Personal genome testing: test characteristics to clarify the discourse on ethical, legal and societal issues

Sharing, reuse, and storage of biosamples among biomedical researchers in Jordan: Practice and concerns

BACKGROUND

Sharing and reuse biosamples can facilitate biomedical research. Little is known about researchers' perception and practice about sharing, reusing, and storing biosamples in Jordan. Therefore, the current study aimed to evaluate the practices of biomedical researchers in Jordan regarding biosamples management.

METHODS

The study was cross-sectional and involved biomedical researchers from different parts of Jordan. A questionnaire was designed to achieve the aim of this study. The questionnaire was web-based and distributed via e-mails using Google forms.

RESULTS

Opinions of Jordanian biomedical researchers from different academic ranks and institutional backgrounds were measured and recorded anonymously. The majority of the sample was males (57.9%), from public universities (64.3%), and (64.6%) were from health-related fields. About 82.9% of participants stored biosamples using codes, whereas the rest used the subject's name. Sharing of biosamples was commonly practiced by 61.7% of Jordanian researchers locally, while 47.2% of the Jordanian researchers shared biosamples overseas. The reuse of biosamples in other projects was reported to be 55.4%. The majority explained the possibility of reusing and sharing biosamples in the consent form (range: 53-58%). Sharing and reusing biosamples were associated with gender, the number of publications in peer-reviewed international journals, and academic rank (P<0.05).

CONCLUSION

Sharing and reusing biosamples are common among Jordanian biomedical researchers. Therefore, ethically grounded biosamples sharing and reuse standards are essential for protecting human subjects' rights and privacy in Jordan.

The patients view on genetics and functional imaging for precision medicine: a willingness-to-pay analysis

Purpose: Willingness-to-pay (WTP) analyses can support allocation processes considering the patients preferences in personalized medicine. However, genetic testing especially might imply ethical concerns that have to be considered. Methods: A WTP questionnaire was designed to compare preferences for imaging and genetic testing in cancer patients and to evaluate potential ethical concerns. Results: Comparing the options of imaging and genetics showed comparable WTP values. Ethical concerns about genetic testing seemed to be minor. Treatment success was the top priority irrespective of the diagnostic modality. In general, the majority of patients considered personalized medicine to be beneficial. Conclusion: Most patients valued personalized approaches and rated the benefits of precision medicine of overriding importance irrespective of modality or ethical concerns.

A systematic approach to the disclosure of genomic findings in clinical practice and research: a proposed framework with colored matrix and decision-making pathways

Background

Whether and how to disclose genomic findings obtained in the course of genomic clinical practice and medical research has been a controversial global bioethical issue over the past two decades. Although several recommendations and judgment tools for the disclosure of genomic findings have been proposed, none are sufficiently systematic or inclusive or even consistent with each other. In order to approach the disclosure/non-disclosure practice in an ethical manner, optimal and easy-to-use tools for supporting the judgment of physicians/researchers in genomic medicine are necessary.

Methods

The bioethics literature on this topic was analyzed to parse and deconstruct the somewhat overlapping and therefore ill-defined key concepts of genomic findings, such as incidental, primary, secondary, and other findings. Based on the deconstruction and conceptual analyses of these findings, we then defined key parameters from which to identify the strength of duty to disclose (SDD) for a genomic finding. These analyses were then applied to develop a framework with the SDD matrix and systematic decision-making pathways for the disclosure of genomic findings.

Results

The following six major parameters (axes), along with sub-axes, were identified: Axis 1 (settings and institutions where findings emerge); Axis 2 (presence or absence of intention and anticipatability in discovery); Axis 3 (maximal actionability at the time of discovery); Axis 4 (net medical importance); Axis 5 (expertise of treating physician/researcher); and Axis 6 (preferences of individual patients/research subjects for disclosure). For Axes 1 to 4, a colored SDD matrix for genomic findings was developed in which levels of obligation for disclosing a finding can be categorized. For Axes 5 and 6, systematic decision-making pathways were developed via the SDD matrix.

Conclusion

We analyzed the SDD of genomic findings and developed subsequent systematic decision-making pathways of whether and how to disclose genomic findings to patients/research subjects and their relatives in an ethical manner. Our comprehensive framework may help physicians and researchers in genomic medicine make consistent ethical judgments regarding the disclosure of genomic findings.

Predictors of empowerment in parents of children with autism and related neurodevelopmental disorders who are undergoing genetic testing

Background

There is limited empirical data quantifying the utility of genetic testing for families of children with autism spectrum disorder (ASD) or related neurodevelopmental disorders (NDD). We assessed the utility of clinical chromosomal microarray analysis (CMA), defined by diagnostic yield and parental empowerment, in population‐based sample of parents of affected children; and explored child, family, and health services factors predictive of empowerment.

Methods

Participants were families of children undergoing diagnostic assessments, between 2016 and 2019. Diagnostic yield of CMA in affected children was determined. Parental empowerment was measured through adapted version of the Genetics Counseling Outcome Scale‐24. Parents completed questionnaires to capture child, family, and health service factors.

Results

The diagnostic yield of CMA was 2.8% for pathogenic variants. Parental empowerment was significantly correlated with family functioning and aspects of perceived family‐centeredness of care. The model accounted for 49.8% of the variation in parental empowerment, F (10,37) = 3.67, p = 0.002. After accounting for other predictors, parental perception of the provision of general information remained significantly associated with empowerment.

Conclusion

The informational needs of families play an important role in their empowerment during genetic testing. Meeting these needs and monitoring empowerment can aid genomic technologies integration in personalized healthcare for ASD/NDD.

The attitude of young people in the city of Yakutsk to DNA-testing

This pilot research was one of the first sociological studies with general questions on genetic testing with 300 participants, 75% of which were representatives of one people - the Sakha. A quantitative method was used: a sociological survey with quota sampling (Δ ± 5%), held in February - March 2018 in the City of Yakutsk (n = 350).Analysis of the survey results have shown that the respondents have low levels of awareness about the DNA-testing method: 72.3% "do not know about the method". Only 18.7% of respondents knew that since 2000 the Medical-Genetic Centre of the Sakha Republic (Yakutia) conducts DNA diagnostics for hereditary diseases, with 81.0% replying that they didn't know that. The questionnaire has shown that 90.3% of participants would like to undergo DNA-testing to identify their susceptibility to genetic diseases. Our questionnaire has shown high levels of self-identity among the young Sakha and their desire to learn about their belonging to a specific ethnicity (49.3%) with the assistance of DNA-testing. Furthermore, based on the answers relating to motivations for undergoing DNA-testing, we can say that the respondents have confirmed the peculiarities of their national mindset, specifically, high value of children for a family: "concern for the health of my future children" was a great motivator for taking the test (50.3%).

Preferences of Italian patients for return of secondary findings from clinical genome/exome sequencing

Exome/genome sequencing (ES/GS) is increasingly becoming routine in clinical genetic diagnosis, yet issues regarding how to disclose and manage secondary findings (SFs) remain to be addressed, and limited evidence is available on patients' preferences. We carried out semi-structured interviews with 307 individuals undergoing clinical genetic testing to explore their preferences for return of SFs in the hypothetical scenario that their test would be performed using ES/GS. Participants were 254 females (82.7%) and 53 males (17.3%), aged 18-86 years; 73.9% (81.1% of those with lower education levels) reported no prior knowledge of ES/GS. Prior knowledge of ES/GS was more common among patients tested for Mendelian conditions (34.5%), compared to those undergoing cancer genetic testing (22.3%) or carrier screening (7.4%). Despite this reported lack of knowledge, most participants (213, 69.6%) stated they would prefer to be informed of all possible results. Reasons in favor of disclosure included wanting to be aware of any risks (168; 83.6%) and to help relatives (23; 11.4%), but also hope that preventive measures might become available in the future (10, 5%). Conversely, potential negative impact on quality of life was the commonest motivation against disclosure. Among 179 participants seen for cancer genetic counseling who were interviewed again after test disclosure, 81.9% had not heard about ES/GS in the meantime; however, the proportion of participants opting for disclosure of any variants was lower (116; 64.8%), with 36 (20.1%) changing opinion compared to the first interview. Based on these findings, we conclude that genetic counseling for ES/GS should involve enhanced education and decision-making support to enable informed consent to SFs disclosure.

Clinical application of next-generation sequencing to the practice of neurology

Next-generation sequencing technologies allow for rapid and inexpensive large-scale genomic analysis, creating unprecedented opportunities to integrate genomic data into the clinical diagnosis and management of neurological disorders. However, the scale and complexity of these data make them difficult to interpret and require the use of sophisticated bioinformatics applied to extensive datasets, including whole exome and genome sequences. Detailed analysis of genetic data has shown that accurate phenotype information is essential for correct interpretation of genetic variants and might necessitate re-evaluation of the patient in some cases. A multidisciplinary approach that incorporates bioinformatics, clinical evaluation, and human genetics can help to address these challenges. However, despite numerous studies that show the efficacy of next-generation sequencing in establishing molecular diagnoses, pathogenic mutations are generally identified in fewer than half of all patients with genetic neurological disorders, exposing considerable gaps in the understanding of the human genome and providing opportunities to focus research on improving the usefulness of genomics in clinical practice. Looking forward, the emergence of precision health in neurological care will increasingly apply genomic data analysis to pharmacogenetics, preventive medicine, and patient-targeted therapies.

Attitudes toward the right to autonomous decision-making in psychiatric genetic testing: Controversial and context-dependent

Recent breakthroughs in psychiatric genetics have identified genetic risk factors of yet unknown clinical value. A main ethical principal in the context of psychiatric research as well as future clinical genetic testing is the respect for a person's autonomy to decide whether to undergo genetic testing, and whom to grant access to genetic data. However, experience within the psychiatric genetic research setting has indicated controversies surrounding attitudes toward this ethical principal. This study aimed to explore attitudes concerning the right of individuals to self-determine testing and disclosure of results, and to determine whether these attitudes are context-dependent, that is, not directly related to the test result but rather to specific circumstances. N = 160 individuals with major depression or bipolar disorder and n = 29 relatives of individuals with either illness completed an online-questionnaire assessing attitudes toward genetic testing, genetic research, disclosure of results, incidental findings, and access to psychiatric genetic test results. Generally, the right of the person's autonomy was considered very important, but attitudes varied. For example, half of those who considered that children should have the right to refuse psychiatric genetic testing even against their parents' will, also state that they should be tested upon their parents' wishes. Also, the majority of respondents considered the physician entitled to disregard their stated wishes concerning the disclosure of incidental findings in case of good treatment options. Thus, researchers and clinicians must be aware that attitudes toward psychiatric genetic testing are often mutable and should discuss these prior to testing.

Value-based genomic screening: exploring genomic screening for chronic diseases using triple value principles

Background

Genomic screening has unique challenges which makes it difficult to easily implement on a wide scale. If the costs, benefits and tradeoffs of investing in genomic screening are not evaluated properly, there is a risk of wasting finite healthcare resources and also causing avoidable harm.

Main text

If healthcare professionals – including policy makers, payers and providers – wish to incorporate genomic screening into healthcare while minimizing waste, maximizing benefits, and considering results that matter to patients, using the principles of triple value (allocative, technical, and personal value) could help them to evaluate tough decisions and tradeoffs. Allocative value focuses on the optimal distribution of limited healthcare resources to maximize the health benefits to the entire population while also accounting for all the costs of care delivery. Technical value ensures that for any given condition, the right intervention is chosen and delivered in the right way. Various methods (e.g. ACCE, HTA, and Wilson and Jungner screening criteria) exist that can help identify appropriate genomic applications. Personal value incorporates preference based informed decision making to ensure that patients are informed about the benefits and harms of the choices available to them and to ensure they make choices based on their values and preferences.

Conclusions

Using triple value principles can help healthcare professionals make reasoned and tough judgements about benefits and tradeoffs when they are exploring the role genomic screening for chronic diseases could play in improving the health of their patients and populations.

The Evolution of Public Health Genomics: Exploring Its Past, Present, and Future

Public health genomics has evolved to responsibly integrate advancements in genomics into the fields of personalized medicine and public health. Appropriate, effective and sustainable integration of genomics into healthcare requires an organized approach. This paper outlines the history that led to the emergence of public health genomics as a distinguishable field. In addition, a range of activities are described that illustrate how genomics can be incorporated into public health practice. Finally, it presents the evolution of public health genomics into the new era of "precision public health."

Reconceptualizing harms and benefits in the genomic age

As new, high-powered sequencing technologies are increasingly incorporated into genomics research, we believe that there has been a break point in how risks and benefits associated with genetic information are being characterized and understood. Genomic sequencing provides the potential benefit of a wealth of information, but also has the potential to alter how we conceptualize risks of sequencing. Until now, our conceptions of risks and benefits have been generally static, arising out of the early ethical, legal and social implications studies conducted in the context of targeted genetics. This paper investigates how the increasing availability of genetic information is changing views about risks and benefits, particularly examining our evolving understanding of psychosocial harms and our expanding conception of benefit. We argue that the lack of robust empirical evidence of psychosocial harms and the expanding view that benefits of genomic research include indirect familial benefit necessitate continued ethical, legal and social implications research.

Legislation of direct-to-consumer genetic testing in Europe: a fragmented regulatory landscape

Despite the increasing availability of direct-to-consumer (DTC) genetic testing, it is currently unclear how such services are regulated in Europe, due to the lack of EU or national legislation specifically addressing this issue. In this article, we provide an overview of laws that could potentially impact the regulation of DTC genetic testing in 26 European countries, namely Austria, Belgium, Cyprus, the Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Ireland, Italy, Latvia, Lithuania, Luxembourg, Norway, Poland, Portugal, Romania, Slovakia, Slovenia, Spain, Sweden, the Netherlands and the United Kingdom. Emphasis is placed on provisions relating to medical supervision, genetic counselling and informed consent. Our results indicate that currently there is a wide spectrum of laws regarding genetic testing in Europe. There are countries (e.g. France and Germany) which essentially ban DTC genetic testing, while in others (e.g. Luxembourg and Poland) DTC genetic testing may only be restricted by general laws, usually regarding health care services and patients' rights.

Advancing Global Precision Medicine: An Overview of Genomic Testing and Counseling Services in Malaysia

Precision medicine, genomic and diagnostic services are no longer limited to developed countries. This broadening in geography of biomarker applications and omics diagnostics also demands empirical study of implementation, diagnostic testing, and counseling practices in the field. For example, the Malaysian population has large ethnic diversity and high prevalence of genetic disorders such as hemoglobinopathies and metabolic disorders. Increased morbidity and mortality from such diseases have a direct impact on society and health system sustainability and for this, decision-making becomes of outmost importance. We report here on our findings on the landscape of genomic testing and genetic counseling services in Malaysia. We first defined the framework of all Malaysian stakeholders that offer genomics services and next, we identified the related information gaps, as depicted through the service providers' online websites. Our research framework revealed that there is a very diverse spectrum of genomics services in Malaysia, in which wet- and dry-laboratory services integrate. Moreover, we identify the current gaps and possible remedies to improve the quality of genomic and predictive analytics, not to mention considerations to ensure robust ethics and responsible innovation. To our knowledge, this is the first such study to be performed for a Southeast Asian country. Our genomics and precision medicine services mapping strategy presented in this study may serve as a model for field assessment at regional, national, and international levels as precision medicine is expanding globally and new governance challenges and opportunities continue to emerge for smart implementation science.

Third party interpretation of raw genetic data: an ethical exploration

In the wake of recent regulations targeting direct-to-consumer genetic testing (DTC-GT), an increasing number of websites have emerged that offer consumers alternative means to derive health information from their DTC-GT raw data. While the ethical concerns associated with DTC-GT have been extensively discussed in the literature, the implications of third party interpretation (TPI) websites have remained largely unexplored. Here we sought to describe these services and elucidate their ethical implications in the context of the current DTC-GT debate. We reviewed five popular TPI websites that use SNP-based genomic data to report health-related information: Promethease, Interpretome, LiveWello, Codegen.eu, and Enlis Personal. We found that many of the ethical concerns previously described in DTC-GT also applied to TPI websites, including inadequate informed consent, questionable clinical validity and utility, and lack of medical supervision. However, some concerns about data usage and privacy reported in DTC-GT were less prominent in the five TPI websites we studied: none of them sold or shared user data, and 3/5 sites did not retain data in the long term. In addition, while exaggerated claims and inaccurate advertising have been frequently problematic in DTC-GT, advertising was minimal in the TPI sites we assessed, and 4/5 made no claims of health benefits. Overall, TPI adds a new dimension to the ethical debate surrounding DTC-GT, and awareness of these services will become increasingly important as personal genomics continues to expand. This study constitutes the first detailed ethical analysis of these services, and presents a starting point for further research and ethical reflection.

Personal utility in genomic testing: a systematic literature review

Researchers and clinicians refer to outcomes of genomic testing that extend beyond clinical utility as 'personal utility'. No systematic delineation of personal utility exists, making it challenging to appreciate its scope. Identifying empirical elements of personal utility reported in the literature offers an inventory that can be subsequently ranked for its relative value by those who have undergone genomic testing. A systematic review was conducted of the peer-reviewed literature reporting non-health-related outcomes of genomic testing from 1 January 2003 to 5 August 2016. Inclusion criteria specified English language, date of publication, and presence of empirical evidence. Identified outcomes were iteratively coded into unique domains. The search returned 551 abstracts from which 31 studies met the inclusion criteria. Study populations and type of genomic testing varied. Coding resulted in 15 distinct elements of personal utility, organized into three domains related to personal outcomes: affective, cognitive, and behavioral; and one domain related to social outcomes. The domains of personal utility may inform pre-test counseling by helping patients anticipate potential value of test results beyond clinical utility. Identified elements may also inform investigations into the prevalence and importance of personal utility to future test users.

Attitudes to incorporating genomic risk assessments into population screening programs: the importance of purpose, context and deliberation

Background

The use of an overall risk assessment based on genomic information is consistent with precision medicine. Despite the enthusiasm, there is a need for public engagement on the appropriate use of such emerging technologies in order to frame meaningful evaluations of utility, including the practical implementation and acceptability issues that might emerge. Doing so requires the involvement of the end users of these services, including patients, and sections of the public who are the target group for population based screening. In the present study we sought to explore public attitudes to the potential integration of personal genomic profiling within existing population screening programs; and to explore the evolution of these attitudes as part of a deliberative process.

Methods

We conducted a mixed methods study presented in the format of a deliberative workshop. Participants were drawn from communities in Ottawa, Ontario (ON) and St John’s, Newfoundland and Labrador (NL), Canada. Individuals were approached to take part in a workshop on the incorporation of genomic risk profiling for either colorectal cancer screening (CRC), or newborn screening for type 1 diabetes mellitus (T1DM).

Results

A total of N = 148 (N = 65 ON, N = 83 NL) participants provided data for analysis. Participants in both groups were supportive of public funding for genomic risk profiling, although participants in the T1DM groups expressed more guarded positive attitudes than participants in the CRC groups. These views were stable throughout the workshop (CRC, p = 0.15, T1DM, p =0.39). Participants were less positive about individual testing, with a significant decrease in support over the course of the workshop (CRC p = 0.02, T1DM, p = 0.003). Common concerns related to access to test results by third parties.

Conclusions

The findings of this study suggest that members of the target populations for potential genomic profiling tests (designed for screening or risk prediction purposes) can engage in meaningful deliberation about their general acceptability and personal utility. Evaluations of whether a test would be personally useful may depend on the experience of the participants in personal health decision making, the purpose of the test, and the availability of interventions to reduce disease risk.

Electronic supplementary material

The online version of this article (doi:10.1186/s12920-016-0186-5) contains supplementary material, which is available to authorized users.

Potential Uses and Inherent Challenges of Using Genome-Scale Sequencing to Augment Current Newborn Screening

Since newborn screening (NBS) began in the 1960s, technological advances have enabled its expansion to include an increasing number of disorders. Recent developments now make it possible to sequence an infant's genome relatively quickly and economically. Clinical application of whole-exome and whole-genome sequencing is expanding at a rapid pace but presents many challenges. Its utility in NBS has yet to be demonstrated and its application in the pediatric population requires examination, not only for potential clinical benefits, but also for the unique ethical challenges it presents.

Success rates for consent and collection of prenatal biological specimens in an epidemiologic survey of child health

BACKGROUND

The National Children's Study (NCS) Vanguard Study began enrollment in January 2009 as an initial pilot study for a planned large-scale, longitudinal U.S. cohort study of the effect of environmental influences on child health and development, with biological and environmental sample collection conducted in seven locations from April 2009 to October 2010. We sought to determine rates of consent for, and success of collection of, maternal and paternal biospecimens before and during pregnancy in the NCS Vanguard Study.

METHODS

Samples of blood, saliva, vaginal swabs, urine, hair, and nails were collected before and during pregnancy. All specimens were sent to a central repository for processing, storage, and quality assessment.

RESULTS

Of 780 pregnant women asked to consent to sample collection, 773 (>99%) agreed, and of 295 nonpregnant women, 292 (99%) agreed. Of 440 fathers asked to consent to sample collection, 435 (99%) agreed. Frequency of successful collection of biospecimens varied depending on sample and visit type. In descending order, the ranges over all visit types of the proportion of expected samples successfully collected from women were: urine, 92.5 to 95.7%; hair, 89.6 to 92.5%; vaginal swab, 84.2 to 88.5%; blood, 74.9 to 78.5%; 2-day saliva, 65.8 to 81.6%; and nails, 76.4 to 76.7%. For fathers, rates were highest for urine (94.9%) and lowest for hair (63.0%).

CONCLUSION

High rates of consent for and collection of a wide variety of biospecimens can be achieved in prospective epidemiologic cohort studies of pregnant women. Ease of sample collection may be a primary factor influencing successful biospecimen collection.

Sharing and Reuse of Sensitive Data and Samples: Supporting Researchers in Identifying Ethical and Legal Requirements

Availability of and access to data and biosamples are essential in medical and translational research, where their reuse and repurposing by the wider research community can maximize their value and accelerate discovery. However, sharing human-related data or samples is complicated by ethical, legal, and social sensitivities. The specific ethical and legal requirements linked to sensitive data are often unfamiliar to life science researchers who, faced with vast amounts of complex, fragmented, and sometimes even contradictory information, may not feel competent to navigate through it. In this case, the impulse may be not to share the data in order to safeguard against unintentional misuse. Consequently, helping data providers to identify relevant ethical and legal requirements and how they might address them is an essential and frequently neglected step in removing possible hurdles to data and sample sharing in the life sciences. Here, we describe the complex regulatory context and discuss relevant online tools-one which the authors co-developed-targeted at assisting providers of sensitive data or biosamples with ethical and legal questions. The main results are (1) that the different approaches of the tools assume different user needs and prior knowledge of ethical and legal requirements, affecting how a service is designed and its usefulness, (2) that there is much potential for collaboration between tool providers, and (3) that enriched annotations of services (e.g., update status, completeness of information, and disclaimers) would increase their value and facilitate quick assessment by users. Further, there is still work to do with respect to providing researchers using sensitive data or samples with truly 'useful' tools that do not require pre-existing, in-depth knowledge of legal and ethical requirements or time to delve into the details. Ultimately, separate resources, maintained by experts familiar with the respective fields of research, may be needed while-in the longer term-harmonization and increase in ease of use will be very desirable.

Management of Incidental Findings in the Era of Next-generation Sequencing

Next-generation sequencing (NGS) technologies allow for the generation of whole exome or whole genome sequencing data, which can be used to identify novel genetic alterations associated with defined phenotypes or to expedite discovery of functional variants for improved patient care. Because this robust technology has the ability to identify all mutations within a genome, incidental findings (IF)- genetic alterations associated with conditions or diseases unrelated to the patient's present condition for which current tests are being performed- may have important clinical ramifications. The current debate among genetic scientists and clinicians focuses on the following questions: 1) should any IF be disclosed to patients, and 2) which IF should be disclosed - actionable mutations, variants of unknown significance, or all IF? Policies for disclosure of IF are being developed for when and how to convey these findings and whether adults, minors, or individuals unable to provide consent have the right to refuse receipt of IF. In this review, we detail current NGS technology platforms, discuss pressing issues regarding disclosure of IF, and how IF are currently being handled in prenatal, pediatric, and adult patients.

A road toward better education in personalized medicine at universities and beyond

Personalized medicine is likely to become a future direction of medicine. There is increased knowledge about gene functions in human health and disease and a rapid advance of biotechnologies. Personal genetic testing is available outside the medical room, as direct-to-consumer testing. There is concern about genetic literacy of general public and healthcare professionals which are to handle genetic results and their clinical interpretation. Education and training in personalized medicine and genetic/genomics/pharmacogenomics issues at different levels (high school, university, continuing medical education) is needed. Examples of innovated educational tools and curricula over the world are presented. The educational initiatives in the field of personalized medicine in the Czech Republic are followed from the very beginning.

Parent and public interest in whole-genome sequencing

OBJECTIVE

The aim of this study was to assess the baseline interest of the public in whole-genome sequencing (WGS) for oneself, parents' interest in WGS for their youngest children, and factors associated with such interest.

METHODS

A random sample of adults from a probability-based nationally representative online panel was surveyed. All participants were provided basic information about WGS and then asked about their interest in WGS for themselves. Those participants who were parents were additionally asked about their interest in WGS for their children. The order in which parents were asked about their interest in WGS for themselves and for their child was randomized. The relationship between parent/child characteristics and interest in WGS was examined.

RESULTS

The overall response rate was 62% (55% among parents). 58.6% of the total population (parents and nonparents) was interested in WGS for themselves. Similarly, 61.8% of the parents were interested in WGS for themselves and 57.8% were interested in WGS for their youngest children. Of note, 84.7% of the parents showed an identical interest level in WGS for themselves and their youngest children. Mothers as a group and parents whose youngest children had ≥2 health conditions had significantly more interest in WGS for themselves and their youngest children, while those with conservative political ideologies had considerably less.

CONCLUSIONS

While US adults have varying interest levels in WGS, parents appear to have similar interests in genome testing for themselves and their youngest children. As WGS technology becomes available in the clinic and private market, clinicians should be prepared to discuss WGS risks and benefits with their patients.

The Human Genome Project, and recent advances in personalized genomics

The language of “personalized medicine” and “personal genomics” has now entered the common lexicon. The idea of personalized medicine is the integration of genomic risk assessment alongside other clinical investigations. Consistent with this approach, testing is delivered by health care professionals who are not medical geneticists, and where results represent risks, as opposed to clinical diagnosis of disease, to be interpreted alongside the entirety of a patient’s health and medical data. In this review we consider the evidence concerning the application of such personalized genomics within the context of population screening, and potential implications that arise from this. We highlight two general approaches which illustrate potential uses of genomic information in screening. The first is a narrowly targeted approach in which genetic profiling is linked with standard population-based screening for diseases; the second is a broader targeting of variants associated with multiple single gene disorders, performed opportunistically on patients being investigated for unrelated conditions. In doing so we consider the organization and evaluation of tests and services, the challenge of interpretation with less targeted testing, professional confidence, barriers in practice, and education needs. We conclude by discussing several issues pertinent to health policy, namely: avoiding the conflation of genetics with biological determinism, resisting the “technological imperative”, due consideration of the organization of screening services, the need for professional education, as well as informed decision making and public understanding.

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.

Implementing risk-stratified screening for common cancers: a review of potential ethical, legal and social issues

BACKGROUND

The identification of common genetic variants associated with common cancers including breast, prostate and ovarian cancers would allow population stratification by genotype to effectively target screening and treatment. As scientific, clinical and economic evidence mounts there will be increasing pressure for risk-stratified screening programmes to be implemented.

METHODS

This paper reviews some of the main ethical, legal and social issues (ELSI) raised by the introduction of genotyping into risk-stratified screening programmes, in terms of Beauchamp and Childress's four principles of biomedical ethics--respect for autonomy, non-maleficence, beneficence and justice. Two alternative approaches to data collection, storage, communication and consent are used to exemplify the ELSI issues that are likely to be raised.

RESULTS

Ultimately, the provision of risk-stratified screening using genotyping raises fundamental questions about respective roles of individuals, healthcare providers and the state in organizing or mandating such programmes, and the principles, which underpin their provision, particularly the requirement for distributive justice.

CONCLUSIONS

The scope and breadth of these issues suggest that ELSI relating to risk-stratified screening will become increasingly important for policy-makers, healthcare professionals and a wide diversity of stakeholders.

"Would you test your children without their consent?" and other sticky dilemmas in the field of cancer genetic testing

Cancer genetic testing is surrounded by myriad ethical, legal, and psychosocial implications which are being revisited as testing expands into an everyday practice and into more complicated areas like whole exome and direct-to-consumer testing. We chose to survey cancer genetic counselors and physicians from a wide range of non-genetics specialties to determine what they would do if faced with the complex decisions associated with cancer genetic testing, how their views compare, and how they align with current guidelines and data. Genetic counselors were significantly more likely than non-genetics physicians to bill their insurance for testing (94.9 vs. 86.8 %; p = 0.001) and purchase life insurance before testing (86.6 vs. 68.6 %; p = 0.000) and were less likely to use an alias (3.2 vs. 13.2 %; p = 0.000) or order testing on their own DNA (15.3 vs. 24.2 %; p = 0.004). They were also less likely to test their minor children (0.9 vs. 33.1 %; p = 0.000) or test their children without their knowledge and consent/assent (1.4 vs.11.5 %; p = 0.000). The results of our study indicate that there is wide variation regarding what clinicians predict they would do in the areas of ethical, legal and psychosocial issues in cancer genetic testing. Cancer genetic counselors' choices are more aligned with professional guidelines, likely due to their experience in the field and awareness of current guidelines. These data are a starting point for a broader discussion of who should offer cancer genetic counseling and testing to patients, particularly as the complexity of the available testing options and associated issues increase with whole exome sequencing.

Navigating the rapids: the development of regulated next-generation sequencing-based clinical trial assays and companion diagnostics

Over the past decade, next-generation sequencing (NGS) technology has experienced meteoric growth in the aspects of platform, technology, and supporting bioinformatics development allowing its widespread and rapid uptake in research settings. More recently, NGS-based genomic data have been exploited to better understand disease development and patient characteristics that influence response to a given therapeutic intervention. Cancer, as a disease characterized by and driven by the tumor genetic landscape, is particularly amenable to NGS-based diagnostic (Dx) approaches. NGS-based technologies are particularly well suited to studying cancer disease development, progression and emergence of resistance, all key factors in the development of next-generation cancer Dxs. Yet, to achieve the promise of NGS-based patient treatment, drug developers will need to overcome a number of operational, technical, regulatory, and strategic challenges. Here, we provide a succinct overview of the state of the clinical NGS field in terms of the available clinically targeted platforms and sequencing technologies. We discuss the various operational and practical aspects of clinical NGS testing that will facilitate or limit the uptake of such assays in routine clinical care. We examine the current strategies for analytical validation and Food and Drug Administration (FDA)-approval of NGS-based assays and ongoing efforts to standardize clinical NGS and build quality control standards for the same. The rapidly evolving companion diagnostic (CDx) landscape for NGS-based assays will be reviewed, highlighting the key areas of concern and suggesting strategies to mitigate risk. The review will conclude with a series of strategic questions that face drug developers and a discussion of the likely future course of NGS-based CDx development efforts.

Ethical, legal, and social implications of incorporating genomic information into electronic health records

The inclusion of genomic data in the electronic health record raises important ethical, legal, and social issues. In this article, we highlight these challenges and discuss potential solutions. We provide a brief background on the current state of electronic health records in the context of genomic medicine, discuss the importance of equitable access to genome-enabled electronic health records, and consider the potential use of electronic health records for improving genomic literacy in patients and providers. We highlight the importance of privacy, access, and security, and of determining which genomic information is included in the electronic health record. Finally, we discuss the challenges of reporting incidental findings, storing and reinterpreting genomic data, and nondocumentation and duty to warn family members at potential genetic risk.

Pairomics, the omics way to mate choice

The core aspects of the biology and evolution of sexual reproduction are reviewed with a focus on the diploid, sexually reproducing, outbreeding, polymorphic, unspecialized, altricial and cultural human species. Human mate choice and pair bonding are viewed as central to individuals' lives and to the evolution of the species, and genetic assistance in reproduction is viewed as a universal human right. Pairomics is defined as an emerging branch of the omics science devoted to the study of mate choice at the genomic level and its consequences for present and future generations. In pairomics, comprehensive genetic information of individual genomes is stored in a database. Computational tools are employed to analyze the mating schemes and rules that govern mating among the members of the database. Mating models and algorithms simulate the outcomes of mating any given genome with each of a number of genomes represented in the database. The analyses and simulations may help to understand mating schemes and their outcomes, and also contribute a new cue to the multicued schemes of mate choice. The scientific, medical, evolutionary, ethical, legal and social implications of pairomics are far reaching. The use of genetic information as a search tool in mate choice may influence our health, lifestyle, behavior and culture. As knowledge on genomics, population genetics and gene-environment interactions, as well as the size of genomic databases expand, so does the ability of pairomics to investigate and predict the consequences of mate choice for the present and future generations.

Genetic data and electronic health records: a discussion of ethical, logistical and technological considerations

Objective

The completion of sequencing the human genome in 2003 has spurred the production and collection of genetic data at ever increasing rates. Genetic data obtained for clinical purposes, as is true for all results of clinical tests, are expected to be included in patients’ medical records. With this explosion of information, questions of what, when, where and how to incorporate genetic data into electronic health records (EHRs) have reached a critical point. In order to answer these questions fully, this paper addresses the ethical, logistical and technological issues involved in incorporating these data into EHRs.

Materials and methods

This paper reviews journal articles, government documents and websites relevant to the ethics, genetics and informatics domains as they pertain to EHRs.

Results and discussion

The authors explore concerns and tasks facing health information technology (HIT) developers at the intersection of ethics, genetics, and technology as applied to EHR development.

Conclusions

By ensuring the efficient and effective incorporation of genetic data into EHRs, HIT developers will play a key role in facilitating the delivery of personalized medicine.

Incorporating genomics into breast and prostate cancer screening: assessing the implications

Individual risk prediction and stratification based on polygenic profiling may be useful in disease prevention. Risk-stratified population screening based on multiple factors including a polygenic risk profile has the potential to be more efficient than age-stratified screening. In this article, we summarize the implications of personalized screening for breast and prostate cancers. We report the opinions of multidisciplinary international experts who have explored the scientific, ethical, and logistical aspects of stratified screening. We have identified (i) the need to recognize the benefits and harms of personalized screening as compared with existing screening methods, (ii) that the use of genetic data highlights complex ethical issues including discrimination against high-risk individuals by insurers and employers and patient autonomy in relation to genetic testing of minors, (iii) the need for transparency and clear communication about risk scores, about harms and benefits, and about reasons for inclusion and exclusion from the risk-based screening process, and (iv) the need to develop new professional competences and to assess cost-effectiveness and acceptability of stratified screening programs before implementation. We conclude that health professionals and stakeholders need to consider the implications of incorporating genetic information in intervention strategies for health-care planning in the future.

Genetics professionals' perspectives on reporting incidental findings from clinical genome-wide sequencing

Whole exome or whole genome analysis using massively parallel sequencing technologies will undoubtedly solve diagnostic dilemmas; however, incidental findings (IF) that may have medical and social implications will also be discovered. While there is consensus in the literature that analytically valid and medically actionable IF should be returned to patients if requested, there is debate regarding the return of other IF. There are currently no guidelines established for managing IF in the clinical context. We therefore distributed an online questionnaire to 496 geneticists and genetic counselors in Canada to explore this unresolved issue, and 210 professionals participated (response rate = 42%). The proportion of respondents who indicated that they would return IF to patients depended on the nature of the finding, ranging from 95% for information pertaining to a serious and treatable condition to 12% for information with only social implications (e.g., non-paternity). There was a lack of consensus around the disclosure of certain IF such as genetic carrier status, especially for pediatric patients. The most important considerations identified as impacting IF disclosure included condition-specific factors such as treatment availability, test accuracy, and evidence indicating pathogenicity. This is the first study to document the views of geneticists and genetic counselors in Canada towards the disclosure of IF, and represents a step towards evidence-based guidelines for clinical genome-wide sequencing investigations.

Genetics specialists' perspectives on disclosure of genomic incidental findings in the clinical setting

OBJECTIVE

Evidence documenting management of incidental findings (IFs) from clinical genomic testing is limited. The aim of this study was to examine genetics specialists' perspectives regarding current and preferred disclosure of clinical genomic IFs.

METHODS

50 genetics specialists, including medical geneticists, laboratory professionals, genetic counselors, and nurses participated in structured telephone interviews. Data were analyzed using qualitative content analysis and descriptive statistics.

RESULTS

Most specialists had encountered IFs, but definitions of IFs varied. They discussed challenges with informing patients about the prospect of IFs and disclosing IFs to patients. Causing psychological harm to patients was a concern. Participants were divided on whether IFs needed to be clinically significant and/or actionable in order to be disclosed to patients. Creating formal disclosure guidelines was considered useful, but only if they were flexible. Additional counseling, more interdisciplinary communication, maintaining contact with patients, and a centralized database to interpret IFs were also proposed.

CONCLUSION

Genetics specialists offer insights into the challenges of defining IFs, knowing when and how to disclose them, and the potential need for flexible disclosure guidelines.

PRACTICE IMPLICATIONS

Further discussion between practicing genetics specialists is needed to develop consensus on the development of best-practice guidelines for IF management.

Experiences of early users of direct-to-consumer genomics in Switzerland: an exploratory study

AIMS

This study explores attitudes, motivations and self-reported impact in connection with direct-to-consumer (DTC) genomic testing amongst a group of life scientists in Switzerland.

METHODS

Data were collected through: (1) a self-completion online questionnaire, and (2) semi-structured qualitative interviews. Forty participants completed the questionnaire and 10 were interviewed.

RESULTS

Curiosity was mentioned as the primary reason for undergoing testing, while less significance was attributed to receiving actionable health information. The opportunity to contribute to research ranked high as a motive for testing. Overall, participants assessed their experience with the test as positive and were willing to recommend it to others. Some reported that the testing had an impact on how they view their health, but only a third of participants planned on showing the results to health practitioners. Participants consistently referred to 'fun' when describing several aspects of the testing experience. The 'fun factor' manifested itself in different phases of the process, including the motivation for taking the test, receiving the information and putting the test results to use (including sharing and discussing it with others). This finding suggests the need to further explore the concept of personal utility in DTC genomics.

CONCLUSIONS

Although this group is not representative of the broader population due to both their scientific expertise and their willingness to try out a controversial new technology, their experiences provide valuable insights into the role of personal curiosity and altruism (fostering medical research) as motivations for testing and the utility attributed to both.

Translational Genomic Research: Protocol Development and Initial Outcomes following SNP Testing for Colon Cancer Risk

Although single nucleotide polymorphism (SNP) testing for disease susceptibility is commercially available, translational studies are necessary to understand how to communicate genomic information and potential implications for public health. We explored attitudes about and initial responses to genomic testing for colon cancer risk. Following development of the educational materials, we offered testing for three colon cancer SNPs in a pilot study with primary care patients. Participants completed pre- and post-test sessions and interviews. We analyzed interview transcripts with qualitative software using thematic analysis. All 20 participants opted for SNP testing. Qualitative analysis identified several themes: Motivations for SNP Testing, Before/After: Meaning of Results, Emotional Responses to SNP Results and Genomic Literacy/ Information Delivery. Results demonstrate that individuals will pursue SNP testing in the context of pre and post-test education. SNP results may influence health behaviors like healthy eating and exercise yet did not appear to impact colon cancer screening intentions.

High-throughput sequencing to decipher the genetic heterogeneity of deafness

Identifying genes causing non-syndromic hearing loss has been challenging using traditional approaches. We describe the impact that high-throughput sequencing approaches are having in discovery of genes related to hearing loss and the implications for clinical diagnosis.

The role of disease characteristics in the ethical debate on personal genome testing

BACKGROUND

Companies are currently marketing personal genome tests directly-to-consumer that provide genetic susceptibility testing for a range of multifactorial diseases simultaneously. As these tests comprise multiple risk analyses for multiple diseases, they may be difficult to evaluate. Insight into morally relevant differences between diseases will assist researchers, healthcare professionals, policy-makers and other stakeholders in the ethical evaluation of personal genome tests.

DISCUSSION

In this paper, we identify and discuss four disease characteristics--severity, actionability, age of onset, and the somatic/psychiatric nature of disease--and show how these lead to specific ethical issues. By way of illustration, we apply this framework to genetic susceptibility testing for three diseases: type 2 diabetes, age-related macular degeneration and clinical depression. For these three diseases, we point out the ethical issues that are relevant to the question whether it is morally justifiable to offer genetic susceptibility testing to adults or to children or minors, and on what conditions.

SUMMARY

We conclude that the ethical evaluation of personal genome tests is challenging, for the ethical issues differ with the diseases tested for. An understanding of the ethical significance of disease characteristics will improve the ethical, legal and societal debate on personal genome testing.

Applications of targeted gene capture and next-generation sequencing technologies in studies of human deafness and other genetic disabilities

The goal of sequencing the entire human genome for $1000 is almost in sight. However, the total costs including DNA sequencing, data management, and analysis to yield a clear data interpretation are unlikely to be lowered significantly any time soon to make studies on a population scale and daily clinical uses feasible. Alternatively, the targeted enrichment of specific groups of disease and biological pathway-focused genes and the capture of up to an entire human exome (~1% of the genome) allowing an unbiased investigation of the complete protein-coding regions in the genome are now routine. Targeted gene capture followed by sequencing with massively parallel next-generation sequencing (NGS) has the advantages of 1) significant cost saving, 2) higher sequencing accuracy because of deeper achievable coverage, 3) a significantly shorter turnaround time, and 4) a more feasible data set for a bioinformatic analysis outcome that is functionally interpretable. Gene capture combined with NGS has allowed a much greater number of samples to be examined than is currently practical with whole-genome sequencing. Such an approach promises to bring a paradigm shift to biomedical research of Mendelian disorders and their clinical diagnoses, ultimately enabling personalized medicine based on one's genetic profile. In this review, we describe major methodologies currently used for gene capture and detection of genetic variations by NGS. We will highlight applications of this technology in studies of genetic disorders and discuss issues pertaining to applications of this powerful technology in genetic screening and the discovery of genes implicated in syndromic and non-syndromic hearing loss.

Advising patients about obtaining genomic profiles

Neurologists, as all physicians, should begin to familiarize themselves with elements of genomic medicine to help their patients navigate the promises and pitfalls of obtaining genomic profiles. The neurologist should encourage a realistic assessment of the patient's expectations regarding the genetic information to be provided and apprise the patient of the challenges involved in obtaining interpretable, clinically useful information. A review of risks of obtaining genomic information is equally important. Discrimination, loss of privacy, receiving inaccurate or unwanted information, and learning information that may create obligations to disclose to others are all possibilities. As genomic research and direct-to-consumer opportunities to obtain genomic information expand, reliance on personal physicians for ethical advice based on current advancements in genomic profiling should be anticipated.

Whole exome and whole genome sequencing

PURPOSE OF REVIEW

The purpose of this review is to describe the new DNA sequencing technologies referred to as next-generation sequencing (NGS). These new methods are becoming central to research in human disease and are starting to be used in routine clinical care.

RECENT FINDINGS

Advances in instrumentation have dramatically reduced the cost of DNA sequencing. An individual's entire genome can now be sequenced for $7500. In addition, the software needed to analyze and help interpret this data is rapidly improving. This technology has been used by researchers to discover new genetic disorders and new disease associations. In the clinic, it can define the etiology in patients with undiagnosed genetic disorders and identify mutations in a cancer to help guide chemotherapy.

SUMMARY

Here we discuss how whole-exome sequencing and whole-genome sequencing are used in basic research and clinical care. These new techniques promise to speed research and affect how healthcare is delivered.