Implementing genomic medicine in the clinic: the future is here

Secondary findings from whole-exome/genome sequencing evaluating stakeholder perspectives. A review of the literature

With the development of next generation sequencing, beyond identifying the cause of manifestations that justified prescription of the test, other information with potential interest for patients and their families, defined as secondary findings (SF), can be provided once patients have given informed consent, in particular when therapeutic and preventive options are available. The disclosure of such findings has caused much debate. The aim of this work was to summarize all opinion-based studies focusing on SF, so as to shed light on the concerns that this question generate. A review of the literature was performed, focusing on all PubMed articles reporting qualitative, quantitative or mixed studies that interviewed healthcare providers, participants, or society regarding this subject. The methodology was carefully analysed, in particular whether or not studies made the distinction between actionable and non-actionable SF, in a clinical or research context. From 2010 to 2016, 39 articles were compiled. A total of 14,868 people were interviewed (1259 participants, 6104 healthcare providers, 7505 representatives of society). When actionable and non-actionable SF were distinguished (20 articles), 92% of respondents were keen to have results regarding actionable SF (participants: 88%, healthcare providers: 86%, society: 97%), against 70% (participants: 83%, healthcare providers: 62%, society: 73%) for non-actionable SF. These percentages were slightly lower in the specific situation of children probands. For respondents, the notion of the «patient's choice» is crucial. For healthcare providers, the importance of defining policies for SF among diagnostic lab, learning societies and/or countries is outlined, in particular regarding the content and extension of the list of actionable genes to propose, the modalities of information, and the access to information about adult-onset diseases in minors. However, the existing literature should be taken with caution, since most articles lack a clear definition of SF and actionability, and referred to hypothetical scenarios with limited information to respondents. Studies conducted by multidisciplinary teams involving patients with access to results are sadly lacking, in particular in the medium term after the results have been given. Such studies would feed the debate and make it possible to measure the impact of such findings and their benefit-risk ratio.

Academic Medical Centers as Innovation Ecosystems: Evolution of Industry Partnership Models Beyond the Bayh-Dole Act

Innovation ecosystems tied to academic medical centers (AMCs) are inextricably linked to policy, practices, and infrastructure resulting from the Bayh-Dole Act in 1980. Bayh-Dole smoothed the way to patenting and licensing new drugs and, to some degree, medical devices and diagnostic reagents. Property rights under Bayh-Dole provided significant incentive for industry investments in clinical trials, clinical validation, and industrial scale-up of products that advanced health care. Bayh-Dole amplified private investment in biotechnology drug development and, from the authors' perspective, did not significantly interfere with the ability of AMCs to produce excellent peer-reviewed science. In today's policy environment, it is increasingly difficult to patent and license products based on the laws of nature-as the scope of patentability has been narrowed by case law and development of a suitable clinical and business case for the technology is increasingly a gating consideration for licensees. Consequently, fewer academic patents are commercially valuable. The role of technology transfer organizations in engaging industry partners has thus become increasingly complex. The partnering toolbox and organizational mandate for commercialization must evolve toward novel collaborative models that exploit opportunities for future patent creation (early drug discovery), data exchange (precision medicine using big data), cohort assembly (clinical trials), and decision rule validation (clinical trials). These inputs contribute to intellectual property rights, and their clinical exploitation manifests the commercialization of translational science. New collaboration models between AMCs and industry must be established to leverage the assets within AMCs that industry partners deem valuable.

Harmonizing Outcomes for Genomic Medicine: Comparison of eMERGE Outcomes to ClinGen Outcome/Intervention Pairs

Genomic medicine is moving from research to the clinic. There is a lack of evidence about the impact of genomic medicine interventions on health outcomes. This is due in part to a lack of standardized outcome measures that can be used across different programs to evaluate the impact of interventions targeted to specific genetic conditions. The eMERGE Outcomes working group (OWG) developed measures to collect information on outcomes following the return of genomic results to participants for several genetic disorders. These outcomes were compared to outcome intervention pairs for genetic disorders developed independently by the ClinGen Actionability working group (AWG). In general, there was concordance between the defined outcomes between the two groups. The ClinGen outcomes tended to be from a higher level and the AWG scored outcomes represented a subset of outcomes referenced in the accompanying AWG evidence review. eMERGE OWG outcomes were more detailed and discrete, facilitating a collection of relevant information from the health records. This paper demonstrates that common outcomes for genomic medicine interventions can be identified. Further work is needed to standardize outcomes across genomic medicine implementation projects and to make these publicly available to enhance dissemination and assist in making precision public health a reality.

Cytochrome P450 genotype-guided drug therapies: An update on current states

Over the past 2 decades, knowledge of the role and clinical value of pharmacogenetic markers has expanded so that individualized pre-emptive therapy based on genetic background of patients could be within reach for clinical implementation. This is evidenced from the frequent updating of drug labels that incorporates pharmacogenetic information (where compelling data become available) by the regulatory agencies (such as the US FDA), and the periodical publication of guidelines of specific therapeutic recommendations based on the results of pharmacogenetic tests by the pharmacogenetics working groups or consortiums of professional bodies. Clinical relevance of the cytochrome P450 (CYP) polymorphism related to dose, effectiveness and/or toxicity of key drugs are presented in this review, including that of warfarin, clopidogrel, tricyclic antidepressants, and proton pump inhibitors. Prospect for routine clinical application of CYP genotyping before prescribing drugs is still currently unclear due to challenges and barriers associated with availability of well-defined and validated pharmacogenetic studies, the interpretation, result reporting and potential error of genotype testing, involvement of non-genetic factors, and other patient's demographic and disease conditions. Further studies to provide additional supporting clinical data and acceleration of pharmacogenetic testing standards and techniques should help improve the evidence base needed for clinical utility and hence move the implementation of genotype-guided therapy in clinical practice a step closer to reality.

Genomics-informed weight management in primary care: anticipated public interest

Aim: An exploratory survey assessed the influence of current and potential future genomic applications for weight management on individuals’ desires to address weight management within primary care. Materials & methods: A convenience sample of 714 US adults aged 18–70 completed an online survey that presented three scenarios: no genomic information; current genomic capabilities; and potential future applications of genomics for weight management. Results: Participants had increased interest in weight management assistance through primary care when considering genomic applications in weight management, p (1,1.68) = 24.66, p < 0.001; this increase was more robust among individuals who felt their weight was important for their health, p (1,1.68) = 20.85, p < 0.001. Conclusion: Primary care systems may need to accommodate a rise in the volume of patients seeking weight management assistance as genomic approaches come to fruition.

Generation and Implementation of a Patient-Centered and Patient-Facing Genomic Test Report in the EHR

Context

Communication of genetic laboratory results to patients and providers is impeded by the complexity of results and reports. This can lead to misinterpretation of results, causing inappropriate care. Patients often do not receive a copy of the report leading to possible miscommunication. To address these problems, we conducted patient-centered research to inform design of interpretive reports. Here we describe the development and deployment of a specific patient-centered clinical decision support (CDS) tool, a multi-use patient-centered genomic test report (PGR) that interfaces with an electronic health record (EHR).

Implementation Process

A PGR with a companion provider report was configured for implementation within the EHR using locally developed software (COMPASS™) to manage secure data exchange and access.

Findings

We conducted semi-structured interviews with patients, family members, and clinicians that showed they sought clear information addressing findings, family implications, resources, prognosis and next steps relative to the genomic result. Providers requested access to applicable, available clinical guidelines. Initial results indicated patients and providers found the PGR contained helpful, valuable information and would provide a basis for result-related conversation between patients, providers and family.

Major Themes

Direct patient involvement in the design and development of a PGR identified format and presentation preferences, and delivery of relevant information to patients and providers, prompting the creation of a CDS tool.

Conclusions

Research and development of patient-centered CDS tools designed to support improved patient outcomes, are enhanced by early and substantial engagement of patients in contributing to all phases of tool design and development.

Internet Versus Virtual Reality Settings for Genomics Information Provision

Current models of genomic information provision will be unable to handle large-scale clinical integration of genomic information, as may occur in primary care settings. Therefore, adoption of digital tools for genetic and genomic information provision is anticipated, primarily using Internet-based, distributed approaches. The emerging consumer communication platform of virtual reality (VR) is another potential intermediate approach between face-to-face and distributed Internet platforms to engage in genomics education and information provision. This exploratory study assessed whether provision of genomics information about body weight in a simulated, VR-based consultation (relative to a distributed, Internet platform) would be associated with differences in health behavior-related attitudes and beliefs, and interpersonal reactions to the avatar-physician. We also assessed whether outcomes differed depending upon whether genomic versus lifestyle-oriented information was conveyed. There were significant differences between communication platforms for all health behavior-oriented outcomes. Following communication in the VR setting, participants reported greater self-efficacy, dietary behavioral intentions, and exercise behavioral intentions than in the Internet-based setting. There were no differences in trust of the physician by setting, and no interaction between setting effects and the content of the information. This study was a first attempt to examine the potential capabilities of a VR-based communication setting for conveying genomic content in the context of weight management. There may be benefits to use of VR settings for communication about genomics, as well as more traditional health information, when it comes to influencing the attitudes and beliefs that underlie healthy lifestyle behaviors.

Physician Knowledge of Human Genetic Variation, Beliefs About Race and Genetics, and Use of Race in Clinical Decision-making

BACKGROUND

Race in the USA has an enduring connection to health and well-being. It is often used as a proxy for ancestry and genetic variation, although self-identified race does not establish genetic risk of disease for an individual patient. How physicians reconcile these seemingly paradoxical facts as they make clinical decisions is unknown.

OBJECTIVE

To examine physicians' genetic knowledge and beliefs about race with their use of race in clinical decision-making DESIGN: Cross-sectional survey of a national sample of clinically active general internists RESULTS: Seven hundred eighty-seven physicians completed the survey. Regression models indicate that genetic knowledge was not significantly associated with use of race. However, physicians who agreed with notions of race as a biological phenomenon and those who agreed that race has clinical importance were more likely to report using race in their decision-making.

CONCLUSIONS

Genomic and precision medicine holds considerable promise for narrowing the gap in health among racial groups in the USA. For this promise to be realized, our findings suggest that future research and education efforts related to race, genomics, and health must go beyond educating health care providers about common genetic conditions to delving into assumptions about race and genetics.

Pharmacogenetic testing in the Veterans Health Administration (VHA): policy recommendations from the VHA Clinical Pharmacogenetics Subcommittee

Purpose:

The Veterans Health Administration (VHA) Clinical Pharmacogenetics Subcommittee is charged with making recommendations about whether specific pharmacogenetic tests should be used in healthcare at VHA facilities. We describe a process to inform VHA pharmacogenetic testing policy.

Methods:

After developing consensus definitions of clinical validity and utility, the Subcommittee identified salient drug-gene pairs with potential clinical application in VHA. Members met monthly to discuss each drug-gene pair, the evidence of clinical utility for the associated pharmacogenetic test, and any VHA-specific testing considerations. The Subcommittee classified each test as strongly recommended, recommended, or not routinely recommended before drug initiation.

Results:

Of 30 drug-gene pair tests reviewed, the Subcommittee classified 4 (13%) as strongly recommended, including HLA-B*15:02 for carbamazepine-associated Stevens-Johnston syndrome and G6PD for rasburicase-associated hemolytic anemia; 12 (40%) as recommended, including CYP2D6 for codeine toxicity; and 14 (47%) as not routinely recommened, such as CYP2C19 for clopidogrel dosing.

Conclusion:

Only half of drug-gene pairs with high clinical validity received Subcommittee support for policy promoting their widespread use across VHA. The Subcommittee generally found insufficient evidence of clinical utility or available, effective alternative strategies for the remainders. Continual evidence review and rigorous outcomes research will help promote the translation of pharmacogenetic discovery to healthcare.

Implementation of a patient-facing genomic test report in the electronic health record using a web-application interface

Background

Genomic medicine is emerging into clinical care. Communication of genetic laboratory results to patients and providers is hampered by the complex technical nature of the laboratory reports. This can lead to confusion and misinterpretation of the results resulting in inappropriate care. Patients usually do not receive a copy of the report leading to further opportunities for miscommunication. To address these problems, interpretive reports were created using input from the intended end users, patients and providers. This paper describes the technical development and deployment of the first patient-facing genomic test report (PGR) within an electronic health record (EHR) ecosystem using a locally developed standards-based web-application interface.

Methods

A patient-facing genomic test report with a companion provider report was configured for implementation within the EHR using a locally developed software platform, COMPASS™. COMPASS™ is designed to manage secure data exchange, as well as patient and provider access to patient reported data capture and clinical display tools. COMPASS™ is built using a Software as a Service (SaaS) approach which exposes an API that apps can interact with.

Results

An authoring tool was developed that allowed creation of patient-specific PGRs and the accompanying provider reports. These were converted to a format that allowed them to be presented in the patient portal and EHR respectively using the existing COMPASS™ interface thus allowing patients, caregivers and providers access to individual reports designed for the intended end user.

Conclusions

The PGR as developed was shown to enhance patient and provider communication around genomic results. It is built on current standards but is designed to support integration with other tools and be compatible with emerging opportunities such as SMART on FHIR. This approach could be used to support genomic return of results as the tool is scalable and generalizable.

The Genomic Consultation Service: A clinical service designed to improve patient selection for genome-wide sequencing in British Columbia

BACKGROUND

Access to clinical diagnostic genome-wide sequencing (GWS; exome or whole genome sequencing) is limited in British Columbia. The establishment of a translational research initiative (CAUSES) to provide diagnostic genome-wide sequencing for 500 children necessitated the development of a genomic consultation service, a clinical service established to provide consultation for physicians considering GWS for their pediatric patients throughout British Columbia. The Genomic Consultation Service provides patient-specific genomic advice that may include: GWS, multi-gene panel, single gene test, referral to medical genetics for clinical evaluation, or no genetic testing. Here, we describe and evaluate this service.

METHODS

We analyzed referral patterns, patient demographics, clinical indications, and genomic advice provided during the first year of this service. Comparison of outcomes from the first 6 months versus the last 6 months was performed.

RESULTS

A total of 407 referrals (238 males and 169 females [p = .0006]) were processed in the first year. Only children were eligible for referral and average patient age was 8 years. Medical genetics was the most frequent referring discipline, followed by biochemical disease and pediatric neurology, respectively. Most patients (68%) had syndromic intellectual disability. There was a significant difference in the frequency of referrals not appropriate for GWS in the first versus the second 6 months of the service (75/220 vs. 42/187; p = .01) suggesting increasing awareness of testing criteria by referring physicians.

CONCLUSION

This triage service is utilized throughout the province and appears to be an important factor in the high diagnostic rate (>40%) achieved in our GWS program.

Clinical Application of Genome and Exome Sequencing as a Diagnostic Tool for Pediatric Patients: a Scoping Review of the Literature

PURPOSE

Availability of clinical genomic sequencing (CGS) has generated questions about the value of genome and exome sequencing as a diagnostic tool. Analysis of reported CGS application can inform uptake and direct further research. This scoping literature review aims to synthesize evidence on the clinical and economic impact of CGS.

METHODS

PubMed, Embase, and Cochrane were searched for peer-reviewed articles published between 2009 and 2017 on diagnostic CGS for infant and pediatric patients. Articles were classified according to sample size and whether economic evaluation was a primary research objective. Data on patient characteristics, clinical setting, and outcomes were extracted and narratively synthesized.

RESULTS

Of 171 included articles, 131 were case reports, 40 were aggregate analyses, and 4 had a primary economic evaluation aim. Diagnostic yield was the only consistently reported outcome. Median diagnostic yield in aggregate analyses was 33.2% but varied by broad clinical categories and test type.

CONCLUSION

Reported CGS use has rapidly increased and spans diverse clinical settings and patient phenotypes. Economic evaluations support the cost-saving potential of diagnostic CGS. Multidisciplinary implementation research, including more robust outcome measurement and economic evaluation, is needed to demonstrate clinical utility and cost-effectiveness of CGS.

Clinical pharmacogenomics testing in the era of next generation sequencing: challenges and opportunities for precision medicine

INTRODUCTION

The rapid development and dramatic decrease in cost of sequencing techniques have ushered the implementation of genomic testing in patient care. Next generation DNA sequencing (NGS) techniques have been used increasingly in clinical laboratories to scan the whole or part of the human genome in order to facilitate diagnosis and/or prognostics of genetic disease. Despite many hurdles and debates, pharmacogenomics (PGx) is believed to be an area of genomic medicine where precision medicine could have immediate impact in the near future. Areas covered: This review focuses on lessons learned through early attempts of clinically implementing PGx testing; the challenges and opportunities that PGx testing brings to precision medicine in the era of NGS. Expert commentary: Replacing targeted analysis approach with NGS for PGx testing is neither technically feasible nor necessary currently due to several technical limitations and uncertainty involved in interpreting variants of uncertain significance for PGx variants. However, reporting PGx variants out of clinical whole exome or whole genome sequencing (WES/WGS) might represent additional benefits for patients who are tested by WES/WGS.

Tensions in ethics and policy created by National Precision Medicine Programs

Precision medicine promises to use genomics and other data-intensive approaches to improve diagnosis and develop new treatments for major diseases, but also raises a range of ethical and governance challenges. Implementation of precision medicine in “real world” healthcare systems blurs the boundary between research and care. This has implications for the meaning and validity of consent, and increased potential for discrimination, among other challenges. Increased sharing of personal information raises concerns about privacy, commercialization, and public trust. This paper considers national precision medicine schemes from the USA, the UK, and Japan, comparing how these challenges manifest in each national context and examining the range of approaches deployed to mitigate the potential undesirable social consequences. There is rarely a “one size” fits all solution to these complex problems, but the most viable approaches are those which take account of cultural preferences and attitudes, available resources, and the wider political landscape in which national healthcare systems are embedded.

Paediatricians underuse recommended genetic tests in children with global developmental delay

Objectives

To assess paediatricians' use of genetic testing for children with global developmental delay (GDD).

Study Design

We developed and piloted a questionnaire assessing the use of genetic tests in children with GDD and awareness of relevant guidelines. All practicing Quebec paediatricians were contacted. Paediatricians who did not evaluate children with GDD in their practice were excluded. Descriptive and statistical analyses were performed with SPSS.

Results

Of the 651 paediatricians, 225 answered (34.5%) and 141 were eligible. Only 31.9% were familiar with at least one guideline about genetic tests for the investigation of children with GDD, but 93.6% had ordered genetic testing for children with GDD (Fragile X testing [92.9%], karyotype [87.2%] and chromosomal microarray [63.8%]). Based on vignettes, 20.6% of participants would order genetic tests for isolated GDD and 95.0% for GDD with dysmorphic features and microcephaly. Only 56.7% ordered Fragile X testing for a girl with GDD and a known family history of Fragile X syndrome. Use of tests for isolated GDD was increased in presence of maternal pregnancy, compared with absence of pregnancy (44.7% and 27.7%, respectively). More participants would order genetic tests for a child with GDD and fetal exposure to alcohol (69.5%) than isolated GDD (20.6%).

Conclusions

Even though paediatricians often order genetic testing for children with GDD, practices and knowledge regarding testing are not optimal. As new and more complex genetic tests are developed, up-to-date training about the use of genetic tests for children with GDD needs to be integrated into paediatrics residency programs and continuous medical education.

The challenges of the expanded availability of genomic information: an agenda-setting paper

Rapid advances in microarray and sequencing technologies are making genotyping and genome sequencing more affordable and readily available. There is an expectation that genomic sequencing technologies improve personalized diagnosis and personalized drug therapy. Concurrently, provision of direct-to-consumer genetic testing by commercial providers has enabled individuals' direct access to their genomic data. The expanded availability of genomic data is perceived as influencing the relationship between the various parties involved including healthcare professionals, researchers, patients, individuals, families, industry, and government. This results in a need to revisit their roles and responsibilities. In a 1-day agenda-setting meeting organized by the COST Action IS1303 "Citizen's Health through public-private Initiatives: Public health, Market and Ethical perspectives," participants discussed the main challenges associated with the expanded availability of genomic information, with a specific focus on public-private partnerships, and provided an outline from which to discuss in detail the identified challenges. This paper summarizes the points raised at this meeting in five main parts and highlights the key cross-cutting themes. In light of the increasing availability of genomic information, it is expected that this paper will provide timely direction for future research and policy making in this area.

Research Directions in the Clinical Implementation of Pharmacogenomics: An Overview of US Programs and Projects

Response to a drug often differs widely among individual patients. This variability is frequently observed not only with respect to effective responses but also with adverse drug reactions. Matching patients to the drugs that are most likely to be effective and least likely to cause harm is the goal of effective therapeutics. Pharmacogenomics (PGx) holds the promise of precision medicine through elucidating the genetic determinants responsible for pharmacological outcomes and using them to guide drug selection and dosing. Here we survey the US landscape of research programs in PGx implementation, review current advances and clinical applications of PGx, summarize the obstacles that have hindered PGx implementation, and identify the critical knowledge gaps and possible studies needed to help to address them.

Patient perspectives following pharmacogenomics results disclosure in an integrated health system

Aim: To assess patient perceptions and utilization of pharmacogenomics (PGx) testing in an integrated community health system. Methods: Fifty-seven patients completed an online survey assessing their experiences with PGx testing offered through two methods: a designated PGx clinic or direct access in-home testing. Results: The majority of participants perceived PGx testing as helpful in their healthcare and reported understanding their results. Some had concerns about privacy and discrimination; most lacked familiarity with the Genetic Information Nondiscrimination Act. There were no significant differences in views between participants tested through either model. Conclusion: Participants reported value in both methods of PGx testing. Patient experiences, understanding and result utilization will play an important role in informing future development and implementation of PGx programs.

Clinical application of pharmacogenetics in pain management

There is growing experience translating genomic data into clinical practice, as seen with the Implementing GeNomics In pracTicE (IGNITE) network. A primary example is the influence of CYP2D6 genotype on the beneficial and adverse effects of some opioids. Clinical recommendations exist to guide drug therapy based on CYP2D6 genotype for codeine, tramadol, oxycodone and hydrocodone, although the level of supporting evidence differs by drug. Limited evidence also supports the use of genetic data to guide other medications in chronic pain therapy, including tricyclic antidepressants and celecoxib. Pragmatic clinical trial data are needed in this area to better understand the impact of diverse populations, therapeutic interventions and clinical care environments on genotype-guided drug therapy for chronic pain.

Toward the implementation of genomic applications for smoking cessation and smoking-related diseases

The incorporation of genomic information into routine care settings is a burgeoning area for investigation in behavioral medicine. The past decade has witnessed rapid advancements in knowledge of genetic biomarkers associated with smoking behaviors and tobacco-related morbidity and mortality, providing the basis for promising genomic applications in clinical and community settings. We assessed the current state of readiness for implementing genomic applications involving variation in the α5 nicotinic cholinergic receptor subunit gene CHRNA5 and smoking outcomes (behaviors and related diseases) using a process that could be translatable to a wide range of genomic applications in behavioral medicine. We reviewed the scientific literature involving CHRNA5 genetic variation and smoking cessation, and then summarized and synthesized a chain of evidence according to analytic validity, clinical validity, clinical utility, and ethical, legal, and social implications (ACCE), a well-established set of criteria used to evaluate genomic applications. Our review identified at least three specific genomic applications for which implementation may be considered, including the use of CHRNA5 genetic test results for informing disease risk, optimizing smoking cessation treatment, and motivating smoking behavior change. For these genomic applications, we rated analytic validity as convincing, clinical validity as adequate, and clinical utility and ethical, legal, and social implications as inadequate. For clinical genomic applications involving CHRNA5 variation and smoking outcomes, research efforts now need to focus on establishing clinical utility. This approach is compatible with pre-implementation research, which is also needed to accelerate translation, improve innovation design, and understand and refine system processes involved in implementation. This study informs the readiness to incorporate smoking-related genomic applications in real-world settings and facilitates cross-disciplinary collaboration to accelerate the integration of evidence-based genomics in behavioral medicine.

Ethical Considerations Related to Return of Results from Genomic Medicine Projects: The eMERGE Network (Phase III) Experience

We examined the Institutional Review Board (IRB) process at 9 academic institutions in the electronic Medical Records and Genomics (eMERGE) Network, for proposed electronic health record-based genomic medicine studies, to identify common questions and concerns. Sequencing of 109 disease related genes and genotyping of 14 actionable variants is being performed in ~28,100 participants from the 9 sites. Pathogenic/likely pathogenic variants in actionable genes are being returned to study participants. We examined each site’s research protocols, informed-consent materials, and interactions with IRB staff. Research staff at each site completed questionnaires regarding their IRB interactions. The time to prepare protocols for IRB submission, number of revisions and time to approval ranged from 10–261 days, 0–11, and 11–90 days, respectively. IRB recommendations related to the readability of informed consent materials, specifying the full range of potential risks, providing options for receiving limited results or withdrawal, sharing of information with family members, and establishing the mechanisms to answer participant questions. IRBs reviewing studies that involve the return of results from genomic sequencing have a diverse array of concerns, and anticipating these concerns can help investigators to more effectively engage IRBs.

Care and cost consequences of pediatric whole genome sequencing compared to chromosome microarray

The clinical use of whole-genome sequencing (WGS) is expected to alter pediatric medical management. The study aimed to describe the type and cost of healthcare activities following pediatric WGS compared to chromosome microarray (CMA). Healthcare activities prompted by WGS and CMA were ascertained for 101 children with developmental delay over 1 year. Activities following receipt of non-diagnostic CMA were compared to WGS diagnostic and non-diagnostic results. Activities were costed in 2016 Canadian dollars (CDN). Ongoing care accounted for 88.6% of post-test activities. The mean number of lab tests was greater following CMA than WGS (0.55 vs. 0.09; p = 0.007). The mean number of specialist visits was greater following WGS than CMA (0.41 vs. 0; p = 0.016). WGS results (diagnostic vs. non-diagnostic) modified the effect of test type on mean number of activities (p < 0.001). The cost of activities prompted by diagnostic WGS exceeded $557CDN for 10% of cases. In complex pediatric care, CMA prompted additional diagnostic investigations while WGS prompted tailored care guided by genotypic variants. Costs for prompted activities were low for the majority and constitute a small proportion of total test costs. Optimal use of WGS depends on robust evaluation of downstream care and cost consequences.

Pharmacogenomics-Based Point-of-Care Clinical Decision Support Significantly Alters Drug Prescribing

Changes in behavior are necessary to apply genomic discoveries to practice. We prospectively studied medication changes made by providers representing eight different medicine specialty clinics whose patients had submitted to preemptive pharmacogenomic genotyping. An institutional clinical decision support (CDS) system provided pharmacogenomic results using traffic light alerts: green = genomically favorable, yellow = genomic caution, red = high risk. The influence of pharmacogenomic alerts on prescribing behaviors was the primary endpoint. In all, 2,279 outpatient encounters were analyzed. Independent of other potential prescribing mediators, medications with high pharmacogenomic risk were changed significantly more often than prescription drugs lacking pharmacogenomic information (odds ratio (OR) = 26.2 (9.0-75.3), P < 0.0001). Medications with cautionary pharmacogenomic information were also changed more frequently (OR = 2.4 (1.7-3.5), P < 0.0001). No pharmacogenomically high-risk medications were prescribed during the entire study when physicians consulted the CDS tool. Pharmacogenomic information improved prescribing in patterns aimed at reducing patient risk, demonstrating that enhanced prescription decision-making is achievable through clinical integration of genomic medicine.

The current state of funded NIH grants in implementation science in genomic medicine: a portfolio analysis

Purpose

Implementation science offers methods to evaluate the translation of genomic medicine research into practice. The extent in which the NIH human genomics grant portfolio includes implementation science is unknown. This brief report’s objective is to describe recently funded implementation science studies in genomic medicine in the NIH grant portfolio, and identify remaining gaps.

Methods

We identified investigator-initiated NIH research grants on implementation science in genomic medicine (funding initiated 2012–2016). A codebook was adapted from the literature, three authors coded grants, and descriptive statistics were calculated for each code.

Results

42 grants fit the inclusion criteria (~1.75% of investigator-initiated genomics grants). The majority of included grants proposed qualitative and/or quantitative methods with cross sectional study designs, and described clinical settings and primarily white, non-Hispanic study populations. Most grants were in oncology and examined genetic testing for risk assessment. Finally, grants lacked the use of implementation science frameworks, and most examined uptake of genomic medicine and/or assessed patient centeredness.

Conclusion

We identified large gaps in implementation science studies in genomic medicine in the funded NIH portfolio over the past five years. To move the genomics field forward, investigator-initiated research grants should employ rigorous implementation science methods within diverse settings and populations.

Pharmacogenetics in Cardiovascular Medicine

PURPOSE OF REVIEW

Pharmacogenetics is an important component of precision medicine. Even within the genomic era, several challenges lie ahead in the road towards clinical implementation of pharmacogenetics in the clinic. This review will summarize the current state of knowledge regarding pharmacogenetics of cardiovascular drugs, focusing on those with the most evidence supporting clinical implementation- clopidogrel, warfarin and simvastatin.

RECENT FINDINGS

There is limited translation of pharmacogenetics into clinical practice primarily due to the absence of outcomes data from prospective, randomized, genotype-directed clinical trials. There are several ongoing randomized controlled trials that will provide some answers as to the clinical utility of genotype-directed strategies. Several academic medical centers have pushed towards clinical implementation where the clinical validity data are strong. Their experiences will inform operational requirements of a clinical pharmacogenetics testing including the timing of testing, incorporation of test results into the electronic health record, reimbursement and ethical issues.

SUMMARY

Pharmacogenetics of clopidogrel, warfarin and simvastatin are three examples where pharmacogenetics testing may provide added clinical value. Continued accumulation of evidence surrounding clinical utility of pharmacogenetics markers is imperative as this will inform reimbursement policy and drive adoption of pharamcogenetics into routine care.

Radiogenomics: Identification of Genomic Predictors for Radiation Toxicity

The overall goal of radiogenomics is the identification of genomic markers that are predictive for the development of adverse effects resulting from cancer treatment with radiation. The principal rationale for a focus on toxicity in radiogenomics is that for many patients treated with radiation, especially individuals diagnosed with early-stage cancers, the survival rates are high, and therefore a substantial number of people will live for a significant period of time beyond treatment. However, many of these patients could suffer from debilitating complications resulting from radiotherapy. Work in radiogenomics has greatly benefited from creation of the Radiogenomics Consortium (RGC) that includes investigators at multiple institutions located in a variety of countries. The common goal of the RGC membership is to share biospecimens and data so as to achieve large-scale studies with increased statistical power to enable identification of relevant genomic markers. A major aim of research in radiogenomics is the development of a predictive instrument to enable identification of people who are at greatest risk for adverse effects resulting from cancer treatment using radiation. It is anticipated that creation of a predictive assay characterized by a high level of sensitivity and specificity will improve precision radiotherapy and assist patients and their physicians to select the optimal treatment for each individual.

Simplifying the use of pharmacogenomics in clinical practice: Building the genomic prescribing system

BACKGROUND

A barrier to the use of genomic information during prescribing is the limited number of software solutions that combine a user-friendly interface with complex medical data. We built and designed an online, secure, electronic custom interface termed the Genomic Prescribing System (GPS).

METHODS

Actionable pharmacogenomic (PGx) information was reviewed, collected, and stored in the back-end of GPS to enable creation of customized drug- and variant-specific clinical decision support (CDS) summaries. The database architecture utilized the star schema to store information. Patient raw genomic data underwent transformation via custom-designed algorithms to enable gene and phenotype-level associations. Multiple external data sets (PubMed, The Systematized Nomenclature of Medicine (SNOMED), National Drug File - Reference Terminology (ND-FRT), and a publically-available PGx knowledgebase) were integrated to facilitate the delivery of patient, drug, disease, and genomic information. Institutional security infrastructure was leveraged to securely store patient genomic and clinical data on a HIPAA-compliant server farm.

RESULTS

As of May 17, 2016, the GPS back-end housed 257 CDS encompassing 112 genetic variants, 42 genes, and 46 PGx-actionable drugs. The GPS user interface presented patient-specific CDS alongside a recognizable traffic light symbol (green/yellow/red), denoting PGx risk for each genomic result. The number of traffic lights per visit increased with the corresponding increase in the number of available PGx-annotated drugs over time. An integrated drug and disease search functionality, links to primary literature sources, and potential alternative PGx drugs were indicated. The system, which was initially used as stand-alone CDS software within our clinical environment, was then integrated with the institutional electronic medical record for enhanced usability. There have been nearly 2000 logins in 43months since inception, with usage exceeding 56 logins per month and system up-times of 99.99%. For all patient-provider visits encompassing >3years of implementation, unique alert click-through rates corresponded to genomic risk: red lights clicked 100%, yellow lights 79%, green lights 43%.

CONCLUSIONS

Successful deployment of GPS by combining complex data and recognizable iconography led to a tool that enabled point-of-care genomic delivery with high usability. Continued scalability and incorporation of additional clinical elements to be considered alongside PGx information could expand future impact.

Developing a common framework for evaluating the implementation of genomic medicine interventions in clinical care: the IGNITE Network's Common Measures Working Group

Purpose

Implementation research provides a structure for evaluating the clinical integration of genomic medicine interventions. This paper describes the Implementing GeNomics In PracTicE (IGNITE) Network’s efforts to promote: 1) a broader understanding of genomic medicine implementation research; and 2) the sharing of knowledge generated in the network.

Methods

To facilitate this goal the IGNITE Network Common Measures Working Group (CMG) members adopted the Consolidated Framework for Implementation Research (CFIR) to guide their approach to: identifying constructs and measures relevant to evaluating genomic medicine as a whole, standardizing data collection across projects, and combining data in a centralized resource for cross network analyses.

Results

CMG identified ten high-priority CFIR constructs as important for genomic medicine. Of those, eight didn’t have standardized measurement instruments. Therefore, we developed four survey tools to address this gap. In addition, we identified seven high-priority constructs related to patients, families, and communities that did not map to CFIR constructs. Both sets of constructs were combined to create a draft genomic medicine implementation model.

Conclusion

We developed processes to identify constructs deemed valuable for genomic medicine implementation and codified them in a model. These resources are freely available to facilitate knowledge generation and sharing across the field.

Genetic identification of a common collagen disease in puerto ricans via identity-by-descent mapping in a health system

Achieving confidence in the causality of a disease locus is a complex task that often requires supporting data from both statistical genetics and clinical genomics. Here we describe a combined approach to identify and characterize a genetic disorder that leverages distantly related patients in a health system and population-scale mapping. We utilize genomic data to uncover components of distant pedigrees, in the absence of recorded pedigree information, in the multi-ethnic BioMe biobank in New York City. By linking to medical records, we discover a locus associated with both elevated genetic relatedness and extreme short stature. We link the gene, COL27A1, with a little-known genetic disease, previously thought to be rare and recessive. We demonstrate that disease manifests in both heterozygotes and homozygotes, indicating a common collagen disorder impacting up to 2% of individuals of Puerto Rican ancestry, leading to a better understanding of the continuum of complex and Mendelian disease.

Diseases often run in families. These disease are frequently linked to changes in DNA that are passed down through generations. Close family members may share these disease-causing mutations; so may distant relatives who inherited the same mutation from a common ancestor long ago. Geneticists use a method called linkage mapping to trace a disease found in multiple members of a family over generations to genetic changes in a shared ancestor. This allows scientists to pinpoint the exact place in the genome the disease-causing mutation occurred. Using computer algorithms, scientists can apply the same technique to identify mutations that distant relatives inherited from a common ancestor.

Belbin et al. used this computational technique to identify a mutation that may cause unusually short stature or bone and joint problems in up to 2% of people of Puerto Rican descent. In the experiments, the genomes of about 32,000 New Yorkers who have volunteered to participate in the BioMe Biobank and their health records were used to search for genetic changes linked to extremely short stature. The search revealed that people who inherited two copies of this mutation from their parents were likely to be extremely short or to have bone and joint problems. People who inherited one copy had an increased likelihood of joint or bone problems.

This mutation affects a gene responsible for making a form of protein called collagen that is important for bone growth. The analysis suggests the mutation first arose in a Native American ancestor living in Puerto Rico around the time that European colonization began. The mutation had previously been linked to a disorder called Steel syndrome that was thought to be rare. Belbin et al. showed this condition is actually fairly common in people whose ancestors recently came from Puerto Rico, but may often go undiagnosed by their physicians. The experiments emphasize the importance of including diverse populations in genetic studies, as studies of people of predominantly European descent would likely have missed the link between this disease and mutation.

The Pharmacogenomics Research Network Translational Pharmacogenetics Program: Outcomes and Metrics of Pharmacogenetic Implementations Across Diverse Healthcare Systems

Numerous pharmacogenetic clinical guidelines and recommendations have been published, but barriers have hindered the clinical implementation of pharmacogenetics. The Translational Pharmacogenetics Program (TPP) of the National Institutes of Health (NIH) Pharmacogenomics Research Network was established in 2011 to catalog and contribute to the development of pharmacogenetic implementations at eight US healthcare systems, with the goal to disseminate real-world solutions for the barriers to clinical pharmacogenetic implementation. The TPP collected and normalized pharmacogenetic implementation metrics through June 2015, including gene-drug pairs implemented, interpretations of alleles and diplotypes, numbers of tests performed and actionable results, and workflow diagrams. TPP participant institutions developed diverse solutions to overcome many barriers, but the use of Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines provided some consistency among the institutions. The TPP also collected some pharmacogenetic implementation outcomes (scientific, educational, financial, and informatics), which may inform healthcare systems seeking to implement their own pharmacogenetic testing programs.

High-Definition Medicine

The foundation for a new era of data-driven medicine has been set by recent technological advances that enable the assessment and management of human health at an unprecedented level of resolution-what we refer to as high-definition medicine. Our ability to assess human health in high definition is enabled, in part, by advances in DNA sequencing, physiological and environmental monitoring, advanced imaging, and behavioral tracking. Our ability to understand and act upon these observations at equally high precision is driven by advances in genome editing, cellular reprogramming, tissue engineering, and information technologies, especially artificial intelligence. In this review, we will examine the core disciplines that enable high-definition medicine and project how these technologies will alter the future of medicine.

Navigating the research-clinical interface in genomic medicine: analysis from the CSER Consortium

Purpose

The Clinical Sequencing Exploratory Research (CSER) Consortium encompasses nine National Institutes of Health–funded U-award projects investigating translation of genomic sequencing into clinical care. Previous literature has distinguished norms and rules governing research versus clinical care. This is the first study to explore how genomics investigators describe and navigate the research–clinical interface.

Methods

A CSER working group developed a 22-item survey. All nine U-award projects participated. Descriptive data were tabulated and qualitative analysis of text responses identified themes and characterizations of the research–clinical interface.

Results

Survey responses described how studies approached the research–clinical interface, including in consent practices, recording results, and using a research versus clinical laboratory. Responses revealed four characterizations of the interface: clear separation between research and clinical care, interdigitation of the two with steps to maintain separation, a dynamic interface, and merging of the two. All survey respondents utilized at least two different characterizations. Although research has traditionally been differentiated from clinical care, respondents pointed to factors blurring the distinction and strategies to differentiate the domains.

Conclusion

These results illustrate the difficulty in applying the traditional bifurcation of research versus clinical care to translational models of clinical research, including in genomics. Our results suggest new directions for ethics and oversight.

Exploring Genetic Numeracy Skills in a Sample of U.S. University Students

Misconceptions concerning numerical genetic risk exist even within educated populations. To more fully characterize and understand the extent of these risk misunderstandings, which have large potential impact on clinical care, we analyzed the responses from 2,576 students enrolled at 2 Southwestern universities using the PGRID tool, a 138-item web-based survey comprising measures of understanding of genetics, genetic disease, and genetic risk. The primary purpose of this study was to characterize the intersection of risk perception and knowledge, termed genetic numeracy (GN). Additionally, we identify sociodemographic factors that might shape varying levels of GN skills within the study sample and explore the impact of GN on genetic testing intentions using both the Marascuilo procedure and logistic regression analysis. Despite having some college coursework or at least one college degree, most respondents lacked high-level aptitude in understanding genetic inheritance risk, especially with respect to recessive disorders. Prior education about genetics and biology, as well as exposure to biomedical models of genetics, was associated with higher GN levels; exposure to popular media models of genetics was inversely associated with higher GN levels. Differing GN levels affects genetic testing intentions. GN will become more relevant as genetic testing is increasingly incorporated into general clinical care.

Genomic sequencing in clinical practice: applications, challenges, and opportunities

The development of massively parallel sequencing (or next-generation sequencing) has facilitated a rapid implementation of genomic sequencing in clinical medicine. Genomic sequencing (GS) is now an essential tool for evaluating rare disorders, identifying therapeutic targets in neoplasms, and screening for prenatal aneuploidy. Emerging applications, such as GS for preconception carrier screening and predisposition screening in healthy individuals, are being explored in research settings and utilized by members of the public eager to incorporate genomic information into their health management. The rapid pace of adoption has created challenges for all stakeholders in clinical GS, from standardizing variant interpretation approaches in clinical molecular laboratories to ensuring that nongeneticist clinicians are prepared for new types of clinical information. Clinical GS faces a pivotal moment, as the vast potential of new quantities and types of data enable further clinical innovation and complicated implementation questions continue to be resolved.

The Impact of Whole-Genome Sequencing on the Primary Care and Outcomes of Healthy Adult Patients: A Pilot Randomized Trial

Background

Whole-genome sequencing (WGS) in asymptomatic adults might prevent disease but increase health care use without clinical value.

Objective

To describe the effect on clinical care and outcomes of adding WGS to standardized family history assessment in primary care.

Design

Pilot randomized trial. (ClinicalTrials.gov: NCT01736566).

Setting

Academic primary care practices.

Participants

9 primary care physicians (PCPs) and 100 generally healthy patients recruited at ages 40 to 65 years.

Intervention

Patients were randomly assigned to receive a family history report alone (FH group) or in combination with an interpreted WGS report (FH + WGS group), which included monogenic disease risk (MDR) results (associated with Mendelian disorders), carrier variants, pharmacogenomic associations, and polygenic risk estimates for cardiometabolic traits. Each patient met with his or her PCP to discuss the report.

Measurements

Clinical outcomes and health care use through 6 months were obtained from medical records and audio-recorded discussions between PCPs and patients. Patients' health behavior changes were surveyed 6 months after receiving results. A panel of clinician-geneticists rated the appropriateness of how PCPs managed MDR results.

Results

Mean age was 55 years; 58% of patients were female. Eleven FH + WGS patients (22% [95% CI, 12% to 36%]) had new MDR results. Only 2 (4% [CI, 0.01% to 15%]) had evidence of the phenotypes predicted by an MDR result (fundus albipunctatus due to RDH5 and variegate porphyria due to PPOX). Primary care physicians recommended new clinical actions for 16% (CI, 8% to 30%) of FH patients and 34% (CI, 22% to 49%) of FH + WGS patients. Thirty percent (CI, 17% to 45%) and 41% (CI, 27% to 56%) of FH and FH + WGS patients, respectively, reported making a health behavior change after 6 months. Geneticists rated PCP management of 8 MDR results (73% [CI, 39% to 99%]) as appropriate and 2 results (18% [CI, 3% to 52%]) as inappropriate.

Limitation

Limited sample size and ancestral and socioeconomic diversity.

Conclusion

Adding WGS to primary care reveals new molecular findings of uncertain clinical utility. Nongeneticist providers may be able to manage WGS results appropriately, but WGS may prompt additional clinical actions of unclear value.

Primary Funding Source

National Institutes of Health.

The current state of implementation science in genomic medicine: opportunities for improvement

PURPOSE

The objective of this study was to identify trends and gaps in the field of implementation science in genomic medicine.

METHODS

We conducted a literature review using the Centers for Disease Control and Prevention's Public Health Genomics Knowledge Base to examine the current literature in the field of implementation science in genomic medicine. We selected original research articles based on specific inclusion criteria and then abstracted information about study design, genomic medicine, and implementation outcomes. Data were aggregated, and trends and gaps in the literature were discussed.

RESULTS

Our final review encompassed 283 articles published in 2014, the majority of which described uptake (35.7%, n = 101) and preferences (36.4%, n = 103) regarding genomic technologies, particularly oncology (35%, n = 99). Key study design elements, such as racial/ethnic composition of study populations, were underreported in studies. Few studies incorporated implementation science theoretical frameworks, sustainability measures, or capacity building.

CONCLUSION

Although genomic discovery provides the potential for population health benefit, the current knowledge base around implementation to turn this promise into a reality is severely limited. Current gaps in the literature demonstrate a need to apply implementation science principles to genomic medicine in order to deliver on the promise of precision medicine.Genet Med advance online publication 12 January 2017.

Physicians' pharmacogenomics information needs and seeking behavior: a study with case vignettes

Background

Genetic testing, especially in pharmacogenomics, can have a major impact on patient care. However, most physicians do not feel that they have sufficient knowledge to apply pharmacogenomics to patient care. Online information resources can help address this gap. We investigated physicians’ pharmacogenomics information needs and information-seeking behavior, in order to guide the design of pharmacogenomics information resources that effectively meet clinical information needs.

Methods

We performed a formative, mixed-method assessment of physicians’ information-seeking process in three pharmacogenomics case vignettes. Interactions of 6 physicians’ with online pharmacogenomics resources were recorded, transcribed, and analyzed for prominent themes. Quantitative data included information-seeking duration, page navigations, and number of searches entered.

Results

We found that participants searched an average of 8 min per case vignette, spent less than 30 s reviewing specific content, and rarely refined search terms. Participants’ information needs included a need for clinically meaningful descriptions of test interpretations, a molecular basis for the clinical effect of drug variation, information on the logistics of carrying out a genetic test (including questions related to cost, availability, test turn-around time, insurance coverage, and accessibility of expert support).Also, participants sought alternative therapies that would not require genetic testing.

Conclusion

This study of pharmacogenomics information-seeking behavior indicates that content to support their information needs is dispersed and hard to find. Our results reveal a set of themes that information resources can use to help physicians find and apply pharmacogenomics information to the care of their patients.

Electronic supplementary material

The online version of this article (doi:10.1186/s12911-017-0510-9) contains supplementary material, which is available to authorized users.

Reactions to clinical reinterpretation of a gene variant by participants in a sequencing study

PurposeAs genome science advances, people receiving personalized genetic information may receive reinterpretations of pathogenicity. Little is known about responses to adjusted results. We examined how reinterpretations might affect attitudes about genetic testing and intentions to share results with family.MethodsData were collected from high-socioeconomic-status participants (n = 58) in a genome sequencing study. Twenty-nine originally learned they were carriers of Duarte variant galactosemia, based on a variant that was reclassified as benign. Positive testers (n = 19) had a newly identified causative variant and remained carriers. Negative testers (n = 10) learned they were no longer carriers. Twenty-nine controls were carriers for a disease of comparable severity with no reclassification. Participants completed baseline, immediate, and 3-month follow-up surveys.ResultsApproximately 80% of participants demonstrated complete or partially accurate recall of their results and reported positive or neutral reactions to their result and about genetic information more generally. Positive testers reported lower intentions to share the change in their result with family. Controls reported the lowest intentions to learn future results. There were no significant group differences or changes over time in perceived ambiguity or negative emotions.ConclusionThe results suggest that high-socioeconomic-status participants understand reinterpretations conferring a neutral change or a change from carrier to noncarrier status. Participants' responses to changes in carrier results for a low-risk condition indicated minimal adverse effects.

Clinical Genomics in Inflammatory Bowel Disease

Genomic technologies inform the complex genetic basis of polygenic inflammatory bowel disease (IBD) as well as Mendelian disease-associated IBD. Aiming to diagnose patients that present with extreme phenotypes due to monogenic forms of IBD, genomics has progressed from 'orphan disease' research towards an integrated standard of clinical care. Advances in diagnostic clinical genomics are increasingly complemented by pathway-specific therapies that aim to correct the consequences of genetic defects. This highlights the exceptional potential for personalized precision medicine. IBD is nevertheless a challenging example for genomic medicine because the overall fraction of patients with Mendelian defects is low, the number of potential candidate genes is high, and interventional evidence is still emerging. We discuss requirements and prospects of explanatory and predictive clinical genomics in IBD.

"Matching" consent to purpose: The example of the Matchmaker Exchange

The Matchmaker Exchange (MME) connects rare disease clinicians and researchers to facilitate the sharing of data from undiagnosed patients for the purpose of novel gene discovery. Such sharing raises the odds that two or more similar patients with candidate genes in common may be found, thereby allowing their condition to be more readily studied and understood. Consent considerations for data sharing in MME included both the ethical and legal differences between clinical and research settings and the level of privacy risk involved in sharing varying amounts of rare disease patient data to enable patient matches. In this commentary, we discuss these consent considerations and the resulting MME Consent Policy as they may be relevant to other international data sharing initiatives.

Lessons learned from a multidisciplinary renal genetics clinic

BACKGROUND

Inherited renal disorders comprise a significant proportion of cases in both paediatric and adult nephrology services. Genetic advances have advanced rapidly while clinical models of care delivery have remained static.

AIM

To describe a cohort of patients attending a multidisciplinary renal genetics clinic and the insights gained from this experience.

DESIGN AND METHODS

A retrospective review of clinic cases and their molecular genetic diagnosis over a 5-year period.

RESULTS

We report details of 244 individuals including 80 probands who attended the clinic. The commonest reasons for referral was familial haematuria which accounted for 37.5% of cases and cystic kidney disease, accounting for 31% of cases. Eighteen probands had a known molecular genetic diagnosis and were referred for genetic counselling and screening of at risk relatives and management plans. About 62 probands and their families were referred for a precise molecular diagnosis and this was achieved in 26 cases (42%). The most frequent new genetic diagnoses were COL4A5 mutations underlying familial haematuria and familial end stage renal disease. The clinic also allowed for patients with rare renal syndromes to be reviewed, such as ciliopathy syndromes, allowing detailed phenotyping and often a precise molecular genetic diagnosis to be provided.

CONCLUSIONS

The integration of modern day genetics and genomics into multidisciplinary clinics often allows a precise diagnosis which benefits patients, their relatives and the clinicians providing care and future management.

Healthcare provider education to support integration of pharmacogenomics in practice: the eMERGE Network experience

Ten organizations within the Electronic Medical Records and Genomics Network developed programs to implement pharmacogenomic sequencing and clinical decision support into clinical settings. Recognizing the importance of informed prescribers, a variety of strategies were used to incorporate provider education to support implementation. Education experiences with pharmacogenomics are described within the context of each organization's prior involvement, including the scope and scale of implementation specific to their Electronic Medical Records and Genomics projects. We describe common and distinct education strategies, provide exemplars and share challenges. Lessons learned inform future perspectives. Future pharmacogenomics clinical implementation initiatives need to include funding toward implementing provider education and evaluating outcomes.

Great expectations: patient perspectives and anticipated utility of non-diagnostic genomic-sequencing results

The management of secondary findings is a challenge to health-care providers relaying clinical genomic-sequencing results to patients. Understanding patients' expectations from non-diagnostic genomic sequencing could help guide this management. This study interviewed 14 individuals enrolled in the eMERGE (Electronic Medical Records and Genomics) study. Participants in eMERGE consent to undergo non-diagnostic genomic sequencing, receive results, and have results returned to their physicians. The interviews assessed expectations and intended use of results. The majority of interviewees were male (64%) and 43% identified as non-Caucasian. A unique theme identified was that many participants expressed uncertainty about the type of diseases they expected to receive results on, what results they wanted to learn about, and how they intended to use results. Participant uncertainty highlights the complex nature of deciding to undergo genomic testing and a deficiency in genomic knowledge. These results could help improve how genomic sequencing and secondary findings are discussed with patients.

Translating genome-wide association findings into new therapeutics for psychiatry

Genome-wide association studies (GWAS) in psychiatry, once they reach sufficient sample size and power, have been enormously successful. The Psychiatric Genomics Consortium (PGC) aims for mega-analyses with sample sizes that will grow to >1 million individuals in the next 5 years. This should lead to hundreds of new findings for common genetic variants across nine psychiatric disorders studied by the PGC. The new targets discovered by GWAS have the potential to restart largely stalled psychiatric drug development pipelines, and the translation of GWAS findings into the clinic is a key aim of the recently funded phase 3 of the PGC. This is not without considerable technical challenges. These approaches complement the other main aim of GWAS studies, risk prediction approaches for improving detection, differential diagnosis, and clinical trial design. This paper outlines the motivations, technical and analytical issues, and the plans for translating PGC phase 3 findings into new therapeutics.

Information Topics of Greatest Interest for Return of Genome Sequencing Results among Women Diagnosed with Breast Cancer at a Young Age

We investigated what information women diagnosed with breast cancer at a young age would want to learn when genome sequencing results are returned. We conducted 60 semi-structured interviews with women diagnosed with breast cancer at age 40 or younger. We examined what specific information participants would want to learn across result types and for each type of result, as well as how much information they would want. Genome sequencing was not offered to participants as part of the study. Two coders independently coded interview transcripts; analysis was conducted using NVivo10. Across result types, participants wanted to learn about health implications, risk and prevalence in quantitative terms, causes of variants, and causes of diseases. Participants wanted to learn actionable information for variants affecting risk of preventable or treatable disease, medication response, and carrier status. The amount of desired information differed for variants affecting risk of unpreventable or untreatable disease, with uncertain significance, and not health-related. Women diagnosed with breast cancer at a young age recognize the value of genome sequencing results in identifying potential causes and effective treatments and expressed interest in using the information to help relatives and to further understand their other health risks. Our findings can inform the development of effective feedback strategies for genome sequencing that meet patients' information needs and preferences.