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10023 Background: Advances in sequencing technologies allow for provision of genome-scale data to oncologists and geneticists caring for pediatric cancer patients. The goal of the BASIC3 (Baylor Advancing Sequencing into Childhood Cancer Care) study is to determine the clinical impact of incorporating CLIA-certified tumor and constitutional exome sequencing into the care of children with newly diagnosed solid tumors. Methods: Blood and frozen tumor samples obtained at initial surgery are submitted for clinical exome sequencing (target enrollment 280 patients). Results are deposited into the electronic medical record and disclosed to families by their oncologist and a genetic counselor. Identification of germline cancer susceptibility mutations is compared with standard testing practices. Oncologists are surveyed on prioritization of treatment options in the hypothetical event of tumor recurrence before and after receiving tumor exome results. Patients will be followed for two years to assess the clinical utility of exome data. Preferences for reporting this complex information are obtained by interviews and audiorecording of disclosure visits. Results: Initial results reveal that41 of 49 (84%) ethnically diverse families have consented to enroll on study. Adequate tumor samples were available from 35 of 41 patients (85%), including 11 of 15 (73%) patients with CNS tumors and 24 of 26 (92%) with non-CNS tumors. Pathogenic germline cancer susceptibility mutations (TP53, MSH2) were reported in 2 of the first 11 patients, with a medically-actionable mutation in a gene (SCN5A) unrelated to cancer in 1 patient and 0-4 (median of 2) recessive carrier mutations per patient. Between 9 and 33 protein altering mutations (median of 11) have been identified in tumors, including known cancer genes such as TP53 and others with no known link to pediatric cancer. Conclusions: A robust clinical pipeline for exome sequencing of blood and tumor samples has been successfully developed with significant parental interest. Data assessing the clinical utility of both the tumor and constitutional exomes and the preferences of oncologists and parents for reporting of these results are under study. Supported by NHGRI 1U01HG006485.

The Human Microbiome Project (HMP) [1],[2] is a concept that was long in the making. After the Human Genome Project, interest grew in sequencing the “other genome" of microbes carried in and on the human body [3],[4]. Microbial ecologists, realizing that >99% of environmental microbes could not be easily cultured, developed approaches to study microorganisms in situ [5], primarily by sequencing the 16S ribosomal RNA gene (16S) as a phylogenetic and taxonomic marker to identify members of microbial communities [6]. The need to develop corresponding new methods for culture-independent studies [7],[8] in turn precipitated a sea change in the study of microbes and human health, inspiring the new term “metagenomics" [9] both to describe a technological approach—sequencing and analysis of the genes from whole communities rather than from individual genomes—and to emphasize that microbes function within communities rather than as individual species. This shift from a focus on individual organisms to microbial interactions [10] culminated in a National Academy of Science report [11], which outlined challenges and promises for metagenomics as a way of understanding the foundational role of microbial communities both in the environment and in human health., National Institutes of Health (U.S.) (grant U54HG004969), National Institutes of Health (U.S.) (grant U54HG004973), National Institutes of Health (U.S.) (grant U54AI084844), National Institutes of Health (U.S.) (grant U01HG004866), National Institutes of Health (U.S.) (grant R01HG005969), National Institutes of Health (U.S.) (grant R01HG004872), United States. Army Research Office (grant W911NF-11-1-0473), National Science Foundation (U.S.) (NSF DBI-1053486), Howard Hughes Medical Institute (Early Career Scientist)

A report on the National Human Genome Research Institute's Ethical, Legal, and Social Implications Research Program 2011 Congress, 'Exploring the ELSI Universe', Chapel Hill, North Carolina, USA, 12-14 April 2011.

Using cadaveric specimens in genome research presents many benefits: investigators can study multiple organs from one individual, including those impossible to collect from living donors (for example, brains), and health risks are minimized as the individual is deceased. Several genomic research initiatives plan to collect cadaveric tissues. For instance, the Genotype-Tissue Expression (GTEx) project, a US National Institutes of Health Roadmap initiative, is seeking insights into the mechanics of gene regulation by identifying variations in gene expression that are highly correlated with genetic variation (1). Another example is the Allen Institute for Brain Science's human brain atlases, which seek to create a comprehensive three-dimensional map of gene expression in the human brain (2). However, in many countries, including the United States, there are not adequate ethical guidelines in place for this type of research. Scandals involving the removal and retention of organs from cadavers in the United Kingdom led to enactment of the Human Tissue Act, which makes it a crime to conduct genome research using tissues from cadavers without consent (3). In the United States, cadaveric specimens can be obtained and used for most research with little regulatory oversight, no ethical review and without informed consent. Deceased individuals are not human subjects under US federal regulations (4). Although the Revised Uniform Anatomical Gift Act recommends that states require individual or family permission to retain cadaveric tissues for use in research (5), permission is not the same as providing informed consent. When an anatomical gift is made, only the purpose of the gift is specified (for example, transplantation, therapy, research, or education); no discussion of the nature of the research or its risks, benefits and alternatives is required. However, ethically, individuals retain certain interests after death, including an interest in having their bodies treated with respect and in having their ante-mortem wishes upheld (6). Living individuals whose organs may be used for research post-mortem may also suffer present harm in anticipation that their corpse will be treated in ways that violate their values or beliefs. Also, family members (whether genetically related or not) have an interest in the disposition of a loved one's remains. Finally, the use of cadaveric tissues in genome research raises additional ethical concerns about privacy. Some have argued that deceased individuals can suffer nonexperiential harm, such as loss of reputation that may result from a privacy breach after death (6), and close genetic relatives have privacy interests that deserve protection (7). Research has shown that DNA is a unique identifier (8, 9), and in some forensic cases it has been used to identify the biological relatives of a suspect (10). For these reasons, it is recommended that research on the newly dead is subjected to independent ethical review and that informed consent is obtained from the individual before death or from the legally authorized surrogate (7, 11). The informed consent process should be integrated into existing organ procurement processes to allow priority to be given to transplanting viable organs and to avoid duplicate requests, and it should include an explanation of the potential privacy risks for the sample source, as well as her or his close genetic relatives. In addition, precautions should be taken to protect privacy by limiting access to DNA data through restricted databases (12). However, independent informed consent from genetic relatives should not be required because the risks are extremely small in relation to the burdens that such a requirement would impose on research. DNA will only reveal predictive information about biological relatives, and the risk of identifiability is both uncertain and dependent upon the nature of the data and the degree of relatedness to the sample source. Further, in most cases it would be impracticable to identify and locate all potentially affected relatives, and the contact itself might constitute a breach of privacy. Further research will be needed to ensure that new policies are responsive to the concerns and perspectives of potential donors and their families. In the absence of data regarding public perspectives, we recommend a preventative ethics approach that involves institutional review board appraisal and informed consent from the individual or a surrogate. This approach may prevent future scandals and bolster public trust. At the same time, it is not overly burdensome and so should not significantly impede research.

No course in genetics can prepare the practicing physician to interpret whole-genome data. We argue that genetics is a microcosm of the changing dynamics of the practice of medicine. It illustrates the perfect storm of exponential increases in raw data with undetermined clinical relevance, ease of access to large amounts of data via the internet and shifting expectations of the doctor-patient relationship and the very mechanisms of health care delivery. Educational reform is needed across the continuum of medical education, from the student to the faculty training them, and requires a shift in focus from factual knowledge to data management and interpretation.

Technological advances over the past several years have dramatically reduced the cost of whole-genome sequencing. At the same time, understanding of the functional significance of genetic variation has advanced considerably. The routine generation of whole-genome sequence data for individual patients will soon be sufficiently cost-effective for widespread clinical integration. Yet, the clinical utility of whole-genome data is currently limited by an inability to effectively process, store, interpret and update genomic data, while at the same time protecting patient privacy. Enter the electronic health record. We propose that without the integration of a dynamic uniform electronic health record, counseling patients on the basis of genome-wide data will be futile.

The Genetic Information Nondiscrimination Act of 2008 (GINA) was recently enacted in the United States. Its supporters have applauded the passage of GINA, and they hope that it will alleviate public fear about genetic discrimination and facilitate genetic testing and participation in genetic research. Critics worry that GINA does not provide adequate protection because it fails to address discrimination on the basis of non-genetic health-related information, and it only regulates the use of genetic information in health insurance and employment. Despite these limitations, GINA represents a major step forward in US policy. Additional research is needed to assess the impact of GINA on industry practice and public opinion. In the mean time, education about GINA and its limitations can help individuals make more informed decisions about genetic testing and participation in genetic research.

It is now possible for individuals to learn about their genetic susceptibility to dozens of common and complex disorders, such as coronary artery disease, diabetes, obesity, prostate cancer, and Alzheimer’s disease, without ever seeing a physician. Direct-to-consumer personal genome testing companies, such as 23andMe, Navigenics, and deCODEme hope to empower consumers to take control of their health by providing tailored assessments of genetic risk based on reported associations between genomic variation and susceptibility to disease. Several states limit or forbid this practice as a violation of state law that requires the appropriate involvement of a licensed physician when providing medical diagnostic information (1). Personal genome testing companies claim that their services are for informational and educational purposes only. They warn consumers that the information should not be used for diagnosis, treatment, or health ascertainment purposes and direct them to their physician if they have questions or concerns about their health status (2–3). Because of uncertainty about the validity and clinical utility of test results, Hunter and colleagues advise physicians to discourage patients from pursuing personal genome testing and to respond to test results with general statements about their limited predictive value (4). While this response is consistent with current knowledge, a recent survey of online social networking users suggests that at least some potential consumers would expect their physician to help them interpret test results and believe that physicians have a professional obligation to do so (ALM, unpublished data). This expectation has important implications for primary care physicians, even pediatricians, because many direct-to-consumer personal genome testing companies allow testing of children as well as adults. Primary care physicians already spend much of their time helping patients understand and manage health risks. Assessment of cardiac risk factors, occupational exposures and other health indicators allow physicians to identify health risks and counsel patients accordingly. Physicians are also accustomed to talking with patients about health information disclosed on the internet or through other media outlets. At the same time, primary care physicians have limited time with patients, face many competing demands (5), and are poorly reimbursed for time spent counseling patients about preventive care. Patient concerns about direct-to-consumer test results have the potential to exacerbate these problems and strain already limited health care resources.

On 31 May 2007, James Watson was handed a miniature hard drive containing his personal genome sequence, which was subsequently uploaded onto publicly accessible databases. Craig Venter’s personal genome was published a few months later (1). These projects represent research milestones. They also present an opportunity to examine the ethical, social, and clinical implications of personal genomics.

Enhancing patient choice is a central theme of medical ethics and law. Informed consent is the legal process used to promote patient autonomy; shared decision making is a widely promoted ethical approach. These processes may most usefully be seen as distinct in clinically and ethically important respects. The approach outlined in this article uses a model that arrays all medical decisions along 2 axes: risk and certainty. At the extremes of these continua, 4 decision types are produced, each of which constrains the principal actors in predictable ways. Shared decision making is most appropriate in situations of uncertainty, in which 2 or more clinically reasonable alternatives exist. When there is only 1 realistic choice, patient and physician may gather and exchange information; however, the patient cannot be empowered to make choices that do not exist. In contrast, informed consent does not require the presence of clinical choice; it is appropriate for all decisions of significant risk, even if there is only one option. When a clinical decision contains both risk and uncertainty, shared decision making and informed consent are both appropriate. For decisions of lower risk, consent should still be present, but it can be simple rather than informed. Clinicians may use this analysis as a guide to their own interactions with patients. In the continuing effort to provide patients with appropriate decisional authority over their own medical choices, shared decision making, informed consent, and simple consent each has a distinct role to play.

Background Continued advances in human microbiome research and technologies raise a number of ethical, legal, and social challenges. These challenges are associated not only with the conduct of the research, but also with broader implications, such as the production and distribution of commercial products promising maintenance or restoration of good physical health and disease prevention. In this article, we document several ethical, legal, and social challenges associated with the commercialization of human microbiome research, focusing particularly on how this research is mobilized within economic markets for new public health uses. Methods We conducted in-depth, semi-structured interviews (2009–2010) with 63 scientists, researchers, and National Institutes of Health project leaders (“investigators”) involved with human microbiome research. Interviews explored a range of ethical, legal, and social dimensions of human microbiome research, including investigators’ perspectives on commercialization. Using thematic content analysis, we identified and analyzed emergent themes and patterns. Results Investigators discussed the commercialization of human microbiome research in terms of (1) commercialization, probiotics, and issues of safety, (2) public awareness of the benefits and risks of dietary supplements, and (3) regulation. Conclusion The prevailing theme of ethical, legal, social concern focused on the need to find a balance between the marketplace, scientific research, and the public’s health. The themes we identified are intended to serve as points for discussions about the relationship between scientific research and the manufacture and distribution of over-the-counter dietary supplements in the United States.

Background Besides its growing importance in clinical diagnostics and understanding the genetic basis of Mendelian and complex diseases, whole exome sequencing (WES) is a rich source of additional information of potential clinical utility for physicians, patients and their families. We analyzed the frequency and nature of single nucleotide variants (SNVs) considered secondary findings and recessive disease allele carrier status in the exomes of 8554 individuals from a large, randomly sampled cohort study and 2514 patients from a study of presumed Mendelian disease having undergone WES. Methods We used the same sequencing platform and data processing pipeline to analyze all samples and characterized the distributions of reported pathogenic (ClinVar, Human Gene Mutation Database (HGMD)) and predicted deleterious variants in the pre-specified American College of Medical Genetics and Genomics (ACMG) secondary findings and recessive disease genes in different ethnic groups. Results In the 56 ACMG secondary findings genes, the average number of predicted deleterious variants per individual was 0.74, and the mean number of ClinVar reported pathogenic variants was 0.06. We observed an average of 10 deleterious and 0.78 ClinVar reported pathogenic variants per individual in 1423 autosomal recessive disease genes. By repeatedly sampling pairs of exomes, 0.5 % of the randomly generated couples were at 25 % risk of having an affected offspring for an autosomal recessive disorder based on the ClinVar variants. Conclusions By investigating reported pathogenic and novel, predicted deleterious variants we estimated the lower and upper limits of the population fraction for which exome sequencing may reveal additional medically relevant information. We suggest that the observed wide range for the lower and upper limits of these frequency numbers will be gradually reduced due to improvement in classification databases and prediction algorithms. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0171-1) contains supplementary material, which is available to authorized users.

Editorial summary Failure to consider lessons from behavioral economics in the case of whole genome sequencing may cause us to run into the ‘last mile problem’ - the failure to integrate newly developed technology, on which billions of dollars have been invested, into society in a way that improves human behavior and decision-making.

The potential to discover unanticipated clinically significant genetic variants during the course of research has stimulated much debate about the obligations of researchers to communicate such findings to study participants. Published guidelines suggest that researchers have an obligation to communicate valid and significant results, especially if they are clinically actionable. I will present data on the practices and perspectives of investigators conducting genome-wide association studies (GWAS) and will caution against the establishment of a general obligation to return results in research. I will compare the role-specific responsibilities of researchers with those of clinicians and discuss emerging standards for genomic analysis and communication of test results in the clinical setting.

Background Whole genome sequencing (WGS) is already being used in certain clinical and research settings, but its impact on patient well-being, health-care utilization, and clinical decision-making remains largely unstudied. It is also unknown how best to communicate sequencing results to physicians and patients to improve health. We describe the design of the MedSeq Project: the first randomized trials of WGS in clinical care. Methods/Design This pair of randomized controlled trials compares WGS to standard of care in two clinical contexts: (a) disease-specific genomic medicine in a cardiomyopathy clinic and (b) general genomic medicine in primary care. We are recruiting 8 to 12 cardiologists, 8 to 12 primary care physicians, and approximately 200 of their patients. Patient participants in both the cardiology and primary care trials are randomly assigned to receive a family history assessment with or without WGS. Our laboratory delivers a genome report to physician participants that balances the needs to enhance understandability of genomic information and to convey its complexity. We provide an educational curriculum for physician participants and offer them a hotline to genetics professionals for guidance in interpreting and managing their patients’ genome reports. Using varied data sources, including surveys, semi-structured interviews, and review of clinical data, we measure the attitudes, behaviors and outcomes of physician and patient participants at multiple time points before and after the disclosure of these results. Discussion The impact of emerging sequencing technologies on patient care is unclear. We have designed a process of interpreting WGS results and delivering them to physicians in a way that anticipates how we envision genomic medicine will evolve in the near future. That is, our WGS report provides clinically relevant information while communicating the complexity and uncertainty of WGS results to physicians and, through physicians, to their patients. This project will not only illuminate the impact of integrating genomic medicine into the clinical care of patients but also inform the design of future studies. Trial registration ClinicalTrials.gov identifier NCT01736566