Incidental findings from clinical genome-wide sequencing: a review

Impact of whole genome sequencing on the care pathway for patients with cancer of unknown primary

BACKGROUND

Patients with metastatic disease and no identifiable primary tumor, thus diagnosed with cancer of unknown primary (CUP), typically have a poor prognosis. Tumor DNA sequencing has recently shown promise in identifying the molecular tissue of origin. This study evaluated the value of whole genome sequencing (WGS) in the CUP care pathway, by comparing patient outcomes with a historical control cohort. Also, the value of whole transcriptome sequencing (WTS) was explored.

PATIENTS AND METHODS

A prospective intervention cohort was established of provisional CUP patients (≥18 years of age) who had WGS carried out on metastatic tissue between August 2021 and August 2023. A control cohort was established of CUP patients (≥18 years of age) diagnosed between December 2016 and April 2021 without the availability of WGS. The CUP predicting algorithm was applied to WGS data, and data on definitive diagnosis, molecular actionable alterations [ESMO Scale for Clinical Actionability of molecular Targets (ESCAT) tier 1-3], therapy, diagnostic timelines, and overall survival (OS) were captured.

RESULTS

A total of 159 provisional CUP patients (n = 54 intervention cohort, n = 105 control cohort) were included. WGS and WTS were successfully carried out in 46 (85%) and 27 patients (50%). A primary tumor diagnosis was established in 76% of the intervention cohort compared with 16% of the control cohort (P < 0.001). WGS contributed to a primary tumor diagnosis in 34 patients (63%) and identified an actionable alteration in 34 patients (63%). WTS contributed to a primary tumor diagnosis in three patients (6%). Following WGS, treatment recommendations could be made for 38 patients (70%), of whom 22 started the recommended therapies (58%). The median OS was 11 and 9 months in the intervention and control cohorts, respectively (P = 0.345).

CONCLUSION

Incorporation of WGS into the CUP care pathway is of significant value for diagnosing a primary tumor of origin and contributed to the identification of actionable alterations in the majority of patients.

Variants that get straight to your heart - Cardiogenetic secondary findings in exome sequencing

BACKGROUND

Exome sequencing has been established as a fundamental tool in genetic diagnostics. It may also provide information about variants in genes unrelated to the primary purpose, so-called secondary findings. Especially, diagnoses of unnoticed inborn cardiac diseases are of high clinical relevance due to therapeutic options in context of prevention of sudden cardiac death.

METHODS

Exome data of 9962 individuals was analysed for relevant cardiogenetic findings. Genes were selected according to ACMG recommendations for secondary findings (v.3.1). First, a filter for (likely) pathogenic variants, published in the ClinVar database, was used. Second, exome data was screened for loss of function (LoF) variants in genes in which LoF is a known disease pathomechanism. All variants were evaluated by geneticists regarding their pathogenicity.

RESULTS

Pathogenic or likely pathogenic variants were identified in 136 different individuals (136/9962, 1.4%), with the Low-Density Lipoprotein Receptor gene (LDLR, 24/136, 17.6%) and the Titin gene (TTN, 24/136, 17.6%), being the most frequently affected ones. 31.6% (43/136) of the identified variants had been reported beforehand, while 47.1% (64/136) had not been reported. The remaining cases (29/136, 21.3%) were part of research projects with no written reports. In 26.5% (36/136), the finding would have been missed, if only index patients and not their parents had been screened for secondary findings in case of trio ES.

CONCLUSION

As demonstrated in our study, at least one or two out of one hundred people are likely to carry a pathogenic cardiogenetic variant. Counselling geneticist and clinicians need to be aware of these findings in exome and genome sequencing. Informed consent of the patient regarding the report of secondary findings should absolutely be obtained beforehand.

What's in a name? Justifying terminology for genomic findings beyond the initial test indication: A scoping review

Genome sequencing can generate findings beyond the initial test indication that may be relevant to a patient or research participant's health. In the decade since the American College of Medical Genetics and Genomics published its recommendations for reporting these findings, consensus regarding terminology has remained elusive and a variety of terms are in use globally. We conducted a scoping review to explore terminology choice and the justifications underlying those choices. Documents were included if they contained a justification for their choice of term(s) related to findings beyond the initial genomic test indication. From 3571 unique documents, 52 were included, just over half of which pertained to the clinical context (n = 29, 56%). We identified four inter-related concepts used to defend or oppose terms: expectedness of the finding, effective communication, relatedness to the original test indication, and how genomic information was generated. A variety of justifications were used to oppose the term "incidental," whereas "secondary" had broader support as a term to describe findings deliberately sought. Terminology choice would benefit from further work to include the views of patients. We contend that clear definitions will improve ethical debate and support communication about genomic findings beyond the initial test indication.

Challenges Related to the Use of Next-Generation Sequencing for the Optimization of Drug Therapy

Over the last decade, next-generation sequencing (NGS) methods have become increasingly used in various areas of human genomics. In routine clinical care, their use is already implemented in oncology to profile the mutational landscape of a tumor, as well as in rare disease diagnostics. However, its utilization in pharmacogenomics is largely lacking behind. Recent population-scale genome data has revealed that human pharmacogenes carry a plethora of rare genetic variations that are not interrogated by conventional array-based profiling methods and it is estimated that these variants could explain around 30% of the genetically encoded functional pharmacogenetic variability.To interpret the impact of such variants on drug response a multitude of computational tools have been developed, but, while there have been major advancements, it remains to be shown whether their accuracy is sufficient to improve personalized pharmacogenetic recommendations in robust trials. In addition, conventional short-read sequencing methods face difficulties in the interrogation of complex pharmacogenes and high NGS test costs require stringent evaluations of cost-effectiveness to decide about reimbursement by national healthcare programs. Here, we illustrate current challenges and discuss future directions toward the clinical implementation of NGS to inform genotype-guided decision-making.

A systematic literature review of disclosure practices and reported outcomes for medically actionable genomic secondary findings

Purpose:

Secondary findings (SF) are present in 1–4% of individuals undergoing genome/exome sequencing. A review of how SF are disclosed and what outcomes result from their receipt is urgent and timely.

Methods:

We conducted a systematic literature review of SF disclosure practices and outcomes after receipt including cascade testing, family and provider communication, and healthcare actions. Of the 1,184 non-duplicate records screened we summarize findings from 27 included research articles describing SF disclosure practices, outcomes after receipt, or both.

Results:

The included articles reported 709 unique SF index recipients/families. Referrals and/or recommendations were provided 647 SF recipients and outcome data were available for 236. At least one recommended evaluation was reported for 146 SF recipients; 16 reports of treatment or prophylactic surgery were identified. We found substantial variations in how the constructs of interest were defined and described.

Conclusion:

Variation in how SF disclosure and outcomes were described limited our ability to compare findings. We conclude the literature provided limited insight into how the ACMG guidelines have been translated into precision health outcomes for SF recipients. Robust studies of SF recipients are needed and should be prioritized for future research.

Systematic Review of the Economic Evaluation of Returning Incidental Findings in Genomic Research

Objectives: Discussions regarding who and how incidental findings (IFs) should be returned and the ethics behind returning IFs have increased dramatically over the years. However, information on the cost and benefits of returning IFs to patients remains scanty. Design: This study systematically reviews the economic evaluation of returning IFs in genomic sequencing. We searched for published articles on the cost-effectiveness, cost-benefit, and cost-utility of IFs in Medline, Scopus, PubMed, and Google Scholar. Results: We found six published articles that met the eligibility criteria of this study. Two articles used cost analysis only, one used cost-benefit analysis only, two used both cost analysis and cost-effectiveness, and one used both cost-benefit analysis and cost-utility to describe the cost of returning IFs in genomic sequencing. Conclusion: While individuals value the IF results and are willing to pay for them, the cost of returning IFs depends on the primary health condition of the patient. Although patients were willing to pay, there was no clear evidence that returning IFs might be cost-effective. More rigorous economic evaluation studies of IFs are needed to determine whether or not the cost of returning IFs is beneficial to the patient.

Preconception genome medicine: current state and future perspectives to improve infertility diagnosis and reproductive and health outcomes based on individual genomic data

BACKGROUND

Our genetic code is now readable, writable and hackable. The recent escalation of genome-wide sequencing (GS) applications in population diagnostics will not only enable the assessment of risks of transmitting well-defined monogenic disorders at preconceptional stages (i.e. carrier screening), but also facilitate identification of multifactorial genetic predispositions to sub-lethal pathologies, including those affecting reproductive fitness. Through GS, the acquisition and curation of reproductive-related findings will warrant the expansion of genetic assessment to new areas of genomic prediction of reproductive phenotypes, pharmacogenomics and molecular embryology, further boosting our knowledge and therapeutic tools for treating infertility and improving women's health.

OBJECTIVE AND RATIONALE

In this article, we review current knowledge and potential development of preconception genome analysis aimed at detecting reproductive and individual health risks (recessive genetic disease and medically actionable secondary findings) as well as anticipating specific reproductive outcomes, particularly in the context of IVF. The extension of reproductive genetic risk assessment to the general population and IVF couples will lead to the identification of couples who carry recessive mutations, as well as sub-lethal conditions prior to conception. This approach will provide increased reproductive autonomy to couples, particularly in those cases where preimplantation genetic testing is an available option to avoid the transmission of undesirable conditions. In addition, GS on prospective infertility patients will enable genome-wide association studies specific for infertility phenotypes such as predisposition to premature ovarian failure, increased risk of aneuploidies, complete oocyte immaturity or blastocyst development failure, thus empowering the development of true reproductive precision medicine.

SEARCH METHODS

Searches of the literature on PubMed Central included combinations of the following MeSH terms: human, genetics, genomics, variants, male, female, fertility, next generation sequencing, genome exome sequencing, expanded carrier screening, secondary findings, pharmacogenomics, controlled ovarian stimulation, preconception, genetics, genome-wide association studies, GWAS.

OUTCOMES

Through PubMed Central queries, we identified a total of 1409 articles. The full list of articles was assessed for date of publication, limiting the search to studies published within the last 15 years (2004 onwards due to escalating research output of next-generation sequencing studies from that date). The remaining articles' titles were assessed for pertinence to the topic, leaving a total of 644 articles. The use of preconception GS has the potential to identify inheritable genetic conditions concealed in the genome of around 4% of couples looking to conceive. Genomic information during reproductive age will also be useful to anticipate late-onset medically actionable conditions with strong genetic background in around 2-4% of all individuals. Genetic variants correlated with differential response to pharmaceutical treatment in IVF, and clear genotype-phenotype associations are found for aberrant sperm types, oocyte maturation, fertilization or pre- and post-implantation embryonic development. All currently known capabilities of GS at the preconception stage are reviewed along with persisting and forthcoming barriers for the implementation of precise reproductive medicine.

WIDER IMPLICATIONS

The expansion of sequencing analysis to additional monogenic and polygenic traits may enable the development of cost-effective preconception tests capable of identifying underlying genetic causes of infertility, which have been defined as 'unexplained' until now, thus leading to the development of a true personalized genomic medicine framework in reproductive health.

Physicians' Attitudes and Ethical Obligations to Pharmacogenetic Testing

INTRODUCTION

Despite the increased utilization of pharmacogenetic (PGt) testing to guide drug therapy, little is known about the ethical challenges posed by the use of these genetic tools.

METHODS

This cross-sectional study aimed to address ethical issues related to ancillary genetic information, consent forms, and potential confidentiality breaches from physicians' perspectives. A questionnaire was administered to all practicing physicians working in KAUH.

RESULTS

Almost 49% and 65% of physicians were willing to recommend PGt testing for adult and pediatric patients, respectively. The findings showed that physicians attitudes towards the clinical utility of PGt testing became more preceptive. The majority (73.7%) indicated that PGt testing should not be treated as other routine laboratory tests. The finding also focused on potential conflicts regarding ancillary genetic information, in which 78.8% indicated that they would like to preserve the confidentiality and privacy of the patients and only 14.4% of physicians did not feel obligated to let patients know about any future risk that might be uncovered using PGt testing. The findings showed that collecting both verbal and written consents was imperative prior to testing. Seriousness and predictability of the diseases were reported to be legitimate circumstances that allow disclosure of genetic information.

DISCUSSION

Unless the field of PGt testing addresses the ethical challenges that might be encountered during PGt treatment, these issues might influence its acceptance in routine clinical settings. Establishing a minimal set of ethical standards may help emphasize the role of physicians and thus facilitate the implementation of PGt tests.

Clinical application of genomic high-throughput data: Infrastructural, ethical, legal and psychosocial aspects

Genomic high-throughput technologies (GHTT) such as next-generation sequencing represent a fast and cost-effective tool toward a more comprehensive understanding of the molecular background of complex diseases. However, technological advances contrast with insufficient application in clinical practice. Thus, patients, physicians, and other professionals are faced with tough challenges that forestall the efficient and effective implementation. With the increasing application of genetic testing, it is of paramount importance that physicians and other professionals in healthcare recognize the restrictions and potential of GHTT, in order to understand and interpret the complex data in the context of health and disease. At the same time, the growing volume and complexity of data is forever increasing the need for sustainable infrastructure and state-of-the-art tools for efficient data management, including their analysis and integration. The large pool of sensitive information remains difficult to interpret and fundamental questions spanning from billing to legal, social, and ethical issues have still not been resolved. Here we summarize and discuss these obstacles in an interdisciplinary context and suggest ways to overcome them. Continuous discussion with clinicians, data managers, biostatisticians, systems medicine experts, ethicists, legal scholars, and patients illuminates the strengths, weakness, and current practices in the pipeline from biomaterial to sequencing and data management. This discussion also highlights the new, cross-disciplinary working collaborations to realize the wide-ranging challenges in clinical genomics including the exceptional demands placed on the staff preparing and presenting the data, as well as the question as to how to report the data and results to patients.

Genomic Contextualism: Shifting the Rhetoric of Genetic Exceptionalism

As genomic science has evolved, so have policy and practice debates about how to describe and evaluate the ways in which genomic information is treated for individuals, institutions, and society. The term genetic exceptionalism, describing the concept that genetic information is special or unique, and specifically different from other kinds of medical information, has been utilized widely, but often counterproductively in these debates. We offer genomic contextualism as a new term to frame the characteristics of genomic science in the debates. Using stasis theory to draw out the important connection between definitional issues and resulting policies, we argue that the framework of genomic contextualism is better suited to evaluating genomics and its policy-relevant features to arrive at more productive discussion and resolve policy debates.

Genomic information and a person's right not to know: A closer look at variations in hypothetical informational preferences in a German sample

In clinical practice and in research, there is an ongoing debate on how to return incidental and secondary findings of genetic tests to patients and research participants. Previous investigations have found that most of the people most of the time are in favor of full disclosure of results. Yet, the option to reject disclosure, based on the so-called right not to know, can be valuable especially for some vulnerable subgroups of recipients. In the present study we investigated variations in informational preferences in the context of genetic testing in a large and diverse German sample. This survey examined health care professionals, patients, participants of genetic counseling sessions and members of the general population (N = 518). Survey participants were assessed regarding their openness to learning about findings under various hypothetical scenarios, as well as their attitudes about the doctor-patient-relationship in a disclosure situation and about informational transfer to third parties. While the majority of participants wanted to learn about their findings, the extent of support of disclosure varied with features of the hypothetical diagnostic scenarios (e.g., controllability of disease; abstract vs. concrete scenario description) and demographic characteristics of the subjects. For example, subjects with higher levels of education were more selective with regards to the kind of information they want to receive than those with lower levels of education. We discuss implications of these findings for the debate about the right not to know and for the clinical practice of informed consent procedures.

A comparison of Australian and French families affected by sarcoma: perceptions of genetics and incidental findings

AIM

To compare Australian and French perceptions of genetics and preferences regarding the return of incidental findings.

METHODS

Participants from the International Sarcoma Kindred Study received a survey at intake to cancer referral units. A total of 1442 Australian and 479 French individuals affected by sarcoma and their unaffected family members responded to four hypothetical scenarios depicting hereditary conditions of varying treatability and severity.

RESULTS

Australians' preference for the return of incidental findings was consistently higher than French for all scenarios. Country group differences were significant for two scenarios when individual characteristics were controlled through multivariable analyses.

CONCLUSION

Findings support the need for guidelines that are sensitive to sociocultural context and promote autonomous decision-making.

"I would like to discuss it further with an expert": a focus group study of Finnish adults' perspectives on genetic secondary findings

Lowered costs of genomic sequencing facilitate analyzing large segments of genetic data. Ethical debate has focused on whether and what kind of incidental or secondary findings (SFs) to report, and how to obtain valid informed consent. However, people's support needs after receiving SFs have received less attention. We explored Finnish adults' perspectives on reporting genetic SFs. In this qualitative study which included four focus group discussions (N = 23) we used four vignette letters, each reporting a genetic SF predisposing to a different disease: familial hypercholesterolemia, long QT syndrome, Lynch syndrome, and Li-Fraumeni syndrome. Transcribed focus group discussions were analyzed using inductive thematic analysis. Major themes were immediate shock, dealing with worry and heightened risk, fear of being left alone to deal with SFs, disclosing to family, and identified support needs. Despite their willingness to receive SFs, participants were concerned about being left alone to deal with them. Empathetic expert support and timely access to preventive care were seen as essential to coping with shock and worry, and disclosing SFs to family. Discussion around SFs needs to concern not only which findings to report, but also how healthcare systems need to prepare for providing timely access to preventive care and support for individuals and families.

Expect the unexpected: screening for secondary findings in clinical genomics research

BACKGROUND

Due to decreasing cost, and increasing speed and precision, genomic sequencing in research is resulting in the generation of vast amounts of genetic data. The question of how to manage that information has been an area of significant debate. In particular, there has been much discussion around the issue of 'secondary findings' (SF)-findings unrelated to the research that have diagnostic significance.

SOURCES OF DATA

The following includes ethical commentaries, guidelines and policies in respect to large-scale clinical genomics studies.

AREAS OF AGREEMENT

Research participant autonomy and their informed consent are paramount-policies around SF must be made clear and participants must have the choice as to which results they wish to receive, if any.

AREAS OF CONTROVERSY

While many agree that clinically 'actionable' findings should be returned, some question whether they should be actively sought within a research protocol.

GROWING POINTS

SF present challenges to a growing field; diverse policies around their management have the potential to hinder collaboration and future research.

AREAS TIMELY FOR DEVELOPING RESEARCH

The impact of returning SF and accurate estimates of their clinical utility are needed to inform future protocol design.

Genomic newborn screening: public health policy considerations and recommendations

BACKGROUND

The use of genome-wide (whole genome or exome) sequencing for population-based newborn screening presents an opportunity to detect and treat or prevent many more serious early-onset health conditions than is possible today.

METHODS

The Paediatric Task Team of the Global Alliance for Genomics and Health's Regulatory and Ethics Working Group reviewed current understanding and concerns regarding the use of genomic technologies for population-based newborn screening and developed, by consensus, eight recommendations for clinicians, clinical laboratory scientists, and policy makers.

RESULTS

Before genome-wide sequencing can be implemented in newborn screening programs, its clinical utility and cost-effectiveness must be demonstrated, and the ability to distinguish disease-causing and benign variants of all genes screened must be established. In addition, each jurisdiction needs to resolve ethical and policy issues regarding the disclosure of incidental or secondary findings to families and ownership, appropriate storage and sharing of genomic data.

CONCLUSION

The best interests of children should be the basis for all decisions regarding the implementation of genomic newborn screening.

How, who, and when: preferences for delivery of genome sequencing results among women diagnosed with breast cancer at a young age

Background

The increasing use of genome sequencing with patients raises a critical communication challenge: return of secondary findings. While the issue of what sequencing results should be returned to patients has been examined, much less attention has been paid to developing strategies to return these results in ways that meet patients' needs and preferences. To address this, we investigated delivery preferences (i.e., who, how, when) for individual genome sequencing results among women diagnosed with breast cancer at age 40 or younger.

Methods

We conducted 60 semistructured, in‐person individual interviews to examine preferences for the return of different types of genome sequencing results and the reasons underlying these preferences. Two coders independently coded interview transcripts; analysis was conducted using NVivo 10.

Results

The major findings from the study were that: (1) many participants wanted sequencing results as soon as possible, even at the time of breast cancer diagnosis; (2) participants wanted an opportunity for an in‐person discussion of results; and (3) they put less emphasis on the type of person delivering results than on the knowledge and communicative skills of that person. Participants also emphasized the importance of a results return process tailored to a patient's individual circumstances and one that she has a voice in determining.

Conclusions

A critical goal for future transdisciplinary research including clinicians, patients, and communication researchers may be to develop decision‐making processes to help patients make decisions about how they would like various sequencing results returned.

While the issue of what genome sequencing results should be returned to patients has been examined, much less attention has been paid to developing strategies to return these results in ways that meet patients' needs and preferences. To address this, we investigated delivery preferences (i.e., who, how, when) for individual genome sequencing results among women diagnosed with breast cancer at age 40 or younger. The major findings from the study were that: (1) many participants wanted sequencing results as soon as possible, even at the time of breast cancer diagnosis; (2) participants wanted an opportunity for an in‐person discussion of results; and (3) they put less emphasis on the type of person delivering results than on the knowledge and communicative skills of that person.

Stakeholder views on secondary findings in whole-genome and whole-exome sequencing: a systematic review of quantitative and qualitative studies

PURPOSE

As whole-exome sequencing (WES) and whole-genome sequencing (WGS) move into routine clinical practice, it is timely to review data that might inform the debate regarding secondary findings (SF) and the development of policies that maximize participant benefit.

METHODS

We systematically searched for qualitative and quantitative studies that explored stakeholder views on SF in WES/WGS. Framework analysis was undertaken to identify major themes.

RESULTS

Forty-four articles reporting the views of 11,566 stakeholders were included. Stakeholders were broadly supportive of returning "actionable" findings, but definitions of actionability varied. Stakeholder views on SF disclosure exist along a spectrum: potential WES/WGS recipients' views were largely influenced by a sense of rights, whereas views of genomics professionals were informed by a sense of professional responsibility. Experience with genetic illness and testing resulted in greater caution about SF, suggesting that truly informed decisions require an understanding of the implications and limitations of WES/WGS and possible findings.

CONCLUSION

This review suggests that bidirectional interaction during consent might best facilitate informed decision making about SF and that dynamic forms of consent, allowing for changing preferences, should be considered. Research exploring views from wider perspectives and from recipients who have received SF is critical if evidence-based policies are to be achieved.Genet Med 19 3, 283-293.

Screening and overdiagnosis: public health implications

Overdiagnosis is the diagnosis of an abnormality that bears no substantial health hazard and no benefit for patients to be aware of. Resulting mainly from the use of increasingly sensitive screening and diagnostic tests, as well as broadened definitions of conditions requiring an intervention, overdiagnosis is a growing but still largely misunderstood public health issue. Fear of missing a diagnosis or of litigation, financial incentives or patient's need of reassurance are further causes of overdiagnosis. The main consequence of overdiagnosis is overtreatment. Treating an overdiagnosed condition bears no benefit but can cause harms and generates costs. Overtreatment also diverts health professionals from caring for those most severely ill. Recognition of overdiagnosis due to screening is challenging since it is rarely identifiable at the individual level and difficult to quantify precisely at the population level. Overdiagnosis exists even for screening of proven efficacy and efficiency. Measures to reduce overdiagnosis due to screening include heightened sensitization of health professionals and patients, active surveillance and deferred treatment until early signs of disease progression and prognosis estimation through biomarkers (including molecular) profiling. Targeted screening and balanced information on its risk and benefits would also help limit overdiagnosis. Research is needed to assess the public health burden and implications of overdiagnosis due to screening activity.

Research participants in NGS studies want to know about incidental findings

Following the implementation of high-throughput sequencing legal and ethical issues are discussed intensively. The management of incidental findings (IFs) in a research setting have been investigated but there is a lack of literature concerning research participant's perspective. The aim of this study was to investigate whether research participants want disclosure of IFs and what kind of IFs they want to know about. One hundred and twenty-seven research participants in a study of gastrointestinal polyps were informed about whole-exome sequencing and the risk of IFs. They were asked to decide whether they (A) wanted disclosure of IFs no matter whether the variants were associated with a non-treatable or non-preventable condition, (B) wanted disclosure of variants associated with treatable or preventable conditions or (C) wanted no disclosure at all. Participants who wanted disclosure of all the IFs (A) accounted for the majority (n=78), 45 of the participants only wanted disclosure of variants, which could lead to surveillance or treatment (B) and 4 participants did not want IFs to be disclosed at all (C). The study showed that almost all research participants wanted disclosure of at least some types of IFs.

Genome-Wide Sequencing for Prenatal Detection of Fetal Single-Gene Disorders

New sequencing methods capable of rapidly analyzing the genome at increasing resolution have transformed diagnosis of single-gene or oligogenic genetic disorders in pediatric and adult medicine. Targeted tests, consisting of disease-focused multigene panels and diagnostic exome sequencing to interrogate the sequence of the coding regions of nearly all genes, are now clinically offered when there is suspicion for an undiagnosed genetic disorder or cancer in children and adults. Implementation of diagnostic exome and genome sequencing tests on invasively and noninvasively obtained fetal DNA samples for prenatal genetic diagnosis is also being explored. We predict that they will become more widely integrated into prenatal care in the near future. Providers must prepare for the practical, ethical, and societal dilemmas that accompany the capacity to generate and analyze large amounts of genetic information about the fetus during pregnancy.

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.

How can psychological science inform research about genetic counseling for clinical genomic sequencing?

Next generation genomic sequencing technologies (including whole genome or whole exome sequencing) are being increasingly applied to clinical care. Yet, the breadth and complexity of sequencing information raise questions about how best to communicate and return sequencing information to patients and families in ways that facilitate comprehension and optimal health decisions. Obtaining answers to such questions will require multidisciplinary research. In this paper, we focus on how psychological science research can address questions related to clinical genomic sequencing by explaining emotional, cognitive, and behavioral processes in response to different types of genomic sequencing information (e.g., diagnostic results and incidental findings). We highlight examples of psychological science that can be applied to genetic counseling research to inform the following questions: (1) What factors influence patients' and providers' informational needs for developing an accurate understanding of what genomic sequencing results do and do not mean?; (2) How and by whom should genomic sequencing results be communicated to patients and their family members?; and (3) How do patients and their families respond to uncertainties related to genomic information?

Genetics in myeloma: genetic technologies and their application to screening approaches in myeloma

BACKGROUND

Despite advances in the treatment of multiple myeloma (MM), it remains an incurable malignant disease. Myeloma genetics is intrinsically complex, but it offers an opportunity to categorize the disease and apply a personalized medicine approach.

AREAS OF AGREEMENT

Research into the genetics of myeloma is moving at a fast pace and is highlighting areas and patient cohorts likely to benefit from specific treatment. Targeting residual disease is likely to be crucial to improved clinical outcome.

AREAS OF CONTROVERSY

Patients in clinical trials are more likely to receive genetic diagnosis than non-trial patients, for whom access is ad hoc and dependent upon regional commissioning arrangements.

AREAS TIMELY FOR DEVELOPING RESEARCH

Relating genetics to potential treatment pathways will become crucial for improved myeloma outcomes. Universal access to standardized genetic testing will facilitate modern personalized treatments.

Institutional protocol to manage consanguinity detected by genetic testing in pregnancy in a minor

Single-nucleotide polymorphism arrays and other types of genetic tests have the potential to detect first-degree consanguinity and uncover parental rape in cases of minor teenage pregnancy. We present 2 cases in which genetic testing identified parental rape of a minor teenager. In case 1, single-nucleotide polymorphism array in a patient with multiple developmental abnormalities demonstrated multiple long stretches of homozygosity, revealing parental rape of a teenage mother. In case 2, a vague maternal sexual assault history and diagnosis of Pompe disease by direct gene sequencing identified parental rape of a minor. Given the medical, legal, and ethical implications of such revelations, a protocol was developed at our institution to manage consanguinity identified via genetic testing.

Returning a Research Participant's Genomic Results to Relatives: Analysis and Recommendations

Genomic research results and incidental findings with health implications for a research participant are of potential interest not only to the participant, but also to the participant's family. Yet investigators lack guidance on return of results to relatives, including after the participant's death. In this paper, a national working group offers consensus analysis and recommendations, including an ethical framework to guide investigators in managing this challenging issue, before and after the participant's death.

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.

Disease variants in genomes of 44 centenarians

To identify previously reported disease mutations that are compatible with extraordinary longevity, we screened the coding regions of the genomes of 44 Ashkenazi Jewish centenarians. Individual genome sequences were generated with 30× coverage on the Illumina HiSeq 2000 and single-nucleotide variants were called with the genome analysis toolkit (GATK). We identified 130 coding variants that were annotated as “pathogenic” or “likely pathogenic” based on the ClinVar database and that are infrequent in the general population. These variants were previously reported to cause a wide range of degenerative, neoplastic, and cardiac diseases with autosomal dominant, autosomal recessive, and X-linked inheritance. Several of these variants are located in genes that harbor actionable incidental findings, according to the recommendations of the American College of Medical Genetics. In addition, we found risk variants for late-onset neurodegenerative diseases, such as the APOE ε4 allele that was even present in a homozygous state in one centenarian who did not develop Alzheimer's disease. Our data demonstrate that the incidental finding of certain reported disease variants in an individual genome may not preclude an extraordinarily long life. When the observed variants are encountered in the context of clinical sequencing, it is thus important to exercise caution in justifying clinical decisions. In genome sequences of 44 Ashkenazi centenarians, we identified many coding variants that were annotated as “pathogenic” or “likely pathogenic” based on the ClinVar database. Our data demonstrate that the incidental finding of certain reported disease variants in an individual genome may not preclude an extraordinarily long life. When the observed variants are encountered in the context of clinical sequencing, it is thus important to exercise caution in justifying clinical decisions.

The incorporation of predictive genomic testing into genetic counseling programs

This study explored whether genetic counseling programs are incorporating instruction about the applications and techniques of predictive genomic testing (PGT) based on student recollection, and whether this is perceived as adequate by those students. For the purpose of this study, PGT was defined as the use of genome-based testing to assess a person's risk, or susceptibility, of developing a disorder with either a known or suspected genetic component. Surveys from 114 graduates were analyzed. The majority of respondents indicated that PGT was covered in their curriculum including methodology, information generated, benefits, risks, limitations, and impact on the field of genetic counseling. A statistically significant increase in incorporating information about PGT as a whole from 2008 to 2011 was also reported. The majority of respondents reported that coverage of PGT prepared them for the American Board of Genetic Counseling (ABGC) board exam (80.6 %), to interpret PGT test results (60.2 %) and to identify clinical situations warranting testing (53.1 %). Although the majority of respondents indicated learning about a wide variety of aspects surrounding PGT, many recent graduates indicated their training was less likely to cover aspects essential for the clinical application of PGT. Therefore, genetic counseling programs should place a greater emphasis on these skills, and the development of continuing education opportunities aimed at increasing genetic counselors abilities to interpret and discuss PGT tests and identify clinical situations warranting such testing may be helpful.

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.