, (2) the determination of clinical utility and when to disclose incidental findings, (3) the differences in management and disclosure in clinical, research and commercial contexts and (4) ethical and practical issues about familial implications and recontacting those tested. We recommend that greater international consensus is developed around the disclosure and management of incidental findings, with particular attention to when, and how, less clear-cut results should be communicated. We suggest that there is no single term that captures all the issues around these kinds of findings and that different terms may, therefore, need to be used in different settings. We also encourage the use of clear consent processes, but suggest that the absence of consent should not always preclude disclosure. Finally, we recommend further research to identify ways to implement the use of a genome output as a resource, accessible over time, to facilitate appropriate disclosure and recontact when the significance of a previously unclear incidental finding is clarified.

An assessment of clinician and researcher needs for support in the era of genomic medicine

AIM

To assess clinicians' and researchers' past, current and anticipated future use of next-generation sequencing (NGS) and anticipated needs for support. Materials & methods: A web-based survey was conducted at Boston Children's Hospital.

RESULTS

Many clinicians anticipate that they will use exome/genome sequencing (44.8%) and/or candidate gene panels (50%) within the next year. Researcher respondents anticipate the need for exome/genome sequencing (48.0%) and candidate gene panels (31.8%). Few respondents (13.6%) said that they felt 'Completely Ready' or 'Pretty Much Ready' to incorporate NGS into their clinical practice or research.

CONCLUSION

Researchers and clinicians anticipate increased utilization of NGS. Respondents indicated varying degrees of need for a diverse list of support services, ranking interpretation and clinical correlation support as the most needed services.

Incidental findings from clinical sequencing in Greece: reporting experts' attitudes

Unprecedented progress in sequencing technologies and decreasing cost have brought genomic testing into the clinical setting. At the same time, the debate in the literature concerning the return of incidental findings (IFs) has made this an important issue internationally. These developments reflect a shift in genetics that will also affect smaller countries, such as Greece, that are just starting to implement these technologies and may look to other countries for examples of good practice. Ten in-depth interviews were conducted with Greek experts in clinical sequencing. Previous experiences and attitudes toward IFs and clinical sequencing were investigated as well as views on the existing policy regarding managing genetic information generated through testing. . Interviews were analysed using thematic analysis. All participants reported the lack of any legal or other supportive mechanism. IFs are currently managed at a “local” level, i.e. within the clinic or the laboratory in an ad hoc way. All participants thought that clinically valid and actionable IFs should be returned, but always with caution and in respect to patients’ wishes, although several experts reported returning IFs according to their clinical discretion. Experts reported that most patients ask for all tests available but they felt that more counselling is needed to understand and manage genetic information. Due to the lack of any supporting mechanisms, professionals in Greece, even those with established experience in the field of genetic and genomic testing, have difficulties dealing with IFs. All experts agreed that it is now time, before the full integration of genomic testing into everyday clinical practice, for guidance to help Greek physicians work with patients and their families when IFs are discovered.

Exome Sequencing in Fetuses with Structural Malformations

Prenatal diagnostic testing is a rapidly advancing field. An accurate diagnosis of structural anomalies and additional abnormalities in fetuses with structural anomalies is important to allow “triage” and designation of prognosis. This will allow parents to make an informed decision relating to the pregnancy. This review outlines the current tests used in prenatal diagnosis, focusing particularly on “new technologies” such as exome sequencing. We demonstrate the utility of exome sequencing above that of conventional karyotyping and Chromosomal Microarray (CMA) alone by outlining a recent proof of concept study investigating 30 parent-fetus trios where the fetus is known to have a structural anomaly. This may allow the identification of pathological gene anomalies and consequently improved prognostic profiling, as well as excluding anomalies and distinguishing between de novo and inherited mutations, in order to estimate the recurrence risk in future pregnancies. The potential ethical dilemmas surrounding exome sequencing are also considered, and the future of prenatal genetic diagnosis is discussed.

Prenatal diagnosis of chromosomal imbalances

Prenatal array comparative genome hybridisation (aCGH) testing has by and large replaced routine karyotyping in many healthcare settings. While this will lead to more diagnoses, uncertain, unexpected or unhelpful findings are also likely to increase. This is the case for aCGH in any setting, but we discuss the particular challenges the prenatal setting generates and suggest areas that need further debate and discussion as well as some pragmatic ways forward.

To disclose, or not to disclose? Context matters

Progress in understanding childhood disease using next-generation sequencing (NGS) portends vast improvements in the nature and quality of patient care. However, ethical questions surrounding the disclosure of incidental findings (IFs) persist, as NGS and other novel genomic technologies become the preferred tool for clinical genetic testing. Thus, the need for comprehensive management plans and multidisciplinary discussion on the return of IFs in pediatric research has never been more immediate. The aim of this study is to explore the views of investigators concerning the return of IFs in the pediatric oncology research context. Our findings reveal at least four contextual themes underlying the ethics of when, and how, IFs could be disclosed to participants and their families: clinical significance of the result, respect for individual, scope of professional responsibilities, and implications for the healthcare/research system. Moreover, the study proposes two action items toward anticipatory governance of IF in genetic research with children. The need to recognize the multiplicity of contextual factors in determining IF disclosure practices, particularly as NGS increasingly becomes a centerpiece in genetic research broadly, is heightened when children are involved. Sober thought should be given to the possibility of discovering IF, and to proactive discussions about disclosure considering the realities of young participants, their families, and the investigators who recruit them.

Views of primary care providers regarding the return of genome sequencing incidental findings

Sequencing of the entire exome or genome is increasingly used in clinical practice. Debate continues, however, regarding which incidental findings (IFs) should be returned and who should be involved in those decisions. Previous empirical research regarding stakeholder attitudes to the return of IFs has primarily involved genetics professionals; non-genetics health professionals have not been widely surveyed. Given this, a survey regarding return of IFs was administered at the Best Practices in Pediatrics Conference following an educational presentation on genetics terminology and genetic condition examples. A total of 258 participants completed the survey. Of particular note, respondents who were positively disposed to sequencing did not always report wanting to learn about IFs, even if actionable. This is noteworthy given recent American College of Medical Genetics and Genomics guidelines recommending particular actionable IF be returned 'without reference to patient preference'. This study's findings are important because they provide insight regarding the attitudes to the return of genome sequencing results for an important professional group, primary care providers. Ultimately, as likely gatekeepers to referrals for this technology, their opinions about the test will be key to its successful deployment.

The unintended implications of blurring the line between research and clinical care in a genomic age

While the development of next-generation sequencing technology has had a paradigm-changing impact on biomedical research, there is likely to be a gap between discovery of therapeutic benefits in research and actual adoption of the new technology into clinical practice. This gap can create pressure on the research enterprise to provide individualized care more typical of the clinic setting because it is uniquely accessible in research. This blurring of the line between research and clinical care is understandable, and perhaps even inevitable. But even if the gap is only transitory, such a blurring can have lasting implications, both by expanding obligations imposed on researchers, but also by challenging long-held ethical views. We explore this idea, focusing on how the dissolving distinction between research and clinical care has influenced the vigorous debate around how researchers should manage genetic findings (sometimes separated into primary and incidental or secondary findings) resulting from research.

Ethical issues raised by whole genome sequencing

While there is ongoing discussion about the details of implementation of whole genome sequencing (WGS) and whole exome sequencing (WES), there appears to be a consensus amongst geneticists that the widespread use of these approaches is not only inevitable, but will also be beneficial [1]. However, at the present time, we are unable to anticipate the full range of uses, consequences and impact of implementing WGS and WES. Nevertheless, the already known ethical issues, both in research and in clinical practice are diverse and complex and should be addressed properly presently. Herein, we discuss the ethical aspects of WGS and WES by particularly focussing on three overlapping themes: (1) informed consent, (2) data handling, and (3) the return of results.

The challenges, advantages and future of phenome-wide association studies

Over the last decade, significant technological breakthroughs have revolutionized human genomic research in the form of genome-wide association studies (GWASs). GWASs have identified thousands of statistically significant genetic variants associated with hundreds of human conditions including many with immunological aetiologies (e.g. multiple sclerosis, ankylosing spondylitis and rheumatoid arthritis). Unfortunately, most GWASs fail to identify clinically significant associations. Identifying biologically significant variants by GWAS also presents a challenge. The GWAS is a phenotype-to-genotype approach. As a complementary/alternative approach to the GWAS, investigators have begun to exploit extensive electronic medical record systems to conduct a genotype-to-phenotype approach when studying human disease – specifically, the phenome-wide association study (PheWAS). Although the PheWAS approach is in its infancy, this method has already demonstrated its capacity to rediscover important genetic associations related to immunological diseases/conditions. Furthermore, PheWAS has the advantage of identifying genetic variants with pleiotropic properties. This is particularly relevant for HLA variants. For example, PheWAS results have demonstrated that the HLA-DRB1 variant associated with multiple sclerosis may also be associated with erythematous conditions including rosacea. Likewise, PheWAS has demonstrated that the HLA-B genotype is not only associated with spondylopathies, uveitis, and variability in platelet count, but may also play an important role in other conditions, such as mastoiditis. This review will discuss and compare general PheWAS methodologies, describe both the challenges and advantages of the PheWAS, and provide insight into the potential directions in which PheWAS may lead.

Testing personalized medicine: patient and physician expectations of next-generation genomic sequencing in late-stage cancer care

Developments in genomics, including next-generation sequencing technologies, are expected to enable a more personalized approach to clinical care, with improved risk stratification and treatment selection. In oncology, personalized medicine is particularly advanced and increasingly used to identify oncogenic variants in tumor tissue that predict responsiveness to specific drugs. Yet, the translational research needed to validate these technologies will be conducted in patients with late-stage cancer and is expected to produce results of variable clinical significance and incidentally identify genetic risks. To explore the experiential context in which much of personalized cancer care will be developed and evaluated, we conducted a qualitative interview study alongside a pilot feasibility study of targeted DNA sequencing of metastatic tumor biopsies in adult patients with advanced solid malignancies. We recruited 29/73 patients and 14/17 physicians; transcripts from semi-structured interviews were analyzed for thematic patterns using an interpretive descriptive approach. Patient hopes of benefit from research participation were enhanced by the promise of novel and targeted treatment but challenged by non-findings or by limited access to relevant trials. Family obligations informed a willingness to receive genetic information, which was perceived as burdensome given disease stage or as inconsequential given faced challenges. Physicians were optimistic about long-term potential but conservative about immediate benefits and mindful of elevated patient expectations; consent and counseling processes were expected to mitigate challenges from incidental findings. These findings suggest the need for information and decision tools to support physicians in communicating realistic prospects of benefit, and for cautious approaches to the generation of incidental genetic information.

Addressing the ethical challenges in genetic testing and sequencing of children

American Academy of Pediatrics (AAP) and American College of Medical Genetics (ACMG) recently provided two recommendations about predictive genetic testing of children. The Clinical Sequencing Exploratory Research Consortium's Pediatrics Working Group compared these recommendations, focusing on operational and ethical issues specific to decision making for children. Content analysis of the statements addresses two issues: (1) how these recommendations characterize and analyze locus of decision making, as well as the risks and benefits of testing, and (2) whether the guidelines conflict or come to different but compatible conclusions because they consider different testing scenarios. These statements differ in ethically significant ways. AAP/ACMG analyzes risks and benefits using best interests of the child and recommends that, absent ameliorative interventions available during childhood, clinicians should generally decline to order testing. Parents authorize focused tests. ACMG analyzes risks and benefits using the interests of the child and other family members and recommends that sequencing results be examined for additional variants that can lead to ameliorative interventions, regardless of age, which laboratories should report to clinicians who should contextualize the results. Parents must accept additional analysis. The ethical arguments in these statements appear to be in tension with each other.

Translating personalized medicine using new genetic technologies in clinical practice: the ethical issues

The integration of new genetic technologies into clinical practice holds great promise for the personalization of medical care, particularly the use of large-scale DNA sequencing for genome-wide genetic testing. However, these technologies also yield unprecedented amounts of information whose clinical implications are not fully understood, and we are still developing technical standards for measuring sequence accuracy. These technical and clinical challenges raise ethical issues that are similar to but qualitatively different from those that we are accustomed to dealing with for traditional medical genetics. The sheer amount of information afforded by genome sequencing requires rethinking of how to implement core ethical principles including, but not limited to: informed consent, privacy and data ownership and sharing, technology regulation, issues of access, particularly as new technology is integrated into clinical practice, and issues of potential stigma and impact on perceptions of disability. In this article, we will review the issues of informed consent, privacy, data ownership and technology regulation as they relate to the emerging field of personalized medicine and genomics.

Informed consent for exome sequencing in diagnostics: exploring first experiences and views of professionals and patients

Next-generation sequencing is increasingly being chosen as a diagnostic tool for cases of expected genetic, but unresolved origin. The consequential increased need for decisions on disclosure of unsolicited findings poses a challenge for the informed consent procedure. This study explored the first experiences with, and needs for, the informed consent procedure in diagnostic exome sequencing, with the stakeholders involved. Semi-structured interviews were conducted with 11 professional experts and one professional gave a written response. Furthermore, the counseling process was observed in three cases where exome sequencing was offered, followed by interviews with the patient (representative) and the genetic counselor. The respondents not only preferred an opt-out for unsolicited findings but also identified many challenges and therefore more experiences with exome sequencing was considered needed. Context-dependent decision-making was observed and an Advisory Board for unsolicited findings was considered helpful while doubts were raised about the feasibility and the possibility of undermining patients' autonomy. Finally, respondents brought up the complexity of information provision, and division of responsibilities between clinicians and the lab. These challenges and needs, raised by stakeholders involved, provide more insight in the next steps needed for an optimal informed consent procedure for exome sequencing in diagnostics.