Return of results in the genomic medicine projects of the eMERGE network

Studying the impact of translational genomic research: Lessons from eMERGE

Two major goals of the Electronic Medical Record and Genomics (eMERGE) Network are to learn how best to return research results to patient/participants and the clinicians who care for them and also to assess the impact of placing these results in clinical care. Yet since its inception, the Network has confronted a host of challenges in achieving these goals, many of which had ethical, legal, or social implications (ELSIs) that required consideration. Here, we share impediments we encountered in recruiting participants, returning results, and assessing their impact, all of which affected our ability to achieve the goals of eMERGE, as well as the steps we took to attempt to address these obstacles. We divide the domains in which we experienced challenges into four broad categories: (1) study design, including recruitment of more diverse groups; (2) consent; (3) returning results to participants and their health care providers (HCPs); and (4) assessment of follow-up care of participants and measuring the impact of research on participants and their families. Since most phases of eMERGE have included children as well as adults, we also address the particular ELSI posed by including pediatric populations in this research. We make specific suggestions for improving translational genomic research to ensure that future projects can effectively return results and assess their impact on patient/participants and providers if the goals of genomic-informed medicine are to be achieved.

Identifying the prevalence of clinically actionable drug-gene interactions in a health system biorepository to guide pharmacogenetics implementation services

Understanding patterns of drug-gene interactions (DGIs) is important for advancing the clinical implementation of pharmacogenetics (PGx) into routine practice. Prior studies have estimated the prevalence of DGIs, but few have confirmed DGIs in patients with known genotypes and prescriptions, nor have they evaluated clinician characteristics associated with DGI-prescribing. This retrospective chart review assessed prevalence of DGI, defined as a medication prescription in a patient with a PGx phenotype that has a clinical practice guideline recommendation to adjust therapy or monitor drug response, for patients enrolled in a research genetic biorepository linked to electronic health records (EHRs). The prevalence of prescriptions for medications with pharmacogenetic (PGx) guidelines, proportion of prescriptions with DGI, location of DGI prescription, and clinical service of the prescriber were evaluated descriptively. Seventy-five percent (57,058/75,337) of patients had a prescription for a medication with a PGx guideline. Up to 60% (n = 26,067/43,647) of patients had at least one DGI when considering recommendations to adjust or monitor therapy based on genotype. The majority (61%) of DGIs occurred in outpatient prescriptions. Proton pump inhibitors were the most common DGI medication for 11 of 12 clinical services. Almost 25% of patients (n = 10,706/43,647) had more than one unique DGI, and, among this group of patients, 61% had a DGI with more than one gene. These findings can inform future clinical implementation by identifying key stakeholders for initial DGI prescriptions, helping to inform workflows. The high prevalence of multigene interactions identified also support the use of panel PGx testing as an implementation strategy.

Advancing Pharmacogenomics from Single-Gene to Preemptive Testing

Pharmacogenomic testing can be an effective tool to enhance medication safety and efficacy. Pharmacogenomically actionable medications are widely used, and approximately 90-95% of individuals have an actionable genotype for at least one pharmacogene. For pharmacogenomic testing to have the greatest impact on medication safety and clinical care, genetic information should be made available at the time of prescribing (preemptive testing). However, the use of preemptive pharmacogenomic testing is associated with some logistical concerns, such as consistent reimbursement, processes for reporting preemptive results over an individual's lifetime, and result portability. Lessons can be learned from institutions that have implemented preemptive pharmacogenomic testing. In this review, we discuss the rationale and best practices for implementing pharmacogenomics preemptively.

Return of individual research results: What do participants prefer and expect?

Newer data platforms offer increased opportunity to share multidimensional health data with research participants, but the preferences of participants for which data to receive and how is evolving. Our objective is to describe the preferences and expectations of participants for the return of individual research results within Project Baseline Health Study (PBHS). The PBHS is an ongoing, multicenter, longitudinal cohort study with data from four initial enrollment sites. PBHS participants are recruited from the general population along with groups enriched for heart disease and cancer disease risk. Cross-sectional data on return of results were collected in 2017–2018 from an (1) in-person enrollment survey (n = 1,890), (2) benchmark online survey (n = 1,059), and (3) participant interviews (n = 21). The main outcomes included (1) preferences for type of information to be added next to returned results, (2) participant plans for sharing returned results with a non-study clinician, and (3) choice to opt-out of receiving genetic results. Results were compared by sociodemographic characteristics. Enrollment and benchmark survey respondents were 57.1% and 53.5% female, and 60.0% and 66.2% white, respectively. Participants preferred the following data types be added to returned results in the future: genetics (29.9%), heart imaging, (16.4%), study watch (15.8%), and microbiome (13.3%). Older adults (OR 0.60, 95% CI: 0.41–0.87) were less likely to want their genetic results returned next. Forty percent of participants reported that they would not share all returned results with their non–study clinicians. Black (OR 0.64, 95% CI 0.43–0.95) and Asian (OR 0.47, 95% CI 0.30–0.73) participants were less likely, and older participants more likely (OR 1.45–1.61), to plan to share all results with their clinician than their counterparts. At enrollment, 5.8% of participants opted out of receiving their genetics results. The study showed that substantial heterogeneity existed in participant’s preferences and expectations for return of results, and variations were related to sociodemographic characteristics.

Patient-Reported Outcomes and Experiences with Population Genetic Testing Offered Through a Primary Care Network

Aims: To explore patient experiences in a large-scale primary care-based, preemptive genetic testing program.

Methods: Patients who received genetic results from the initiative were invited to participate in an online survey 3 weeks postresult disclosure. A 6-month follow-up survey was sent to assess changes over time.

Results: The initial survey was completed by 1646 patients, with 544 completing the 6-month follow-up survey. The following outcomes were high overall: patient-reported understanding of results (cancer: 87%; cardiac: 86%); perceived utility (75%); positive emotions (relieved: 66.8%; happy: 62.0%); family result sharing (67.6%); and satisfaction (87%), although analysis by demographic factors identified groups who may benefit from additional education and emotional support. Results-related health behaviors and discussions with providers increased over time (screening procedures 6.1% to 14.2% p < 0.001; provider discussion 10.3% to 25.3%, p < 0.001), and were more likely to take place for patients with positive cancer and/or cardiac results (39.8% vs. 7.6%, p < 0.001). Forty-seven percent of patients reported insurance discrimination concerns, and most (79.4%) were not familiar with privacy and nondiscrimination laws. Concerns regarding discrimination and negative emotions decreased between the two survey time points (privacy issues 44.6% to 35.1% p < 0.001; life insurance discrimination concerns 35.5% to 29.6%, p = 0.001; anxiety 8.1% to 3.3%, p < 0.001; and uncertainty 19.8% to 12.8%, p < 0.001). These findings led to the development and integration of additional patient resources to improve program implementation.

Conclusion: Our findings highlight patient experiences with and areas of need in a community-based genomic screening pilot initiative using a mixed primary care/genetics provider model to deliver precision medicine.

Preferences for and acceptability of receiving pharmacogenomic results by mail: A focus group study with a primarily African-American cohort

Although genetic counseling is traditionally done through in-person, one-on-one visits, workforce shortages call for efficient result return mechanisms. Studies have shown that telephone and in-person return of cancer genetic results are equivalent for patient outcomes. Few studies have been conducted with other modes, result types or racially diverse participants. This study explored participants' perspectives on receiving pharmacogenomic results by mail. Two experienced moderators facilitated six focus groups with 49 individuals who self-identified primarily as African-American and consented to participate in a genome sequencing cohort study. Participants were given a hypothetical pharmacogenomic result report (positive for c.521T>C in SLCO1B1). An accompanying letter explained that the result was associated with statin intolerance along with a recommendation to share it with one's doctor and immediate relatives. Participants reacted to the idea of receiving this type of result by mail, discussing whether the letter's information was sufficient and what they predicted they would do with the result. Two researchers coded the focus group transcripts and identified themes. Many participants thought that it was appropriate to receive the result through the mail, but some suggested a phone call alerting the recipient to the letter. Others emphasized that although a letter was acceptable for disclosing pharmacogenomic results, it would be insufficient for what they perceived as life-threatening results. Most participants found the content sufficient. Some participants suggested resources about statin intolerance and warning signs be added. Most claimed they would share the result with their doctor, yet few participants offered they would share the result with their relatives. This exploratory study advances the evidence that African-American research participants are receptive to return of certain genetic results by approaches that do not involve direct contact with a genetic counselor and intend to share results with providers. ClinSeq: A Large-Scale Medical Sequencing Clinical Research Pilot Study (NCT00410241).

Genomic Sequencing Results Disclosure in Diverse and Medically Underserved Populations: Themes, Challenges, and Strategies from the CSER Consortium

Genomic sequencing results need to be effectively communicated across all populations and practice settings. Projects in the Clinical Sequencing Evidence-Generating Research (CSER) consortium enroll diverse racial/ethnic and medically underserved participants across various clinical contexts. This article explores a set of CSER results disclosure cases to expand the evidence base on experiences returning genomic results. Case details were collected using a structured set of questions. We identified common themes in the case set, and assessed challenges and strategies in achieving six relevant results disclosure objectives. CSER-affiliated patient/community stakeholder impressions of the findings were solicited via video conference calls. Seventeen cases across six CSER projects were included. Case themes sorted into four categories: (1) factors influencing participant understanding, (2) participant emotional response, (3) disease burden, and (4) logistical challenges. Challenges meeting results disclosure objectives included a lack of dialogue, health literacy level, unexpected findings, and complex concepts. Strategies were consistent with traditional genetic counseling practice, but also highlighted approaches being evaluated in CSER projects. Patient/community stakeholders supported the identified themes and provided additional suggestions to improve patient understanding and engagement. These experiences add valuable insights into adapting genomic results disclosure practices to best serve all patient populations.

Communicating unexpected pharmacogenomic results to biobank contributors: A focus group study

OBJECTIVES

The goals of this study were to explore 1) the impact of returning unexpected pharmacogenomic (PGx) results to biobank contributors, and 2) participant views about improving communication.

METHODS

We conducted a qualitative focus group study with biobank participants (N = 54) who were notified by mail of an individual research result indicating increased risk for adverse events associated with the common cancer drug 5-fluorouracil (5-FU). We employed a framework approach for analysis.

RESULTS

Our results revealed three themes illustrating participants' questions and uncertainty, especially regarding how to share results with health providers and family members, and remember them over time. Participants valued results for themselves and others, and for the future of medicine. Risk perception was framed by health identity. "Toxicity narratives," or familiarity with another's adverse reaction to chemotherapy, increased the sense of importance participants reported.

CONCLUSION

These focus group results highlight research participant remaining questions and high valuation of PGx results, even when unexpected.

PRACTICE IMPLICATIONS

We identify PGx research participants' needs for clear clinical translation messaging that attends to health identity, pragmatics of sharing information with family members, and patient perceptions of barriers to transferring research results to a clinical context.

Association between triglycerides, known risk SNVs and conserved rare variation in SLC25A40 in a multi-ancestry cohort

Background

Elevated triglycerides (TG) are associated with, and may be causal for, cardiovascular disease (CVD), and co-morbidities such as type II diabetes and metabolic syndrome. Pathogenic variants in APOA5 and APOC3 as well as risk SNVs in other genes [APOE (rs429358, rs7412), APOA1/C3/A4/A5 gene cluster (rs964184), INSR (rs7248104), CETP (rs7205804), GCKR (rs1260326)] have been shown to affect TG levels. Knowledge of genetic causes for elevated TG may lead to early intervention and targeted treatment for CVD. We previously identified linkage and association of a rare, highly conserved missense variant in SLC25A40, rs762174003, with hypertriglyceridemia (HTG) in a single large family, and replicated this association with rare, highly conserved missense variants in a European American and African American sample.

Methods

Here, we analyzed a longitudinal mixed-ancestry cohort (European, African and Asian ancestry, N = 8966) from the Electronic Medical Record and Genomics (eMERGE) Network. We tested associations between median TG and the genes of interest, using linear regression, adjusting for sex, median age, median BMI, and the first two principal components of ancestry.

Results

We replicated the association between TG and APOC3, APOA5, and risk variation at APOE, APOA1/C3/A4/A5 gene cluster, and GCKR. We failed to replicate the association between rare, highly conserved variation at SLC25A40 and TG, as well as for risk variation at INSR and CETP.

Conclusions

Analysis using data from electronic health records presents challenges that need to be overcome. Although large amounts of genotype data is becoming increasingly accessible, usable phenotype data can be challenging to obtain. We were able to replicate known, strong associations, but were unable to replicate moderate associations due to the limited sample size and missing drug information.

The Implementation Chasm Hindering Genome-informed Health Care

The promises of precision medicine are often heralded in the medical and lay literature, but routine integration of genomics in clinical practice is still limited. While the "last mile' infrastructure to bring genomics to the bedside has been demonstrated in some healthcare settings, a number of challenges remain - both in the receptivity of today's health system and in its technical and educational readiness to respond to this evolution in care. To improve the impact of genomics on health and disease management, we will need to integrate both new knowledge and new care processes into existing workflows. This change will be onerous and time-consuming, but hopefully valuable to the provision of high quality, economically feasible care worldwide.

Are providers prepared for genomic medicine: interpretation of Direct-to-Consumer genetic testing (DTC-GT) results and genetic self-efficacy by medical professionals

Background

Precision medicine is set to deliver a rich new data set of genomic information. However, the number of certified specialists in the United States is small, with only 4244 genetic counselors and 1302 clinical geneticists. We conducted a national survey of 264 medical professionals to evaluate how they interpret genetic test results, determine their confidence and self-efficacy of interpreting genetic test results with patients, and capture their opinions and experiences with direct-to-consumer genetic tests (DTC-GT).

Methods

Participants were grouped into two categories, genetic specialists (genetic counselors and clinical geneticists) and medical providers (primary care, internists, physicians assistants, advanced nurse practitioners, etc.). The survey (full instrument can be found in the Additional file 1) presented three genetic test report scenarios for interpretation: a genetic risk for diabetes, genomic sequencing for symptoms report implicating a potential HMN7B: distal hereditary motor neuropathy VIIB diagnosis, and a statin-induced myopathy risk. Participants were also asked about their opinions on DTC-GT results and rank their own perceived level of preparedness to review genetic test results with patients.

Results

The rates of correctly interpreting results were relatively high (74.4% for the providers compared to the specialist’s 83.4%) and age, prior genetic test consultation experience, and level of trust assigned to the reports were associated with higher correct interpretation rates. The self-selected efficacy and the level of preparedness to consult on a patient’s genetic results were higher for the specialists than the provider group.

Conclusion

Specialists remain the best group to assist patients with DTC-GT, however, primary care providers may still provide accurate interpretation of test results when specialists are unavailable.

Genomic Information for Clinicians in the Electronic Health Record: Lessons Learned From the Clinical Genome Resource Project and the Electronic Medical Records and Genomics Network

Genomic knowledge is being translated into clinical care. To fully realize the value, it is critical to place credible information in the hands of clinicians in time to support clinical decision making. The electronic health record is an essential component of clinician workflow. Utilizing the electronic health record to present information to support the use of genomic medicine in clinical care to improve outcomes represents a tremendous opportunity. However, there are numerous barriers that prevent the effective use of the electronic health record for this purpose. The electronic health record working groups of the Electronic Medical Records and Genomics (eMERGE) Network and the Clinical Genome Resource (ClinGen) project, along with other groups, have been defining these barriers, to allow the development of solutions that can be tested using implementation pilots. In this paper, we present “lessons learned” from these efforts to inform future efforts leading to the development of effective and sustainable solutions that will support the realization of genomic medicine.

Detecting moderate or complex congenital heart defects in adults from an electronic health records system

Background

The prevalence of moderate or complex (moderate-complex) congenital heart defects (CHDs) among adults is increasing due to improved survival, but many patients experience lapses in specialty care or their CHDs are undocumented in the medical system. There is, to date, no efficient approach to identify this population.

Objective

To develop and assess the performance of a risk score to identify adults aged 20-60 years with undocumented specific moderate-complex CHDs from electronic health records (EHR).

Methods

We used a case-control study (596 adults with specific moderate-complex CHDs and 2384 controls). We extracted age, race/ethnicity, electrocardiogram (EKG), and blood tests from routine outpatient visits (1/2009 through 12/2012). We used multivariable logistic regression models and a split-sample (4: 1 ratio) approach to develop and internally validate the risk score, respectively. We generated receiver operating characteristic (ROC) c-statistics and Brier scores to assess the ability of models to predict the presence of specific moderate-complex CHDs.

Results

Out of six models, the non-blood biomarker model that included age, sex, and EKG parameters offered a high ROC c-statistic of 0.96 [95% confidence interval: 0.95, 0.97] and low Brier score (0.05) relative to the other models. The adult moderate-complex congenital heart defect risk score demonstrated good accuracy with 96.4% sensitivity and 80.0% specificity at a threshold score of 10.

Conclusions

A simple risk score based on age, sex, and EKG parameters offers early proof of concept and may help accurately identify adults with specific moderate-complex CHDs from routine EHR systems who may benefit from specialty care.

Return of individual results in epilepsy genomic research: A view from the field

Genomic findings are emerging rapidly in 2 large, closely related epilepsy research consortia: the Epilepsy Phenome/Genome Project and Epi4K. Disclosure of individual results to participants in genomic research is increasingly viewed as an ethical obligation, but strategies for return of results were not included in the design of these consortia, raising complexities in establishing criteria for which results to offer, determining participant preferences, managing the large number of sites involved, and covering associated costs. Here, we describe the challenges faced, alternative approaches considered, and progress to date. Experience from these 2 consortia illustrates the importance, for genomic research in epilepsy and other disorders, of including a specific plan for return of results in the study design, with financial support for obtaining clinical confirmation and providing ongoing support for participants. Participant preferences for return of results should be established at the time of enrollment, and methods for allowing future contacts with participants should be included. In addition, methods should be developed for summarizing meaningful, comprehensible information about findings in the aggregate that participants can access in an ongoing way.

Willingness to Participate in a National Precision Medicine Cohort: Attitudes of Chronic Kidney Disease Patients at a Cleveland Public Hospital

Multiple ongoing, government-funded national efforts longitudinally collect health data and biospecimens for precision medicine research with ascertainment strategies increasingly emphasizing underrepresented groups in biomedical research. We surveyed chronic kidney disease patients from an academic, public integrated tertiary care system in Cleveland, Ohio, to examine local attitudes toward participation in large-scale government-funded studies. Responses (n = 103) indicate the majority (71%) would participate in a hypothetical national precision medicine cohort and were willing to send biospecimens to a national repository and share de-identified data, but <50% of respondents were willing to install a phone app to track personal data. The majority of participants (62%) indicated that return of research results was very important, and the majority (54%) also wanted all of their research-collected health and genetic data returned. Response patterns did not differ by race/ethnicity. Overall, we found high willingness to participate among this Cleveland patient population already participating in a local genetic study. These data suggest that despite common perceptions, subjects from communities traditionally underrepresented in genetic research will participate and agree to store samples and health data in repositories. Furthermore, most participants want return of research results, which will require a plan to provide these data in a secure, accessible, and understandable manner.

Patients' Attitudes Towards the Return of Incidental Findings After Research with Residual Tissue: A Mixed Methods Study

AIMS

To investigate the attitudes of patients toward the return of individual research results from scientific research with residual tissue.

METHODS AND FINDINGS

We recruited 1319 patients from 6 Dutch hospitals. In total, 673 patients (51% response rate) completed the questionnaire and 146 were interviewed. Based on the questionnaire data, the majority of respondents (92%) wanted to be informed of incidental findings about both a curable (92%) and an incurable (76%) disease. Respondents' wishes to be informed about incidental findings did not vary significantly as a function of patient demographics or type of disease. The interview data show that respondents wished to be informed about incidental findings because they considered it to be normal practice; they expected the information to be of benefit for their health. Information should be provided by their physician. Yet, most respondents (84%) would consent to research even if they would not be informed about incidental findings, primarily because they recognized that there might be practical problems in providing such information, and because they valued scientific research highly.

CONCLUSIONS

We conclude that, while the majority of patients want to be informed about incidental findings, they also recognize that this may be difficult.

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.

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.

Preferences for the Return of Individual Results From Research on Pediatric Biobank Samples

Discussions about disclosing individual genetic research results include calls to consider participants' preferences. In this study, parents of Boston Children's Hospital patients set preferences for disclosure based on disease preventability and severity, and could exclude mental health, developmental, childhood degenerative, and adult-onset disorders. Participants reviewed hypothetical reports and reset preferences, if desired. Among 661 participants who initially wanted all results (64%), 1% reset preferences. Among 336 participants who initially excluded at least one category (36%), 38% reset preferences. Participants who reset preferences added 0.9 categories, on average; and their mean satisfaction on 0 to 10 scales increased from 4.7 to 7.2 ( p < .001). Only 2% reduced the number of categories they wanted disclosed. Findings demonstrate the benefits of providing examples of preference options and the tendency of participants to want results disclosed. Findings also suggest that preference-setting models that do not provide specific examples of results could underestimate participants' desires for information.

Choices for return of primary and secondary genomic research results of 790 members of families with Mendelian disease

Although consensus is building that primary (PR) and secondary findings (SF) from genomic research should be offered to participants under some circumstances, data describing (1) actual choices of study participants and (2) factors associated with these choices are limited, hampering study planning. We conducted a cross-sectional analysis of choices made for return of PR and SF during informed consent by members of the first 247 families (790 individuals) enrolled in the Baylor-Hopkins Center for Mendelian Genomics, a genome sequencing study. Most (619; 78.3%) chose to receive SF and PR, 66 (8.4%) chose PR only, 65 (8.2%) wanted no results, and 40 (5.1%) chose SF only. Choosing SF was associated with an established clinical diagnosis in the proband (87.8 vs 79%, P=0.009) and European ancestry (EA) (87.7 vs 73%, P<0.008). Participants of non-European ancestry (NEA) were as likely as those of EA to choose SF when consented by a genetic counselor (GC) (82% NEA vs 88.3% EA, P=0.09) but significantly less likely when consented by a physician (67.4% NEA vs 85.4% EA, P=0.001). Controlling for proband diagnosis, individuals of NEA were 2.13-fold (95% CI: 1.11-4.08) more likely to choose SF when consented by a GC rather than a physician. Participants of NEA were 3-fold more likely than those of EA to decline all study results (14.7% NEA vs 5.4% EA, P<0.008). In this ethnically diverse population, whereas most participants desired PR and SF, more than 20% declined some or all results, highlighting the importance of research participant choice.

Variability in assigning pathogenicity to incidental findings: insights from LDLR sequence linked to the electronic health record in 1013 individuals

Knowledge of variant pathogenicity is key to implementing genomic medicine. We describe variability between expert reviewers in assigning pathogenicity to sequence variants in LDLR, the causal gene in the majority of cases of familial hypercholesterolemia. LDLR was sequenced on the Illumina HiSeq platform (average read depth >200 × ) in 1013 Mayo Biobank participants recruited from 2012 to 2013. Variants with a minor allele frequency (MAF) <5% predicted to be functional or referenced in HGMD (Human Gene Mutation Database) or NCBI-ClinVar databases were reviewed. To assign pathogenicity, variant frequency in population data sets, computational predictions, reported observations and patient-level data including electronic health record-based post hoc phenotyping were leveraged. Of 178 LDLR variants passing quality control, 25 were selected for independent review using either an in-house protocol or a disease/gene-specific semi-quantitative framework based on the American College of Medical Genetics and Genomics-recommended lines of evidence. NCBI-ClinVar included interpretations for all queried variants with 74% (14/19) of variants with >1 submitter showing inconsistency in classification and 26% (5/19) appearing with conflicting clinical actionability. The discordance rate (one-step level of disagreement out of five classes in variant interpretation) between the reviewers was 40% (10/25). Two LDLR variants were independently deemed clinically actionable and returnable. Interpretation of LDLR variants was often discordant among ClinVar submitters and between expert reviewers. A quantitative approach based on strength of each predefined criterion in the context of specific genes and phenotypes may yield greater consistency between different reviewers.

User-centered design of multi-gene sequencing panel reports for clinicians

The objective of this study was to develop a high-fidelity prototype for delivering multi-gene sequencing panel (GS) reports to clinicians that simulates the user experience of a final application. The delivery and use of GS reports can occur within complex and high-paced healthcare environments. We employ a user-centered software design approach in a focus group setting in order to facilitate gathering rich contextual information from a diverse group of stakeholders potentially impacted by the delivery of GS reports relevant to two precision medicine programs at the University of Maryland Medical Center. Responses from focus group sessions were transcribed, coded and analyzed by two team members. Notification mechanisms and information resources preferred by participants from our first phase of focus groups were incorporated into scenarios and the design of a software prototype for delivering GS reports. The goal of our second phase of focus group, to gain input on the prototype software design, was accomplished through conducting task walkthroughs with GS reporting scenarios. Preferences for notification, content and consultation from genetics specialists appeared to depend upon familiarity with scenarios for ordering and delivering GS reports. Despite familiarity with some aspects of the scenarios we proposed, many of our participants agreed that they would likely seek consultation from a genetics specialist after viewing the test reports. In addition, participants offered design and content recommendations. Findings illustrated a need to support customized notification approaches, user-specific information, and access to genetics specialists with GS reports. These design principles can be incorporated into software applications that deliver GS reports. Our user-centered approach to conduct this assessment and the specific input we received from clinicians may also be relevant to others working on similar projects.

Feedback of Individual Genetic Results to Research Participants: Is It Feasible in Europe?

BACKGROUND

There is growing consensus that individual genetic research results that are scientifically robust, analytically valid, and clinically actionable should be offered to research participants. However, the general practice in European research projects is that results are usually not provided to research participants for many reasons. This article reports on the views of European experts and scholars who are members of the European COST Action CHIP ME IS1303 (Citizen's Health through public-private Initiatives: Public health, Market and Ethical perspectives) regarding challenges to the feedback of individual genetic results to research participants in Europe and potential strategies to address these challenges.

MATERIALS AND METHODS

A consultation of the COST Action members was conducted through an email survey and a workshop. The results from the consultation were analyzed following a conventional content analysis approach.

RESULTS

Legal frameworks, professional guidelines, and financial, organizational, and human resources to support the feedback of results are largely missing in Europe. Necessary steps to facilitate the feedback process include clarifying legal requirements to the feedback of results, developing harmonized European best practices, promoting interdisciplinary and cross-institutional collaboration, designing educational programs and cost-efficient IT-based platforms, involving research ethics committees, and documenting the health benefits and risks of the feedback process.

CONCLUSIONS

Coordinated efforts at pan-European level are needed to enable equitable, scientifically sound, and socially robust feedback of results to research participants.

From Genome-Wide Association Study to Phenome-Wide Association Study: New Paradigms in Obesity Research

Obesity is a condition in which excess body fat has accumulated over an extent that increases the risk of many chronic diseases. The current clinical classification of obesity is based on measurement of body mass index (BMI), waist-hip ratio, and body fat percentage. However, these measurements do not account for the wide individual variations in fat distribution, degree of fatness or health risks, and genetic variants identified in the genome-wide association studies (GWAS). In this review, we will address this important issue with the introduction of phenome, phenomics, and phenome-wide association study (PheWAS). We will discuss the new paradigm shift from GWAS to PheWAS in obesity research. In the era of precision medicine, phenomics and PheWAS provide the required approaches to better definition and classification of obesity according to the association of obese phenome with their unique molecular makeup, lifestyle, and environmental impact.

A multi-locus genetic risk score for abdominal aortic aneurysm

BACKGROUND

We investigated whether a multi-locus genetic risk scores (GRS) was associated with presence and progression of abdominal aortic aneurysm (AAA) in a case - control study.

METHODS AND RESULTS

The study comprised of 1124 patients with AAA (74 ± 8 years, 83% men, 52% of them with a maximal AAA size ≤ 5 cm) and 6524 non-cases (67 ± 11 years, 58% men) from the Mayo Vascular Disease Biorepository. AAA was defined as infrarenal abdominal aorta diameter ≥ 3.0 cm or history of AAA repair. Non-cases were participants without known AAA. A GRS was calculated using 4 SNPs associated with AAA at genome-wide significance (P ≤ 10(-8)). The GRS was associated with the presence of AAA after adjustment for age, sex, cardiovascular risk factors, atherosclerotic cardiovascular diseases and family history of aortic aneurysm: odds ratio (OR, 95% confidence interval, CI) 1.06 (1.04-1.09, p < 0.001). Adding GRS to conventional risk factors improved the association of presence of AAA (net reclassification index 14%, p < 0.001). In a subset of patients with AAA who had ≥ 2 imaging studies (n = 651, mean (SE) growth rate 2.47 (0.11) mm/year during a mean time interval of 5.41 years), GRS, baseline size, diabetes and family history were each associated with aneurysm growth rate in univariate association (all p < 0.05). The estimated mean aneurysm growth rate was 0.50 mm/year higher in those with GRS > median (5.78) than those with GRS ≤ median (p = 0.01), after adjustment for baseline size (p < 0.001), diabetes (p = 0.046) and family history of aortic aneurysm (p = 0.02).

CONCLUSIONS

A multi-locus GRS was associated with presence of AAA and greater aneurysm expansion.

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

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

Neonatal medications

Neonatal abstinence syndrome (NAS) is reaching epidemic proportions related to perinatal use of opioids. There are many approaches to assess and manage NAS, including one we have outlined. A standardized approach is likely to reduce length of stay and variability in practice. Circumcision is a frequent, painful procedure performed in the neonatal period. The rationale for providing analgesia is presented as well as a review of methods. Pharmacogenomics and pharmacogenetics have expanded our understanding of diseases and their drug therapy. Some applications of pharmacogenomics to the neonatal period are presented, along with pediatric challenges of developmental expression of drug-metabolizing enzymes.

Disclosing genetic risk for coronary heart disease: effects on perceived personal control and genetic counseling satisfaction

We investigated whether disclosure of coronary heart disease (CHD) genetic risk influences perceived personal control (PPC) and genetic counseling satisfaction (GCS). Participants (n = 207, age: 45-65 years) were randomized to receive estimated 10-year risk of CHD based on a conventional risk score (CRS) with or without a genetic risk score (GRS). Risk estimates were disclosed by a genetic counselor who also reviewed how GRS altered risk in those randomized to CRS+GRS. Each participant subsequently met with a physician and then completed surveys to assess PPC and GCS. Participants who received CRS+GRS had higher PPC than those who received CRS alone although the absolute difference was small (25.2 ± 2.7 vs 24.1 ± 3.8, p = 0.04). A greater proportion of CRS+GRS participants had higher GCS scores (17.3 ± 5.3 vs 15.9 ± 6.3, p = 0.06). In the CRS+GRS group, PPC and GCS scores were not correlated with GRS. Within both groups, PPC and GCS scores were similar in patients with or without family history (p = NS). In conclusion, patients who received their genetic risk of CHD had higher PPC and tended to have higher GCS. Our findings suggest that disclosure of genetic risk of CHD together with conventional risk estimates is appreciated by patients. Whether this results in improved outcomes needs additional investigation.

Automatic Placement of Genomic Research Results in Medical Records: Do Researchers Have a Duty? Should Participants Have a Choice?

In genomics research, it is becoming common practice to return individualized primary and incidental findings to participants and several ongoing major studies have begun to automatically transfer these results to a participant's clinical medical record. This paper explores who should decide whether to place genomic research findings into a clinical medical record. Should participants make this decision, or does a researcher's duty to place this information in a medical record override the participant's autonomy? We argue that there are no clear ethical, legal, professional, or regulatory duties that mandate placement without the consent of the participant. We conclude that informing participants of results, together with a clear explanation, relevant recommendations and referral sources, and the option to consent to placement in the medical records will best discharge researchers' ethical and legal duties towards participants.

Quality standards for DNA sequence variation databases to improve clinical management under development in Australia

Despite the routine nature of comparing sequence variations identified during clinical testing to database records, few databases meet quality requirements for clinical diagnostics. To address this issue, The Royal College of Pathologists of Australasia (RCPA) in collaboration with the Human Genetics Society of Australasia (HGSA), and the Human Variome Project (HVP) is developing standards for DNA sequence variation databases intended for use in the Australian clinical environment. The outputs of this project will be promoted to other health systems and accreditation bodies by the Human Variome Project to support the development of similar frameworks in other jurisdictions.

A perspective on the New American College of Cardiology/American Heart Association guidelines for cardiovascular risk assessment

The recently published American College of Cardiology (ACC)/American Heart Association (AHA) guidelines for cardiovascular risk assessment provide equations to estimate the 10-year and lifetime atherosclerotic cardiovascular disease (ASCVD) risk in African Americans and non-Hispanic whites, include stroke as an adverse cardiovascular outcome, and emphasize shared decision making. The guidelines provide a valuable framework that can be adapted on the basis of clinical judgment and individual/institutional expertise. In this review, we provide a perspective on the new guidelines, highlighting what is new, what is controversial, and potential adaptations. We recommend obtaining family history of ASCVD at the time of estimating ASCVD risk and consideration of imaging to assess subclinical disease burden in patients at intermediate risk. In addition to the adjuncts for ASCVD risk estimation recommended in the guidelines, measures that may be useful in refining risk estimates include carotid ultrasonography, aortic pulse wave velocity, and serum lipoprotein(a) levels. Finally, we stress the need for research efforts to improve assessment of ASCVD risk given the suboptimal performance of available risk algorithms and suggest potential future directions in this regard.

Pragmatic and Ethical Challenges of Incorporating the Genome into the Electronic Medical Record

Recent successes in the use of gene sequencing for patient care highlight the potential of genomic medicine. For genomics to become a part of usual care, pertinent elements of a patient's genomic test must be communicated to the most appropriate care providers. Electronic medical records may serve as a useful tool for storing and disseminating genomic data. Yet, the structure of existing EMRs and the nature of genomic data pose a number of pragmatic and ethical challenges in their integration. Through a review of the recent genome-EMR integration literature, we explore concrete examples of these challenges, categorized under four key questions: What data will we store? How will we store it? How will we use it? How will we protect it? We conclude that genome-EMR integration requires a rigorous, multi-faceted and interdisciplinary approach of study. Problems facing the field are numerous, but few are intractable.

eMERGEing progress in genomics-the first seven years

The electronic MEdical Records & GEnomics (eMERGE) network was established in 2007 by the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) in part to explore the utility of electronic medical records (EMRs) in genome science. The initial focus was on discovery primarily using the genome-wide association paradigm, but more recently, the network has begun evaluating mechanisms to implement new genomic information coupled to clinical decision support into EMRs. Herein, we describe this evolution including the development of the individual and merged eMERGE genomic datasets, the contribution the network has made toward genomic discovery and human health, and the steps taken toward the next generation genotype-phenotype association studies and clinical implementation.