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3.  Clinical Integration of Next Generation Sequencing: A Policy Analysis 
Précis
Clinical next generation sequencing (NGS) technologies are challenging existing regulatory paradigms. We advocate a coordinate policy approach, which first requires a comprehensive understanding of the existing regulatory and legal structures. This paper introduces four key policy domains, including quality assurance, insurance coverage, intellectual property management, and data sharing, that must be addressed to ensure high quality clinical NGS. In bringing these policy issues into conversation through this special issue for the Journal of Law, Medicine, and Ethics we hope to lay the foundation for further discussion by a range of stakeholder groups with diverse and strong interests in the governance of NGS.
doi:10.1111/jlme.12158
PMCID: PMC5095695  PMID: 25298287
4.  Persistent Confusion and Controversy Surrounding Gene Patents 
Nature biotechnology  2016;34(2):145-147.
There is persistent confusion and controversy surrounding basic issues of patent law relevant to the genomics industry. Uncertainty and conflict can lead to the adoption of inefficient practices and exposure to liability. The development of patent-specific educational resources for industry members, as well as the prompt resolution of patentability rules unsettled by recent U.S. Supreme Court decisions, are therefore urgently needed.
doi:10.1038/nbt.3470
PMCID: PMC5094359  PMID: 26849516
5.  Beyond Our Borders? Public Resistance to Global Genomic Data Sharing 
PLoS Biology  2016;14(11):e2000206.
Prospects have never seemed better for a truly global approach to science to improve human health, with leaders of national initiatives laying out their vision of a worldwide network of related projects. An extensive literature addresses obstacles to global genomic data sharing, yet a series of public polls suggests that the scientific community may be overlooking a significant barrier: potential public resistance to data sharing across national borders. In several large United States surveys, university researchers in other countries were deemed the least acceptable group of data users, and a just-completed US survey found a marked increase in privacy and security concerns related to data access by non-US researchers. Furthermore, diminished support for sharing beyond national borders is not unique to the US, although the limited data from outside the US suggest variation across countries as well as demographic groups. Possible sources of resistance include apprehension about privacy and security protections. Strategies for building public support include making the affirmative case for global data sharing, addressing privacy, security, and other legitimate concerns, and investigating public concerns in greater depth.
doi:10.1371/journal.pbio.2000206
PMCID: PMC5091881  PMID: 27806054
6.  Overcoming the Reimbursement Barriers for Clinical Sequencing 
JAMA  2014;312(18):1857-1858.
doi:10.1001/jama.2014.14915
PMCID: PMC5087268  PMID: 25387182
7.  Pediatric cancer genetics research and an evolving preventive ethics approach for return of results after death of the subject 
Précis
The return of genetic research results after death in the pediatric setting comes with unique complexities. Researchers must determine which results and through which processes results are returned. This paper discusses the experience over 15 years in pediatric cancer genetics research of returning research results after the death of a child and proposes a preventive ethics approach to protocol development in order to improve the quality of return of results in pediatric genomic settings.
doi:10.1111/jlme.12295
PMCID: PMC4617204  PMID: 26479562
8.  Barriers to clinical adoption of next generation sequencing: Perspectives of a policy Delphi panel 
This research aims to inform policymakers by engaging expert stakeholders to identify, prioritize, and deliberate the most important and tractable policy barriers to the clinical adoption of next generation sequencing (NGS). A 4-round Delphi policy study was done with a multi-stakeholder panel of 48 experts. The first 2 rounds of online questionnaires (reported here) assessed the importance and tractability of 28 potential barriers to clinical adoption of NGS across 3 major policy domains: intellectual property, coverage and reimbursement, and FDA regulation. We found that: 1) proprietary variant databases are seen as a key challenge, and a potentially intractable one; 2) payer policies were seen as a frequent barrier, especially a perceived inconsistency in standards for coverage; 3) relative to other challenges considered, FDA regulation was not strongly perceived as a barrier to clinical use of NGS. Overall the results indicate a perceived need for policies to promote data-sharing, and a desire for consistent payer coverage policies that maintain reasonably high standards of evidence for clinical utility, limit testing to that needed for clinical care decisions, and yet also flexibly allow for clinician discretion to use genomic testing in uncertain circumstances of high medical need.
doi:10.1016/j.atg.2016.05.004
PMCID: PMC5025465  PMID: 27668172
Next generation sequencing; Coverage and reimbursement; FDA regulation; Intellectual property; Personalized medicine; Clinical genomics
9.  Patients’ perceived utility of whole-genome sequencing for their healthcare: findings from the MedSeq project 
Personalized medicine  2016;13(1):13-20.
Aim
To evaluate patients’ expectations regarding the perceived utility of whole-genome sequencing (WGS).
Materials & methods
We used latent class analysis to characterize individuals enrolled in the MedSeq Project based on their perceived utility of WGS. Multinomial logistic regression was used to evaluate associations between participant characteristics and latent classes.
Results
Findings characterized participants into one of three perceived utility groups: enthusiasts, who had a high probability of agreement with all utility items (23%); health conscious, who perceived utility in medically related areas (60%) or skeptics, who had a low probability of agreement with utility items (17%). Trust significantly predicted latent class.
Conclusion
Understanding differences in perceived utility of WGS may inform strategies for uptake of this technology.
doi:10.2217/pme.15.45
PMCID: PMC4806392  PMID: 27019659
clinical utility; patient perspectives; perceived utility; personal utility; whole-genome sequencing
10.  An open access pilot freely sharing cancer genomic data from participants in Texas 
Scientific Data  2016;3:160010.
Genomic data sharing in cancer has been restricted to aggregate or controlled-access initiatives to protect the privacy of research participants. By limiting access to these data, it has been argued that the autonomy of individuals who decide to participate in data sharing efforts has been superseded and the utility of the data as research and educational tools reduced. In a pilot Open Access (OA) project from the CPRIT-funded Texas Cancer Research Biobank, many Texas cancer patients were willing to openly share genomic data from tumor and normal matched pair specimens. For the first time, genetic data from 7 human cancer cases with matched normal are freely available without requirement for data use agreements nor any major restriction except that end users cannot attempt to re-identify the participants (http://txcrb.org/open.html).
doi:10.1038/sdata.2016.10
PMCID: PMC4755126  PMID: 26882539
Genetics research; Cancer genomics; DNA sequencing; Medical genomics
11.  Responding to moderate breaches in professionalism: An intervention for medical students 
Medical teacher  2014;37(2):136-139.
Much has been written about how we understand, teach and evaluate professionalism in medical training. Less often described are explicit responses to mild or moderate professionalism concerns in medical students. To address this need, Baylor College of Medicine created a mechanism to assess professionalism competency for medical students and policies to address breaches in professional behavior. This article describes the development of an intervention using a guided reflection model, student responses to the intervention, and how the program evolved into a credible resource for deans and other educational leaders.
doi:10.3109/0142159X.2014.911270
PMCID: PMC4229483  PMID: 24819504
12.  A One-Page Summary Report of Genome Sequencing for the Healthy Adult 
Public health genomics  2015;18(2):123-129.
As genome sequencing technologies increasingly enter medical practice, genetics laboratories must communicate sequencing results effectively to non-geneticist physicians. We describe the design and delivery of a clinical genome sequencing report, including a one-page summary suitable for interpretation by primary care physicians. To illustrate our preliminary experience with this report, we summarize the genomic findings from ten healthy patient participants in a study of genome sequencing in primary care.
doi:10.1159/000370102
PMCID: PMC4348325  PMID: 25612602
whole genome sequencing; genomic screening; laboratory reporting; molecular testing
13.  Marginally scientific? Genetic testing of children and adolescents for lifestyle and health promotion 
doi:10.1093/jlb/lsv038
PMCID: PMC5034400  PMID: 27774215
Direct-to-consumer genetic testing; genetic testing of adolescents; genetic testing of children; genetic testing policy; genetic testing regulation
14.  ‘Someday it will be the norm’: physician perspectives on the utility of genome sequencing for patient care in the MedSeq Project 
Personalized medicine  2015;12(1):23-32.
Aim
To describe practicing physicians’ perceived clinical utility of genome sequencing.
Materials & methods
We conducted a mixed-methods analysis of data from 18 primary care physicians and cardiologists in a study of the clinical integration of whole-genome sequencing. Physicians underwent brief genomics continuing medical education before completing surveys and semi-structured interviews.
Results
Physicians described sequencing as currently lacking clinical utility because of its uncertain interpretation and limited impact on clinical decision-making, but they expressed the idea that its clinical integration was inevitable. Potential clinical uses for sequencing included complementing other clinical information, risk stratification, motivating patient behavior change and pharmacogenetics.
Conclusion
Physicians given genomics continuing medical education use the language of both evidence-based and personalized medicine in describing the utility of genome-wide testing in patient care.
doi:10.2217/PME.14.68
PMCID: PMC4306284  PMID: 25642274
genomics; high-throughput nucleotide sequencing; pharmacogenetics; physician’s practice patterns; qualitative research
15.  Do recent US Supreme Court rulings on patenting of genes and genetic diagnostics affect the practice of genetic screening and diagnosis in prenatal and reproductive care? 
Prenatal diagnosis  2014;34(10):921-926.
Thousands of patents have been awarded that claim human gene sequences and their uses, and some have been challenged in court. In a recent high-profile case, Association for Molecular Pathology, et al. vs. Myriad Genetics, Inc., et al., the United States Supreme Court ruled that genes are natural occurring substances and therefore not patentable through “composition of matter” claims. The consequences of this ruling will extend well beyond ending Myriad's monopoly over BRCA testing, and may affect similar monopolies of other commercial laboratories for tests involving other genes. It could also simplify intellectual property issues surrounding genome-wide clinical sequencing, which can generate results for genes covered by intellectual property. Non-invasive prenatal testing (NIPT) for common aneuploidies using cell-free fetal (cff) DNA in maternal blood is currently offered through commercial laboratories and is also the subject of ongoing patent litigation. The recent Supreme Court decision in the Myriad case has already been invoked by a lower district court in NIPT litigation and resulted in invalidation of primary claims in a patent on currently marketed cffDNA-based testing for chromosomal aneuploidies.
doi:10.1002/pd.4445
PMCID: PMC4293120  PMID: 24989832
16.  It depends whose data are being shared: considerations for genomic data sharing policies 
There is an urgent need for consistent data sharing policies that promote the advancement of science while respecting the values and interests of those providing their genetic data for research. Responding to the article of Jalayne J. Arias, Genevieve Pham-Kanter, and Eric G. Campbell, ‘The Growth and Gaps of Genetic Data Sharing Policies in the United States’, this commentary further explores the challenges of human subjects’ protection in existing data sharing policies. We will elaborate on the need for data sharing policies to accommodate variation in individual and group preferences around data sharing and privacy concerns by comparing our previously published data on patients’ and parents’ consent to data sharing and attitudes about privacy to data from focus groups with HIV-positive, underserved individuals who were asked about their willingness to participate in genetic research and share their data broadly. These studies support the observation of Arias, Pham-Kanter, and Campbell that researchers, and funding agencies will need to balance the privacy interests of groups as well as individuals in future genomic data sharing policies.
doi:10.1093/jlb/lsv030
PMCID: PMC5034404  PMID: 27774218
data sharing; genomic; research; policy; privacy; trust
17.  ASSESSING THE UTILITY OF CLINICAL TUMOR SEQUENCING IN THE PEDIATRIC NEURO-ONCOLOGY CLINIC 
Neuro-Oncology  2014;16(Suppl 3):iii24.
BACKGROUND: Additional insight into the molecular alterations driving pediatric central nervous system (CNS) tumors is urgently needed, given the significant morbidity and mortality associated with these cancers and the relative paucity of effective chemotherapeutic options. Advances in sequencing technologies now allow for provision of genome-scale data to oncologists caring for pediatric cancer patients but current experience with the clinical application of genomic sequencing is limited. 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 whole exome sequencing (WES) into the care of children with newly diagnosed solid tumors. METHODS: The study follows pediatric patients with newly diagnosed CNS and non-CNS solid tumors (target enrollment n = 280) at Texas Children's Cancer Center for two years after performing CLIA-certified whole exome sequencing (WES) of blood and frozen tumor samples. Results are deposited into the electronic medical record and disclosed to families by their oncologist and a genetic counselor. The potential impact of tumor exome findings on clinical decision-making is assessed through review of the medical record and through surveys of the oncologists regarding prioritization of treatment options in the hypothetical event of tumor recurrence. RESULTS: To date, 133 subjects have been enrolled, including 47 patients with CNS tumors (35%) comprising a diverse representation of diagnoses. Despite limited diagnostic biopsies in many patients, tumor samples adequate for WES were obtained from 33/47 (70%) patients. Tumor WES results have been reported for the first 22 CNS tumors, revealing a median of 7 (range of 0 to 25) protein-altering mutations per tumor, including alterations of known cancer genes such as ARID1A, SMARCA4, BRAF, CTNNB1, DDX3X, NF2, FANCA, and NOTCH3. Notably, 12/22 (55%) tumors were found to harbour mutations only in genes not known to be recurrently altered in human cancers. CONCLUSIONS: These results demonstrate the feasibility of routine tumor WES in the pediatric neuro- oncology clinic. Potentially clinically-relevant mutations can be identified in a substantial proportion of patients but early results suggest that integration of parallel genomic technologies (e.g. RNAseq) to identify genetic alterations not detectable by WES will be necessary; such studies are ongoing. Orthotopic xenograft models and cell lines are being established to allow in vitro and in vivo analysis of tumors containing alterations of interest. Data further assessing the clinical utility of the tumor exomes are under study. Supported by NHGRI/NCI 1U01HG006485. SECONDARY CATEGORY: Neuropathology & Tumor Biomarkers.
doi:10.1093/neuonc/nou208.5
PMCID: PMC4144597
18.  Secondary findings and carrier test frequencies in a large multiethnic sample 
Genome Medicine  2015;7(1):54.
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.
doi:10.1186/s13073-015-0171-1
PMCID: PMC4507324  PMID: 26195989
19.  Pediatric Data Sharing in Genomic Research: Attitudes and Preferences of Parents 
Pediatrics  2014;133(4):690-697.
OBJECTIVE:
In the United States, data from federally funded genomics studies are stored in national databases, which may be accessible to anyone online (public release) or only to qualified researchers (restricted release). The availability of such data exposes participants to privacy risk and limits the ability to withdraw from research. This exposure is especially challenging for pediatric participants, who are enrolled in studies with parental permission. The current study examines genomic research participants’ attitudes to explore differences in data sharing (DS) preferences between parents of pediatric patients and adult patients.
METHODS:
A total of 113 parents of pediatric patients and 196 adult participants from 6 genomics studies were randomly assigned to 3 experimental consent forms. Participants were invited to a follow-up structured interview exploring DS preferences, study understanding, and attitudes. Descriptive analyses and regression models were built on responses.
RESULTS:
Most parents (73.5%) and adult participants (90.3%) ultimately consented to broad public release. However, parents were significantly more restrictive in their data release decisions, not because of understanding or perceived benefits of participation but rather autonomy and control. Parents want to be more involved in the decision about DS and are significantly more concerned than adult participants about unknown future risks.
CONCLUSIONS:
Parents have the same altruistic motivations and grasp of genomics studies as adult participants. However, they are more concerned about future risks to their child, which probably motivates them to choose more restrictive DS options, but only when such options are made available.
doi:10.1542/peds.2013-1592
PMCID: PMC3966500  PMID: 24616359
data sharing; parents; public release; restricted release; tiered consent; participant perspectives
20.  How behavioral economics can help to avoid ‘The last mile problem’ in whole genome sequencing 
Genome Medicine  2015;7(1):3.
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.
doi:10.1186/s13073-015-0132-8
PMCID: PMC4302430  PMID: 25614766
21.  Experiences and Attitudes of Genome Investigators Regarding Return of Individual Genetic Test Results 
Purpose
Whether and how to return individual genetic results to study participants is among the most contentious policy issues in contemporary genomic research.
Methods
We surveyed corresponding authors of genome-wide association studies (GWAS), identified through the National Human Genome Research Institute's Catalog of Published GWAS, to describe the experiences and attitudes of these stakeholders.
Results
Of 357 corresponding authors, 200 (56%) responded. One hundred twenty-six (63%) had been responsible for primary data and sample collection, whereas 74 (37%) had performed secondary analyses. Only 7 (4%) had returned individual results within their index GWAS. Most (69%) believed that return of results to individual participants was warranted under at least some circumstances. Most respondents identified a desire to benefit participants's health (63%) and respect for participants's; desires for information (57%) as major motivations for returning results. Most also identified uncertain clinical utility (76%), the possibility that participants will misunderstand results (74%), the potential for emotional harm (61%), the need to ensure access to trained clinicians (59%), and the potential for loss of confidentiality (51%) as major barriers to return.
Conclusion
Investigators have limited experience returning individual results from genome-scale research, yet most are motivated to do so in at least some circumstances.
doi:10.1038/gim.2013.58
PMCID: PMC4143384  PMID: 23639901
22.  Social and behavioral research in genomic sequencing: approaches from the Clinical Sequencing Exploratory Research Consortium Outcomes and Measures Working Group 
The routine use of genomic sequencing in clinical medicine has the potential to dramatically alter patient care and medical outcomes. To fully understand the psychosocial and behavioral impact of sequencing integration into clinical practice, it is imperative that we identify the factors that influence sequencing-related decision making and patient outcomes. In an effort to develop a collaborative and conceptually grounded approach to studying sequencing adoption, members of the National Human Genome Research Institute's Clinical Sequencing Exploratory Research Consortium formed the Outcomes and Measures Working Group. Here we highlight the priority areas of investigation and psychosocial and behavioral outcomes identified by the Working Group. We also review some of the anticipated challenges to measurement in social and behavioral research related to genomic sequencing; opportunities for instrument development; and the importance of qualitative, quantitative, and mixed-method approaches. This work represents the early, shared efforts of multiple research teams as we strive to understand individuals' experiences with genomic sequencing. The resulting body of knowledge will guide recommendations for the optimal use of sequencing in clinical practice.
doi:10.1038/gim.2014.26
PMCID: PMC4163120  PMID: 24625446
behavior; genome sequencing; measures; outcomes; psychosocial
23.  Obtaining informed consent for clinical tumor and germline exome sequencing of newly diagnosed childhood cancer patients 
Genome Medicine  2014;6(9):69.
Background
Effectively educating families about the risks and benefits of genomic tests such as whole exome sequencing (WES) offers numerous challenges, including the complexity of test results and potential loss of privacy. Research on best practices for obtaining informed consent (IC) in a variety of clinical settings is needed. The BASIC3 study of clinical tumor and germline WES in an ethnically diverse cohort of newly diagnosed pediatric cancer patients offers the opportunity to study the IC process in the setting of critical illness. We report on our experience for the first 100 families enrolled, including study participation rates, reasons for declining enrollment, assessment of clinical and demographic factors that might impact study enrollment, and preferences of parents for participation in optional genomics study procedures.
Methods
A specifically trained IC team offered study enrollment to parents of eligible children for procedures including clinical tumor and germline WES with results deposited in the medical record and disclosure of both diagnostic and incidental results to the family. Optional study procedures were also offered, such as receiving recessive carrier status and deposition of data into research databases. Stated reasons for declining participation were recorded. Clinical and demographic data were collected and comparisons made between enrolled and non-enrolled patients.
Results
Over 15 months, 100 of 121 (83%) eligible families elected to enroll in the study. No significant differences in enrollment were detected based on factors such as race, ethnicity, use of Spanish interpreters and Spanish consent forms, and tumor features (central nervous system versus non-central nervous system, availability of tumor for WES). The most common reason provided for declining enrollment (10% of families) was being overwhelmed by the new cancer diagnosis. Risks specific to clinical genomics, such as privacy concerns, were less commonly reported (5.5%). More than 85% of parents consented to each of the optional study procedures.
Conclusions
An IC process was developed that utilizes a specialized IC team, active communication with the oncology team, and an emphasis on scheduling flexibility. Most parents were willing to participate in a clinical germline and tumor WES study as well as optional procedures such as genomic data sharing independent of race, ethnicity or language spoken.
Electronic supplementary material
The online version of this article (doi:10.1186/s13073-014-0069-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s13073-014-0069-3
PMCID: PMC4195891  PMID: 25317207
24.  Open Access Data Sharing in Genomic Research 
Genes  2014;5(3):739-747.
The current emphasis on broad sharing of human genomic data generated in research in order to maximize utility and public benefit is a significant legacy of the Human Genome Project. Concerns about privacy and discrimination have led to policy responses that restrict access to genomic data as the means for protecting research participants. Our research and experience show, however, that a considerable number of research participants agree to open access sharing of their genomic data when given the choice. General policies that limit access to all genomic data fail to respect the autonomy of these participants and, at the same time, unnecessarily limit the utility of the data. We advocate instead a more balanced approach that allows for individual choice and encourages informed decision making, while protecting against the misuse of genomic data through enhanced legislation.
doi:10.3390/genes5030739
PMCID: PMC4198928  PMID: 25178093
data sharing; genomics; privacy; genetic discrimination; open access database

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