Whole genome sequencing is quickly becoming more affordable and accessible, with the prospect of personal genome sequencing for under $1,000 now widely said to be in sight. The ethical issues raised by the use of this technology in the research context have received some significant attention, but little has been written on its use in the clinical context, and most of this analysis has been futuristic forecasting. This is problematic, given the speed with which (...) class='Hi'>whole genome sequencing technology is likely to be incorporated into clinical care. This paper explores one particular subset of these issues: the implications of adopting this technology in the prenatal context without a good understanding of when and how it is useful. Prenatal whole genome sequencing differs from current prenatal genetic testing practice in a number of ethically relevant ways. Most notably, whole genome sequencing would radically increase the volume and scope of available prenatal genetic data. The wealth of new data could enhance reproductive decision‐making, promoting parents' freedom to make well‐informed reproductive decisions. We argue, however, that there is potential for prenatal whole genome sequencing to alter clinical practice in undesirable ways, especially in the short term. We are concerned that the technology could (1) change the norms and expectations of pregnancy in ways that complicate parental autonomy and informed decision‐making, (2) exacerbate the deleterious role that genetic determinism plays in child rearing, and (3) undermine children's future autonomy by removing the option of not knowing their genetic information without appropriate justification. (shrink)

This report is grounded in several social concepts: First, the primary goal of genetic testing should be to promote the well-being of the child. Second, the recognition that children are part of a network of family relationships supports an approach to potential conflicts that is not adversarial but, rather, emphasizes a deliberative process that seeks to promote the child's well-being within this context. Third, as children grow through successive stages of cognitive and moral development, parents and professionals should be attentive (...) to the child's increasing interest and ability to participate in decisions about his or her own welfare. (shrink)

Gene retrocopies are generated by reverse transcription and genomic integration of mRNA. As such, retrocopies present an important exception to the central dogma of molecular biology, and have substantially impacted the functional landscape of the metazoan genome. While an estimated 8,000–17,000 retrocopies exist in the human genome reference sequence, the extent of variation between individuals in terms of retrocopy content has remained largely unexplored. Three recent studies by Abyzov et al., Ewing et al. and Schrider et al. have (...) exploited 1,000 Genomes Project Consortium data, as well as other sources of whole‐genome sequencing data, to uncover novel gene retrocopies. Here, we compare the methods and results of these three studies, highlight the impact of retrocopies in human diversity and genome evolution, and speculate on the potential for somatic gene retrocopies to impact cancer etiology and genetic diversity among individual neurons in the mammalian brain. (shrink)

Noninvasive, prenatal whole genome sequencing may be a technological reality in the near future, making available a vast array of genetic information early in pregnancy at no risk to the fetus or mother. Many worry that the timing, safety, and ease of the test will lead to informational overload and reproductive consumerism. The prevailing response among commentators has been to restrict conditions eligible for testing based on medical severity, which imposes disputed value judgments and devalues those living (...) with eligible conditions. To avoid these difficulties, we propose an unrestricted testing policy, under which prospective parents could obtain information on any variant of known significance after a careful informed consent process that uses an interactive decision aid to deliver a mandatory presentation on the purposes, techniques, and limitations of genomic testing, as well as optional resources for reflection and consultation. This process would encourage thoughtful, informed deliberation... (shrink)

Noninvasive, prenatal whole genome sequencing may be a technological reality in the near future, making available a vast array of genetic information early in pregnancy at no risk to the fetus or mother. Many worry that the timing, safety, and ease of the test will lead to informational overload and reproductive consumerism. The prevailing response among commentators has been to restrict conditions eligible for testing based on medical severity, which imposes disputed value judgments and devalues those living (...) with eligible conditions. To avoid these difficulties, we propose an unrestricted testing policy, under which prospective parents could obtain information on any variant of known significance after a careful informed consent process that uses an interactive decision aid to deliver a mandatory presentation on the purposes, techniques, and limitations of genomic testing, as well as optional resources for reflection and consultation. This process would encourage thoughtful, informed deliberation by prospective parents before deciding whether or how to use NIPW. (shrink)

Emerging genomic technologies promise more efficient infectious disease control. Whole genome sequencing is increasingly being used in tuberculosis diagnosis, surveillance, and epidemiology. However, while the use of WGS by public health agencies may raise ethical, legal, and socio-political concerns, these challenges are poorly understood. Between November 2017 and April 2018, we conducted semi-structured interviews with 22 key stakeholders across the fields of governance and policy, public health, and laboratory sciences representing the major jurisdictions currently using WGS in (...) national TB programs. Thematic analysis of the interviews was conducted using NVivo 11. Respondents identified several ethical and practical challenges associated with WGS in TB care and surveillance, all related to issues of trust, including: 1) the power of public health; 2) data sharing and profits derived from surveillance efforts; and 3) concerns regarding who has access to, and can benefit from, the technology. Additional challenges included: the potential utility that WGS adds to a public health program, the risks associated with linking necessary epidemiological metadata to the genomic data, and challenges associated with jurisdictional capacity to implement the technology. Successful implementation of WGS is dependent on fostering relationships of trust between those working with genomics technology and those directly impacted by it, including clinicians. Building trust between the public and the public health agencies and within public health agencies themselves is critical due to the inherent complexity of WGS and its implementation for communicable disease control purposes. (shrink)

As a psychologist and an ethicist, we have explored empirically newborn screening consent and communication processes. In this paper we consider the impact on families if newborn screening uses whole genome sequencing. We frame this within the World Health Organization’s definition of health and contend that proposals to use whole genome sequencing in newborn screening take into account the ethical, practical and psychological impact of such screening. We argue that the important psychological processes occurring (...) in the neonatal phase necessitate a clear justification that providing risk information at this stage provides a health benefit. We illustrate how research on current newborn screening can inform whole genome sequencing debates, whilst highlighting important gaps. Obtaining explicit, voluntary, and sufficiently informed consent for newborn screening is challenging, however we stress that such consent is ethically and legally appropriate and psychologically and practically important. We conclude by outling how this might be done. (shrink)

The anticipation of ethical issues that may arise with the clinical use of genomic technologies is crucial to envision their future implementation in a manner sensitive to local contexts. Yet, populations in low- and middle-income countries are underrepresented in studies that aim to explore stakeholders’ perspectives on the use of such technologies. Within the framework of a research project entitled “Personalized medicine in the treatment of epilepsy”, we sought to increase inclusiveness by widening the reach of our survey, inviting neurologists (...) from around the world to share their views and practices regarding the use of whole-genome sequencing in clinical neurology and its associated ethics. We discuss herein the compelling scientific and ethical reasons that led us to attempt to recruit neurologists worldwide, despite the lack, in many low- or middle-income countries, of access to genomic technologies. Recruitment procedures and their results are presented and discussed, as well as the barriers we faced. We conclude that inclusive recruitment remains a challenging, albeit necessary and legitimate, endeavour. (shrink)

The rise of technologies that can inexpensively sequence entire genomes means that researchers and clinicians have access to ever vaster stores of genomic data, some of which could be of great use to research participants or patients, and most of which, at least for today, will be of little, uncertain, or no use. Those facts are essential features of a new ethical territory we are now entering with genetics research. As we explore that territory, we should try to be as (...) clear as possible about the issues at hand. Clarity about the ethical issues that delineate this new territory requires that we be wary about too hastily importing into it concepts from the old territory. We want to suggest a way in which the term “incidental findings” can impede our ability to see clearly some of the most important issues we face. To show how that term can sometimes obscure more than it illuminates, we focus on how it is being deployed in the context of research. Although it may have been useful, when considering older forms of genetic research, to speak about researchers stumbling across clinically significant findings, and although that way of speaking has certainly not yet become wholly obsolete, it is ever less appropriate as the technology becomes ever more powerful. (shrink)

Progress in gene sequencing could make rapid whole genome sequencing of individuals affordable to millions of persons and useful for many purposes in a future era of genomic medicine. Using the idea of $1000 genome as a focus, this article reviews the main technical, ethical, and legal issues that must be resolved to make mass genotyping of individuals cost-effective and ethically acceptable. It presents the case for individual ownership of a person's genome and its (...) information, and shows the implications of that position for rights to informed consent and privacy over sequencing, testing, and disclosing genomic information about identifiable individuals. Legal recognition of a person's right to control his or her genome and the information that it contains is essential for further progress in applying genomic discoveries to human lives. (shrink)

Whole-genome analysis and whole-exome analysis generate many more clinically actionable findings than traditional targeted genetic analysis. These findings may be relevant to research participants themselves as well as for members of their families. Though researchers performing genomic analyses are likely to find medically significant genetic variations for nearly every research participant, what they will find for any given participant is unpredictable. The ubiquity and diversity of these findings complicate questions about disclosing individual genetic test results. We outline (...) an approach for disclosing a select range of genetic results to the relatives of research participants who have died, developed in response to relatives? requests during a pilot study of large-scale medical genetic sequencing. We also argue that studies that disclose individual research results to participants should, at a minimum, passively disclose individual results to deceased participants? relatives. (shrink)

Rapid advances in high throughput genomic technologies and next generation sequencing are making medical genomic research more readily accessible and affordable, including the sequencing of patient and control whole genomes and exomes in order to elucidate genetic factors underlying disease. Over the next five years, the Human Heredity and Health in Africa (H3Africa) Initiative, funded by the Wellcome Trust (United Kingdom) and the National Institutes of Health (United States of America), will contribute greatly towards sequencing of (...) numerous African samples for biomedical research. (shrink)

Large-scale whole genome sequencing (WGS) studies promise to revolutionize cancer research by identifying targets for therapy and by discovering molecular biomarkers to aid early diagnosis, to better determine prognosis and to improve treatment response prediction. Such projects raise a number of ethical, legal, and social (ELS) issues that should be considered. In this study, we set out to discover how these issues are being handled across different jurisdictions.

The possible integration of genomic sequencing (including whole‐genome and whole‐exome sequencing) into the three contexts addressed in this special report—state‐mandated screening programs, clinical care, and direct‐to‐consumer services—raises related but distinct legal issues. This essay will outline the legal issues surrounding the integration of genomic sequencing into state newborn screening programs, parental rights to refuse and access sequencing for their newborns in clinical and direct‐to‐consumer care, and privacy‐related legal issues attending the use of (...) class='Hi'>sequencing in newborns. (shrink)

Background Massively parallel sequencing techniques, such as whole exome sequencing (WES) and whole genome sequencing (WGS), may reveal unsolicited findings (UFs) unrelated to the diagnostic aim. Such techniques are frequently used for diagnostic purposes in pediatric cases of developmental delay (DD). Yet policy guidelines for informed consent and return of UFs are not well equipped to address specific moral challenges that may arise in these children’s situations. Discussion In previous empirical studies conducted by our (...) research group, we found that it is sometimes uncertain how children with a DD will develop and whether they could come to possess capacities for autonomous decision-making in the future. Parents sometimes felt this brought them into a Catch-22 like situation when confronted with choices about UFs before undergoing WES in trio-analysis (both the parents’ and child’s DNA are sequenced). An important reason for choosing to consent to WES was to gain more insight into how their child might develop. However, to make responsible choices about receiving or declining knowledge of UFs, some idea of their child’s future development of autonomous capacities is needed. This undesirable Catch-22 situation was created by the specific policy configuration in which parents were required to make choices about UFs before being sequencing (trio-analysis). We argue that this finding is relevant for reconfiguring current policies for return of UFs for WES/WGS and propose guidelines that encompass two features. First, the informed consent process ought to be staged. Second, differing guidelines are required for withholding/disclosing a UF in cases of DD appropriate to the level of confidence there is about the child’s future developmental of autonomous capacities. Conclusion When combined with a dynamic consent procedure, these two features of our guidelines could help overcome significant moral challenges that present themselves in the situations of children undergoing genomic sequencing for clarifying a DD. (shrink)

This paper examines three possible justifications for original ACMG recommendations to return incidental findings from whole exome or genome sequencing independent of patient preferences. The first two potential justifications, based on a patient's authentic values, then on harms to others, are founding lacking as a basis of justification for these recommendations. The third, grounded in analogous professional practices, might serve as a potential justification if several controversies can be avoided. However, given the nature of these controversies and (...) the need to instill public trust in this newly emerging science, the paper finds that updated ACMG recommendations that recognize opt-out rights on behalf of patients is the most prudent, and justifiable, approach. (shrink)

Whole–exome sequencing (WES) has increased our ability to analyze large parts of the human genome, bringing with it a plethora of ethical, legal, and social implications. A topic dominating discussion of WES is identification of “secondary findings” (SFs), defined as the identification of risk in an asymptomatic individual unrelated to the indication for the test. SFs can have considerable psychosocial impact on patients and families, and patients with an SF may have concerns regarding genomic privacy and genetic (...) discrimination. The Genetic Information Nondiscrimination Act of 2008 (GINA) currently excludes protections for members of the military. This may cause concern in military members and families regarding genetic discrimination when considering genetic testing. In this report, we discuss a case involving a patient and family in which a secondary finding was discovered by WES. The family members have careers in the U.S. military, and a risk–predisposing condition could negatively affect employment. While beneficial medical management changes were made, the information placed exceptional stress on the family, who were forced to navigate career–sensitive “extra–medical” issues, to consider the impacts of uncovering risk–predisposition, and to manage the privacy of their genetic information. We highlight how information obtained from WES may collide with these issues and emphasize the importance of genetic counseling for anyone undergoing WES. (shrink)

The use of genome-wide association studies in medical research and the increased ability to share data give a new twist to some of the perennial ethical issues associated with genomic research. GWAS create particular challenges because they produce fine, detailed, genotype information at high resolution, and the results of more focused studies can potentially be used to determine genetic variation for a wide range of conditions and traits. The information from a GWA scan is derived from DNA that is (...) a powerful personal identifier, and can provide information not just on the individual, but also on the individual's relatives, related groups, and populations. Furthermore, it creates large amounts of individual-specific digital information that is easy to share across international borders. This paper provides an overview of some of the key ethical issues around GWAS: consent, feedback of results, privacy, and the governance of research. Many of the questions that lie ahead of us in terms of the next generation sequencing methods will have been foreshadowed by GWAS and the debates around ethical and policy issues that these have created. (shrink)

Many scientists and doctors hope that affordable genome sequencing will lead to more personalized medical care and improve public health in ways that will benefit children, families, and society more broadly. One hope in particular is that all newborns could be sequenced at birth, thereby setting the stage for a lifetime of medical care and self‐directed preventive actions tailored to each child's genome. Indeed, commentators often suggest that universal genome sequencing is inevitable. Such optimism can (...) come with the presumption that discussing the potential limits, cost, and downsides of widespread application of genomic technologies is pointless, excessively pessimistic, or overly cautious. We disagree. Given the pragmatic challenges associated with determining what sequencing data mean for the health of individuals, the economic costs associated with interpreting and acting on such data, and the psychosocial costs of predicting one's own or one's child's future life plans based on uncertain testing results, we think this hope and optimism deserve to be tempered.In the analysis that follows, we distinguish between two reasons for using sequencing: to diagnose individual infants who have been identified as sick and to screen populations of infants who appear to be healthy. We also distinguish among three contexts in which sequencing for either diagnosis or screening could be deployed: in clinical medicine, in public health programs, and as a direct‐to‐consumer service. Each of these contexts comes with different professional norms, policy considerations, and public expectations. Finally, we distinguish between two main types of genome sequencing: targeted sequencing, where only specific genes are sequenced or analyzed, and whole‐exome or whole‐genome sequencing, where all the DNA or all the coding segments of all genes are sequenced and analyzed.In a symptomatic newborn, targeted or genome‐wide sequencing can help guide other tests for diagnosis or for specific treatment that is urgently needed. Clinicians use the infant's symptoms (or phenotype) to interrogate the sequencing data. These same complexities and uncertainties, however, limit the usefulness of genome‐wide sequencing as a population screening tool. While we recognize considerable benefit in using targeted sequencing to screen for or detect specific conditions that meet the criteria for inclusion in newborn screening panels, use of genome‐wide sequencing as a sole screening tool for newborns is at best premature. We conclude that sequencing technology can be beneficially used in newborns when that use is nuanced and attentive to context. (shrink)

In this post‐sequencing era, geneticists can focus on functional genomics on a much larger scale than ever before. One goal is the discovery and elucidation of the intricate genetic networks that co‐ordinate transcriptional activation in different regulatory circuitries. High‐throughput gene expression measurement using DNA arrays has thus become routine strategy. This approach, however, does not directly identify gene loci that belong to the same regulatory group; e.g., those that are bound by a common (set of) transcription factor(s). Working in (...) yeast, two groups have recently published an elegant method that could circumvent this problem, by combining chromatin immunoprecipitation and DNA microarrays.(1,2) The method is likely to provide a powerful tool for the dissection of global regulatory networks in eukaryotic cells. BioEssays 23:473–476, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

Whether, and to what degree, do patents granted on human genes cast a shadow of uncertainty over genomics and its applications? Will owners of patents on individual genes or clusters of genes sue those performing whole-genome analyses on human samples for patent infringement? These are related questions that have haunted molecular diagnostics companies and services, coloring scientific, clinical, and business decisions. Can the profusion of whole-genome analysis methods proceed without fear of patent infringement liability?Whole-genome (...) sequencing is proceeding apace. Academic centers have been performing whole-genome and -exome sequencing in research for at least five years, and academic clinical laboratories with national reach have been doing sequencing for clinical applications for almost as long. Companies have also been offering WGS and WES as a clinical service for a few years now. So far as we know, no one has been sued for infringement of “gene patents” for performing WGS. (shrink)

Salmon genomics is an emerging field that represents a convergence between socially important scientific innovation and a politically volatile topic of significant interest to the public. These factors provide a strong rationale for public input. This report describes such input from a public engagement event based on the principles of deliberative democracy. The event involved a random, demographically stratified sample of 25 British Columbians (Canada). While some participants opposed sequencing the salmon genome on principle, on the whole (...) participants responded favourably, citing the value of increased knowledge of human impacts on salmon, potentially slowing or reversing this impact, and assisting sustainable management of salmon resources. Participants discussed many of the potential implications of the sequencing project and formulated recommendations pertaining to regulations, international treaties, public education and engagement. Overall, the project illustrates that the specific design and implementation of this event is capable of producing sound policy advice from the general public on genomic-related issues. (shrink)

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

In lieu of an abstract, here is a brief excerpt of the content:Kennedy Institute of Ethics Journal 14.1 (2004) 47-54 [Access article in PDF] Ethical Guidelines for Human Embryonic Stem Cell Research*(A Recommended Manuscript) Adopted on 16 October 2001Revised on 20 August 2002 Ethics Committee of the Chinese National Human Genome Center at Shanghai, Shanghai 201203 Human embryonic stem cell (ES) research is a great project in the frontier of biomedical science for the twenty-first century. Be- cause the research (...) involves the use of human embryos, it triggers serious debate on ethical issues. Opponents consider the embryo to be an early form of human life that should be respected and not destroyed. However, the majority of scientists support embryonic stem cell research, believing that it offers good prospects for the treatment of diseases that have remained incurable until now and so will benefit humankind. The Ethics Committee of the Department of Ethical, Legal, and Social Implications of the Chinese National Human Genome Center at Shanghai seriously discussed the ethical debate initiated by embryonic stem cell research. We concluded that we should support the scientists of our country in actively carrying out human embryonic stem cell research for the noble cause of "medicine being a beneficent art." For the healthy and orderly development of human embryonic stem cell research in our country, we put forward the following recommended Ethical Guidelines for Human Embryonic Stem Cell Research as a reference for leaders, administrative departments, and related scientists. Preface Article 1. Human embryonic stem cells are the primitive cells that play the main role in the growth and development of a human body. These [End Page 47] primitive cells have the potential for infinite proliferation, self-renewal, and multi-directional differentiation. If scientists can discover the mechanism of differentiation of human embryonic stem cells, it will be possible to induce differentiation of human embryonic stem cells to form various types of human cells for clinical cell therapy. If human embryonic stem cell research can be integrated with modern biomedical engineering techniques, it also will be possible to make repair and replacement of human tissues and organs a reality. Article 2. There are two ways to classify human embryonic stem cells. One way is to classify them according to their potential for differentiation. There could be three kinds of stem cells: totipotent stem cells, pluripotent stem cells, and unipotent stem cells.A totipotent stem cell has the potential to develop into a whole individual. It can differentiate into the more than 200 cell types in the whole body, construct any tissue or organ of the body, and finally develop into a whole individual. The fertilized egg and the cleavage cells at the very early stage of embryonic development are totipotent stem cells.A pluripotent stem cell has the potential to differentiate into many cell types derived from the three embryonic layers. However, it has lost the capacity to develop into a complete organism.A unipotent stem cell is derived from the further differentiation of the pluripotent stem cell. It can differentiate only into one cell type such as a hematopoietic stem cell, neural stem cell, and others.The other way is to classify human stem cells according to their source. There could be two kinds of human stem cells: embryonic stem cells and tissue stem cells (also called adult stem cells). The former involves experimentation with embryos, which has serious ethical implications. Ethical issues associated with the latter are mainly expressed in the various opinions regarding the allocation of health resources. Article 3. Human embryonic stem cells are the group of cells called the blastocyst inner cell mass during the early stage of embryonic development. They are the main source of totipotent stem cells, and hence the focal and hot point in stem cell research. Studies on the clinical application of embryonic stem cells probably will involve use of the somatic cell nucleus transfer (SCNT) technique, which destroys the early human embryo. At present, the ethical and moral debate is very serious in human embryonic stem cell research regarding whether the research will develop... (shrink)

Transcriptome sequencing has identified more than a thousand potentially imprinted genes in the mouse brain. This comes as a revelation to someone who cut his teeth on the identification of imprinted genes when only a handful was known. Genomic imprinting, an epigenetic mechanism that determines expression of alleles according to sex of transmitting parent, was discovered over 25 years ago in mice but remains an enigmatic phenomenon. Why do these genes disobey the normal Mendelian logic of inheritance, do they (...) function in specific processes, and how is their imprinting conferred? Next generation sequencing technologies are providing an unprecedented opportunity to survey the whole genome for imprinted genes and are beginning to reveal that imprinting may be more pervasive than we had come to believe. Such advances should lay the foundation for a definitive account of imprinting, but may also challenge accepted views on what it means to be imprinted.Editor's suggested further reading in BioEssays RNA as the substrate for epigenome‐environment interactions Abstract. (shrink)

Whole genome and exome sequencing techniques raise hope for a new scale of diagnosis, prevention, and prediction of genetic conditions, and improved care for children. For these hopes to materialize, extensive genomic research with children will be needed. However, the use of WGS/WES in pediatric research settings raises considerable challenges for families, researchers, and policy development. In particular, the possibility that these techniques will generate genetic findings unrelated to the primary goal of sequencing has stirred intense (...) debate about whether, which, how, and when these secondary or incidental findings should be returned to parents and minors. The debate is even more pronounced when the subjects are adolescents, for whom decisions about return of SFs may have particular implications. In this paper, we consider the rise of “genomic citizenship” and the main challenges that arise for these stakeholders: adolescents' involvement in decisions relating to return of genomic SFs, the types of SFs that should be offered, privacy protections, and communication between researchers and adolescents about SFs. We argue that adolescents' involvement in genomic SF-related decisions acknowledges their status as valuable stakeholders without detracting from broader familial interests, and promotes more informed genomic citizens. (shrink)

Issues in genetics and genomics have been centre stage in Bioethics for much of its history, and have given rise to both negative and positive imagined futures. Ten years after the completion of the Human Genome Project, it is a good time to assess developments. The promise of whole genome sequencing of individuals requires reflection on personalization, genetic determinism, and privacy.

The rapid advancement from single-gene testing to whole genome sequencing has significantly broadened the type and amount of information available to researchers, physicians, patients, and the public in general. Much debate has ensued about whether genomic test results should be reported to research participants, patients and consumers, and at what stage we can be sure that existing evidence justifies their use in clinical settings. Courts and judges evaluating the utility of these results will not be immune to (...) this uncertainty. As scholars increasingly explore the duty of care standards related to reporting genomic test results, it is timely to provide a framework for understanding how uncertainty about genetic and genomic tests influences evidentiary considerations in the court room. Here, we explore the subtleties and nuances of interpreting genetic data in an environment of substantial discord related to the value that individuals should place on genetic and genomic tests. In conjunction, we discuss the roles courts should play in qualifying experts, expert testimony, and genetic and genomic tests given the intricate and complex nature of genetic and genomic information. (shrink)

Genomic research—including whole genome sequencing and whole exome sequencing—has a growing presence in contemporary biomedical investigation. The capacity of sequencing techniques to generate results that go beyond the primary aims of the research—historically referred to as “incidental findings”—has generated considerable discussion as to how this information should be handled—that is, whether incidental results should be returned, and if so, which ones.Federal regulations governing most human subjects research in the United States require the disclosure of (...) “the procedures to be followed” in the research as part of the informed consent process. It seems reasonable to assume—and indeed, many commentators have concluded—that genomic investigators will be expected to inform participants about, among other procedures, the prospect that incidental findings will become available and the mechanisms for dealing with them. Investigators, most of whom will not have dealt with these issues before, will face considerable challenges in framing meaningful disclosures for research participants.To help in this task, we undertook to identify the elements that should be included in the informed consent process related to incidental findings. We did this by surveying a large number of genomic researchers (n = 241) and by conducting in‐depth interviews with a smaller number of researchers (n = 28) and genomic research participants (n = 20). Based on these findings, it seems clear to us that routine approaches to informed consent are not likely to be effective in genomic research in which the prospect of incidental findings exists. Ensuring that participants’ decisions are informed and meaningful will require innovative approaches to dealing with the consent issue. We have identified four prototypical models of a consent process for return of incidental findings. (shrink)

In many species the mutation rate is higher in males than in females, a phenomenon denoted as male mutation bias. This is often observed in animals where males produce many more sperm than females produce eggs, and is thought to result from differences in the number of replication‐associated mutations accumulated in each sex. Thus, studies of male mutation bias have the capacity to reveal information about the replication‐dependent or replication‐independent nature of different mutations. The availability of whole genome (...) sequences for many species, as well as for multiple individuals within a species, has opened the door to studying factors, both sequence‐specific and those acting on the genome globally, that affect differences in mutation rates between males and females. Here, we assess the advantages that genomic sequences provide for studies of male mutation bias and general mutation mechanisms, discuss major challenges left unresolved, and speculate about the direction of future studies. (shrink)

Recent advances in DNA sequencing have revolutionized the field of genomics, making it possible for even single research groups to generate large amounts of sequence data very rapidly and at a substantially lower cost. These high‐throughput sequencing technologies make deep transcriptome sequencing and transcript quantification, whole genome sequencing and resequencing available to many more researchers and projects. However, while the cost and time have been greatly reduced, the error profiles and limitations of the new (...) platforms differ significantly from those of previous sequencing technologies. The selection of an appropriate sequencing platform for particular types of experiments is an important consideration, and requires a detailed understanding of the technologies available; including sources of error, error rate, as well as the speed and cost of sequencing. We review the relevant concepts and compare the issues raised by the current high‐throughput DNA sequencing technologies. We analyze how future developments may overcome these limitations and what challenges remain. (shrink)

Fusion genes formed by chromosomal rearrangements are common drivers of cancer. Recent innovations in the field of next‐generation sequencing (NGS) have seen a dynamic shift from traditional fusion detection approaches, such as visual characterization by fluorescence, to more precise multiplexed methods. There are many different NGS‐based approaches to fusion gene detection and deciding on the most appropriate method can be difficult. Beyond the experimental approach, consideration needs to be given to factors such as the ease of implementation, processing time, (...) associated costs, and the level of expertise required for data analysis. Here, the different NGS‐based methods for fusion gene detection, the basic principles underlying the techniques, and the benefits and limitations of each approach are reviewed. This article concludes with a discussion of how NGS will impact fusion gene detection in a clinical context and from where the next innovations are evolving. (shrink)

Since the first draft of the human genome was published in 2001, DNA sequencing technology has advanced at a remarkable pace. Launched in 1990, the Human Genome Project sought to sequence all three billion base pairs of the haploid human genome, an endeavor that took more than a decade and cost nearly three billion dollars. The subsequent development of so-called “next generation” sequencing methods has raised the possibility that real-time, affordable genome sequencing will (...) soon be widely available. Currently, NGS methods can be used to sequence up to 60 billion base pairs per day. Whole-genome sequencing costs an estimated $5,000-10,000, with that number predicted to fall to $1000 in the near future.In the past few years, the availability of high-throughput NGS methods has led to a proliferation of potential and actual clinical applications for NGS. NGS therefore has the potential to usher in the long-awaited era of personalized medicine. (shrink)

Rice cultivation is one of the most important agricultural activities on earth, with nearly 90% of it being produced in Asia. It belongs to the family of crops that includes wheat, maize and barley, and it supplies more than 50% of calories consumed by the world population. Its immense economic value and a relatively small genome size makes it a focal point for scientific investigations, so much so that four whole genome sequence drafts with varying qualities have (...) been generated by both public and privately funded ventures. The availability of a complete and high‐quality map‐based sequence has provided the opportunity to study genome organization and evolution. Most importantly, the order and identity of 37,544 genes of rice have been unraveled. The sequence provides the required ingredients for functional genomics and molecular breeding programs aimed at unraveling intricate cellular processes and improving rice productivity. BioEssays 28: 421–432, 2006. © 2006 Wiley Periodicals, Inc. (shrink)