Third party interpretation of raw genetic data: an ethical exploration

Policy Guidance for Direct-to-Consumer Genetic Testing Services: Framework Development Study

BACKGROUND

The online offer of commercial genetic tests, also called direct-to-consumer genetic tests (DTC-GTs), enables citizens to gain insight into their health and disease risk based on their genetic profiles. DTC-GT offers often consist of a combination of services or aspects, including advertisements, information, DNA analysis, and medical or lifestyle advice. The risks and benefits of DTC-GT services have been debated and studied extensively, but instruments that assess DTC-GT services and aid policy are lacking. This leads to uncertainty among policy makers, law enforcers, and regulators on how to ensure and balance both public safety and autonomy and about the responsibilities these 3 parties have toward the public.

OBJECTIVE

This study aimed to develop a framework that outlines aspects of DTC-GTs that lead to policy issues and to help provide policy guidance regarding DTC-GT services.

METHODS

We performed 3 steps: (1) an integrative literature review to identify risks and benefits of DTC-GT services for consumers and society in Embase and Medline (January 2014-June 2022), (2) structuring benefits and risks in different steps of the consumer journey, and (3) development of a checklist for policy guidance.

RESULTS

Potential risks and benefits of DTC-GT services were mapped from 134 papers and structured into 6 phases. In summary, these phases were called the consumer journey: (1) exposure, (2) pretest information, (3) DNA analysis, (4) data management, (5) posttest information, and (6) individual and societal impact. The checklist for evaluation of DTC-GT services consisted of 8 themes, covering 38 items that may raise policy issues in DTC-GT services. The themes included the following aspects: general service content, validity and quality assurance, potential data and privacy risks, scientific evidence and robustness, and quality of the provided information.

CONCLUSIONS

Both the consumer journey and the checklist break the DTC-GT offer down into key aspects that may impact and compromise individual and public health, safety, and autonomy. This framework helps policy makers, regulators, and law enforcers develop methods to interpret, assess, and act in the DTC-GT service market.

Pathological findings and long-term prognosis in Korean BRCA1/2 mutation carriers undergoing risk-reducing salpingo-oophorectomy

OBJECTIVE

Our study aimed to evaluate the incidence of pathological findings in asymptomatic Korean patients with BRCA1/2 pathogenic variants who underwent risk-reducing salpingo-oophorectomy and to assess their long-term prognosis.

METHODS

We retrospectively analyzed the medical records of patients with a germinal BRCA1/2 pathologic variant who had undergone risk-reducing salpingo-oophorectomy at Asan Medical Center (Seoul, Korea) between January 2013 and December 2020. All pathologic reports were made based on the sectioning and extensively examining the fimbriated end of the fallopian tube (SEE/FIM) protocol.

RESULTS

Out of 243 patients who underwent risk-reducing salpingo-oophorectomy, 121 (49.8%) had a BRCA1 mutation, 119 (48.9%) had a BRCA2 mutation, and three (1.2%) had both mutations. During the procedure, four (3.3%) patients with a BRCA1 mutation were diagnosed with serous tubal intraepithelial carcinoma (STIC) or serous tubal intraepithelial lesion (STIL), and another four patients (3.3%) were diagnosed with occult cancer despite no evidence of malignancy on preoperative ultrasound. In the BRCA2 mutation group, we found one (0.8%) case of STIC, but no cases of STIL or occult cancer. During the median follow-up period of 98 months (range, 44-104) for STIC and 54 months (range, 52-56) for STIL, none of the patients diagnosed with these precursor lesions developed primary peritoneal carcinomatosis.

CONCLUSIONS

Risk-reducing salpingo-oophorectomy, in asymptomatic Korean patients with BRCA1/2 pathogenic variants, detected ovarian cancer and precursor lesions, including STIC or STIL. Furthermore, our follow-up period did not reveal any instances of primary peritoneal carcinomatosis, suggesting a limited body of evidence supporting the imperative need for adjuvant treatment in patients diagnosed with these precursor lesions during risk-reducing salpingo-oophorectomy.

An Environmental Scan of Consumer-Initiated Germline Genetic Testing for Health Risks

As patient access to laboratory testing outside the clinic grows, health care providers can expect to confront increasing questions about the utility and interpretation of consumer-initiated genetic testing for health risks. We sought to characterize the marketplace diversity of consumer-initiated germline genetic testing options. An environmental scan was conducted to identify germline genetic testing companies that offer testing for at least one diagnosable health condition and are available for purchase by consumers in the US market without a visit to one's health care provider. We limited our scope to tests available between October 1, 2019, and September 30, 2021. We characterized variability in the content and processes used by 21 companies offering 74 distinct test products that met our inclusion and exclusion criteria. A minority (8 of 21 companies) offered tests that assessed the presence of at least 1 US Centers for Disease Control and Prevention Tier 1 condition for which detection can impact an individual's clinical care and for which evidence-based guidelines for detection and management exist.

A game theoretic approach to balance privacy risks and familial benefits

As recreational genomics continues to grow in its popularity, many people are afforded the opportunity to share their genomes in exchange for various services, including third-party interpretation (TPI) tools, to understand their predisposition to health problems and, based on genome similarity, to find extended family members. At the same time, these services have increasingly been reused by law enforcement to track down potential criminals through family members who disclose their genomic information. While it has been observed that many potential users shy away from such data sharing when they learn that their privacy cannot be assured, it remains unclear how potential users' valuations of the service will affect a population's behavior. In this paper, we present a game theoretic framework to model interdependent privacy challenges in genomic data sharing online. Through simulations, we find that in addition to the boundary cases when (1) no player and (2) every player joins, there exist pure-strategy Nash equilibria when a relatively small portion of players choose to join the genomic database. The result is consistent under different parametric settings. We further examine the stability of Nash equilibria and illustrate that the only equilibrium that is resistant to a random dropping of players is when all players join the genomic database. Finally, we show that when players consider the impact that their data sharing may have on their relatives, the only pure strategy Nash equilibria are when either no player or every player shares their genomic data.

Patient experiences with clinical confirmatory genetic testing after using direct-to-consumer raw DNA and third-party genetic interpretation services

The availability of raw DNA and genetic interpretation tools allow individuals to access genetic health risk information, where analytical false-positives exist. Little is known about the experience of individuals who receive pathogenic or likely pathogenic variant(s) through raw DNA interpretation and follow-up with clinical confirmatory genetic testing. This qualitative study set out to describe the experiences of individuals who pursued clinical confirmatory genetic testing, including their perception of the process. Participants were recruited from social media and eligible if they discovered a potential pathogenic or likely pathogenic variant in a raw DNA interpretation report, completed clinical confirmatory genetic testing in the U.S., and provided documentation of those results. Individuals participated in semi-structured interviews, which were transcribed and inductively coded to identify themes. Of the 12 participants, 3 received clinical genetic testing results that confirmed pathogenic or likely pathogenic variants noted in raw DNA interpretation reports (confirmation positive), and 9 were not confirmed. Nearly all (n = 11) participants described emotional distress and information-seeking behavior as a coping mechanism after discovering a pathogenic or likely pathogenic variant in raw DNA interpretation. When pursuing confirmatory genetic testing, many (n = 9) faced challenges with finding knowledgeable healthcare providers and obtaining insurance coverage. Despite reporting concerns over raw DNA interpretation and a desire for more safeguards, almost all (n = 10) participants stated interest in using the service again. Overall, participants' experiences reveal they find personal utility in raw DNA interpretation results and provide insight into opportunities for patient and provider education.

Elective genomic testing: Practice resource of the National Society of Genetic Counselors

Genetic counseling for patients who are pursuing genetic testing in the absence of a medical indication, referred to as elective genomic testing (EGT), is becoming more common. This type of testing has the potential to detect genetic conditions before there is a significant health impact permitting earlier management and/or treatment. Pre- and post-test counseling for EGT is similar to indication-based genetic testing. Both require a complete family and medical history when ordering a test or interpreting a result. However, EGT counseling has some special considerations including greater uncertainties around penetrance and clinical utility and a lack of published guidelines. While certain considerations in the selection of a high-quality genetic testing laboratory are universal, there are some considerations that are unique to the selection of a laboratory performing EGT. This practice resource intends to provide guidance for genetic counselors and other healthcare providers caring for adults seeking pre- or post-test counseling for EGT. Genetic counselors and other genetics trained healthcare providers are the ideal medical professionals to supply accurate information to individuals seeking counseling about EGT enabling them to make informed decisions about testing and follow-up.

The Role of Genetic Testing for Parkinson's Disease

PURPOSE OF REVIEW

To describe current practices and attitudes about genetic testing for Parkinson's disease (PD) among neurologists, highlight the changing scene of genetic testing for PD, and provide guidance on facilitating PD genetic testing in a clinical practice.

RECENT FINDINGS

Since the 1990s, researchers have discovered several major gene variants contributing to PD etiology. A large body of literature now exists supporting the frequency of these variants in different populations and their effects on phenotype and clinical course. Recently, clinical trials have emerged with therapies targeting genetic forms of PD, specifically LRRK2 and GBA. Despite this growing knowledge, genetic testing for PD is not typically offered by neurologists including movement disorder specialists. Neurologists express concerns about the financial and practical issues of genetic testing as well as the potential impact on their patients. Researchers and specialists in the field are questioning this hesitation as clinical utility and consumer demand increase. Consideration of genetic testing for PD is shifting, as we enter a new era of precision medicine and gain clinical knowledge about PD. Barriers to testing, as perceived by clinicians, can be overcome with education, support, and involvement of multiple stakeholders with the goal of making PD genetic testing accessible to all patients.

Genetic counselor approaches to BRCA1/2 direct-to-consumer genetic testing results

The National Comprehensive Cancer Network recommends clinical-grade genetic testing to confirm commercial results from direct-to-consumer genetic testing (DTC-GT) companies and third-party interpretation (TPI) services; however, the type of confirmatory testing that genetic counselors (GCs) recommend remains uncharacterized. Therefore, we aimed to describe GCs testing strategies for patients who have already obtained DTC-GT results (23andMe) or TPI data (Promethease) that reported a BRCA1/2 pathogenic variant. We invited GCs specializing in clinical cancer genetics to complete an online survey distributed to members of the National Society of Genetic Counselors. The survey, completed by 80 respondents, contained case scenarios featuring probands with variable personal and family histories of cancer. Our results show that the majority of participating GCs have counseled patients for their health-related commercial test results; 94% have encountered patient DTC-GT reports (3 per year), and 69% have encountered patient TPI data (2 per year). Most participating GCs would recommend confirmatory clinical-grade testing for probands with a positive 23andMe BRCA1/2 result (77/80, 96%). However, there was strong variability between the type of recommended testing. Approximately 20% recommended single-site analysis, 11%-14% recommended the three Ashkenazi Jewish BRCA1/2 founder mutations, 4% recommended BRCA1/2 testing, and 61%-64% recommended multi-gene panel testing. The most commonly recommended panels were split between a breast and gynecological cancer-focused panel and a broad pan-cancer panel. The majority of participants (98%-100%) would also recommend confirmatory testing for patients with positive TPI data for BRCA1/2. Similarly, results were mixed between those who recommended targeted, single-site analysis (10%-15%) compared to a multi-gene panel (72%-83%). These data show that while most GCs were uniform in their practice of recommending confirmatory testing, they are mixed in their approach to the specific type of testing they would select. These results may help inform counseling approaches and consensus for this expanding group of patients.

Ethical challenges of precision cancer medicine

Amongst common diseases, cancer is often both a leader in self-regulatory policy, or the field for contentious ethical issues such as the patenting of the BRCA1/2 genes. With the advent of genomic sequencing technologies, achieving precision cancer medicine requires prospective norms due to the large and varied sources of data involved. Here, we discuss the ethical and legal aspects of the policy debate around the relevant topics in precision cancer medicine: the return of incidental findings and sequencing raw data to patients, the communication of genetic results to patients' relatives, privacy and communication risks with concomitant oversight strategies, patient participation and consent models. We present the arguments and empirical data supporting specific policy solutions delineating still contested areas. What type of consent and oversight are required to acquire genomic data or to access it where desired, either by the participant/patient or third-party researchers? Most of the raw sequencing data is still uninterpretable and the variants revealed subject to reinterpretation over time. No doubt the ethical challenges of precision cancer medicine are a prototype of what's to come for other diseases. They are also paradigmatic for regulatory and ethical questions of the translational endeavors since the two worlds - basic science and patient care - are governed by different ethical and legal principles that need to be reconciled in precision cancer medicine.

Health and kinship matter: Learning about direct-to-consumer genetic testing user experiences via online discussions

Background

Millions of people have undergone direct-to-consumer genetic testing (DTC-GT), but little is known about individuals' motivations and experiences (e.g., discussion topics and emotions after obtaining the test results) in engaging with DTC-GT services. Previous studies either involved only a small number of DTC-GT consumers or were based on hypothetical scenarios.

Objective

Our study aimed to fill this gap by investigating online discussions about DTC-GT that developed naturally among tens of thousands of social media users.

Methods

We focused on the posts that were published in the r/23andme and r/AncestryDNA subreddits, which correspond to the two companies with the largest number of consumers in the DTC-GT market. We applied computational methods to infer and examine the topics discussed, temporal trends in posting rates and themes (e.g., aggregation of related topics), and emotions expressed in these online forums.

Results

We collected 157,000 posts published by 16,500 Reddit users between 2013 and 2019. We found that the posting rates increased sharply after popular promotional events (e.g., each Amazon Prime Day and Black Friday) and most posts were inquiries into, or status updates about, testing progress. The inferred themes of Ancestral Origin and Kinship/Feelings were the two most frequently discussed, while discussions about the Health Risks theme focused primarily on submitting DTC-GT raw data to third parties for interpretation. The Kinship/Feelings theme exhibited the largest range of emotional response. A qualitative review of the posts with extreme emotions showed that some people became excited because they found their biological parents or other kin, while others became upset because they unexpectedly found that their parents or other kin were not biologically related to them.

Conclusion

This research demonstrates that online social media platforms can serve as a rich resource for characterizing actual DTC-GT experiences. The findings suggest that DTC-GT consumers' purchasing behaviors are associated with societal events and that future investigations should consider how DTC-GT challenges our understanding of kinship structure and function, genomic privacy, and the interpretation of health risks.

Personal Health Information Inference Using Machine Learning on RNA Expression Data from Patients With Cancer: Algorithm Validation Study

BACKGROUND

As the need for sharing genomic data grows, privacy issues and concerns, such as the ethics surrounding data sharing and disclosure of personal information, are raised.

OBJECTIVE

The main purpose of this study was to verify whether genomic data is sufficient to predict a patient's personal information.

METHODS

RNA expression data and matched patient personal information were collected from 9538 patients in The Cancer Genome Atlas program. Five personal information variables (age, gender, race, cancer type, and cancer stage) were recorded for each patient. Four different machine learning algorithms (support vector machine, decision tree, random forest, and artificial neural network) were used to determine whether a patient's personal information could be accurately predicted from RNA expression data. Performance measurement of the prediction models was based on the accuracy and area under the receiver operating characteristic curve. We selected five cancer types (breast carcinoma, kidney renal clear cell carcinoma, head and neck squamous cell carcinoma, low-grade glioma, and lung adenocarcinoma) with large samples sizes to verify whether predictive accuracy would differ between them. We also validated the efficacy of our four machine learning models in analyzing normal samples from 593 cancer patients.

RESULTS

In most samples, personal information with high genetic relevance, such as gender and cancer type, could be predicted from RNA expression data alone. The prediction accuracies for gender and cancer type, which were the best models, were 0.93-0.99 and 0.78-0.94, respectively. Other aspects of personal information, such as age, race, and cancer stage, were difficult to predict from RNA expression data, with accuracies ranging from 0.0026-0.29, 0.76-0.96, and 0.45-0.79, respectively. Among the tested machine learning methods, the highest predictive accuracy was obtained using the support vector machine algorithm (mean accuracy 0.77), while the lowest accuracy was obtained using the random forest method (mean accuracy 0.65). Gender and race were predicted more accurately than other variables in the samples. On average, the accuracy of cancer stage prediction ranged between 0.71-0.67, while the age prediction accuracy ranged between 0.18-0.23 for the five cancer types.

CONCLUSIONS

We attempted to predict patient information using RNA expression data. We found that some identifiers could be predicted, but most others could not. This study showed that personal information available from RNA expression data is limited and this information cannot be used to identify specific patients.

Sport and exercise genomics: the FIMS 2019 consensus statement update

Rapid advances in technologies in the field of genomics such as high throughput DNA sequencing, big data processing by machine learning algorithms and gene-editing techniques are expected to make precision medicine and gene-therapy a greater reality. However, this development will raise many important new issues, including ethical, moral, social and privacy issues. The field of exercise genomics has also advanced by incorporating these innovative technologies. There is therefore an urgent need for guiding references for sport and exercise genomics to allow the necessary advancements in this field of sport and exercise medicine, while protecting athletes from any invasion of privacy and misuse of their genomic information. Here, we update a previous consensus and develop a guiding reference for sport and exercise genomics based on a SWOT (Strengths, Weaknesses, Opportunities and Threats) analysis. This SWOT analysis and the developed guiding reference highlight the need for scientists/clinicians to be well-versed in ethics and data protection policy to advance sport and exercise genomics without compromising the privacy of athletes and the efforts of international sports federations. Conducting research based on the present guiding reference will mitigate to a great extent the risks brought about by inappropriate use of genomic information and allow further development of sport and exercise genomics in accordance with best ethical standards and international data protection principles and policies. This guiding reference should regularly be updated on the basis of new information emerging from the area of sport and exercise medicine as well as from the developments and challenges in genomics of health and disease in general in order to best protect the athletes, patients and all other relevant stakeholders.

Impute.me: An Open-Source, Non-profit Tool for Using Data From Direct-to-Consumer Genetic Testing to Calculate and Interpret Polygenic Risk Scores

To date, interpretation of genomic information has focused on single variants conferring disease risk, but most disorders of major public concern have a polygenic architecture. Polygenic risk scores (PRSs) give a single measure of disease liability by summarizing disease risk across hundreds of thousands of genetic variants. They can be calculated in any genome-wide genotype data-source, using a prediction model based on genome-wide summary statistics from external studies. As genome-wide association studies increase in power, the predictive ability for disease risk will also increase. Although PRSs are unlikely ever to be fully diagnostic, they may give valuable medical information for risk stratification, prognosis, or treatment response prediction. Public engagement is therefore becoming important on the potential use and acceptability of PRSs. However, the current public perception of genetics is that it provides "yes/no" answers about the presence/absence of a condition, or the potential for developing a condition, which in not the case for common, complex disorders with polygenic architecture. Meanwhile, unregulated third-party applications are being developed to satisfy consumer demand for information on the impact of lower-risk variants on common diseases that are highly polygenic. Often, applications report results from single-nucleotide polymorphisms (SNPs) and disregard effect size, which is highly inappropriate for common, complex disorders where everybody carries risk variants. Tools are therefore needed to communicate our understanding of genetic vulnerability as a continuous trait, where a genetic liability confers risk for disease. Impute.me is one such tool, whose focus is on education and information on common, complex disorders with polygenetic architecture. Its research-focused open-source website allows users to upload consumer genetics data to obtain PRSs, with results reported on a population-level normal distribution. Diseases can only be browsed by International Classification of Diseases, 10th Revision (ICD-10) chapter-location or alphabetically, thus prompting the user to consider genetic risk scores in a medical context of relevance to the individual. Here, we present an overview of the implementation of the impute.me site, along with analysis of typical usage patterns, which may advance public perception of genomic risk and precision medicine.

Genetic Privacy and Data Protection: A Review of Chinese Direct-to-Consumer Genetic Test Services

Background

The existing literature has not examined how Chinese direct-to-consumer (DTC) genetic testing providers navigate the issues of informed consent, privacy, and data protection associated with testing services. This research aims to explore these questions by examining the relevant documents and messages published on websites of the Chinese DTC genetic test providers.

Methods

Using Baidu.com, the most popular Chinese search engine, we compiled the websites of providers who offer genetic testing services and analyzed available documents related to informed consent, the terms of services, and the privacy policy. The analyses were guided by the following inquiries as they applied to each DTC provider: the methods available for purchasing testing products; the methods providers used to obtain informed consent; privacy issues and measures for protecting consumers’ health information; the policy for third-party data sharing; consumers right to their data; and the liabilities in the event of a data breach.

Results

68.7% of providers offer multiple channels for purchasing genetic testing products, and that social media has become a popular platform to promote testing services. Informed consent forms are not available on 94% of providers’ websites and a privacy policy is only offered by 45.8% of DTC genetic testing providers. Thirty-nine providers stated that they used measures to protect consumers’ information, of which, 29 providers have distinguished consumers’ general personal information from their genetic information. In 33.7% of the cases examined, providers stated that with consumers’ explicit permission, they could reuse and share the clients’ information for non-commercial purposes. Twenty-three providers granted consumer rights to their health information, with the most frequently mentioned right being the consumers’ right to decide how their data can be used by providers. Lastly, 21.7% of providers clearly stated their liabilities in the event of a data breach, placing more emphasis on the providers’ exemption from any liability.

Conclusions

Currently, the Chinese DTC genetic testing business is running in a regulatory vacuum, governed by self-regulation. The government should develop a comprehensive legal framework to regulate DTC genetic testing offerings. Regulatory improvements should be made based on periodical reviews of the supervisory strategy to meet the rapid development of the DTC genetic testing industry.

'It's much more grey than black and white': clinical geneticists' views on the oversight of consumer genomics in Europe

Aim: Direct-to-consumer (DTC) genetic tests (GT) have created controversy regarding their risks and benefits. In view of recent regulatory developments, this article aims to explore the attitudes of European clinical geneticists toward the oversight of DTC GT. Materials & methods: Fifteen semi-structured interviews were performed with clinical geneticists based in ten European countries. The transcripts were thematically analysized in an iterative process. Results & conclusion: Respondents strongly supported quality standards for DTC GT equal to those applied within the healthcare setting. Despite participants unanimously considering the involvement of healthcare professionals to be important, mandatory medical supervision was controversial. In this regard, promoting education and truth-in-advertising was considered as being key in maintaining a balance between protecting consumers and promoting their autonomy.

From Expectations to Experiences: Consumer Autonomy and Choice in Personal Genomic Testing

Background: Personal genomic testing (PGT) offers individuals genetic information about relationships, wellness, sporting ability, and health. PGT is increasingly accessible online, including in emerging markets such as Australia. Little is known about what consumers expect from these tests and whether their reflections on testing resonate with bioethics concepts such as autonomy.Methods: We report findings from focus groups and semi-structured interviews that explored attitudes to and experiences of PGT. Focus group participants had little experience with PGT, while interview participants had undergone testing. Recordings were transcribed and analyzed using thematic analysis. Findings were critically interpreted with reference to bioethics scholarship on autonomy.Results: Fifty-six members of the public participated in seven focus groups, and 40 individuals were interviewed separately. Both groups valued the choice of PGT, and believed that it could motivate relevant actions. Focus group themes centered on the perceived value of choices, knowledge enabling action and knowledge about the self. Interview themes suggest that participants reflexively engage with their PGT information to make meaning, and that some appreciate its shortcomings. Critical interpretation of findings shows that while consumers of PGT are able to exercise a degree of autonomy in choosing, they may not be able to achieve a substantive conceptualization of autonomy, one that promotes alignment with higher-order desires.Conclusions: PGT consumers can critically reason about testing. However, they may uncritically accept test results, may not appreciate drawbacks of increased choice, or may overestimate the potential for information to motivate behavioral change. While consumers appear to be capable of substantive autonomy, they do so without ongoing support from companies. PGT companies promote a problematic ("default") account of autonomy, reliant on empowerment rhetoric. This leaves consumers vulnerable to making decisions inconsistent with their higher-order desires. As PGT expands, claims about its power and value need to be carefully drawn.

Direct-to-consumer genetic testing with third party interpretation: beware of spurious results

Direct-to-consumer (DTC) genetic tests aim to provide insights into issues as varied as ancestry, nutrition, athletic ability and child talent, and some also report on disease risks. DTC companies tend to present their tests as uniformly beneficial, but the quality of the information they provide can be doubtful. Tests often invite people to step between territories, from the consumer in search of ‘fun’ information to potential patient, and the boundaries between these roles become even murkier when individuals explore the raw data from their DTC tests using third-party interpretation websites. We discuss two composite cases from U.K. genetics centres where patients used third party interpretation services to analyse raw data from DTC genetic tests. They then presented to NHS clinical services requesting interventions based on the disease-associated variants found, only to find that these variants were not actually present: their ‘pathogenic results’ were spurious. We highlight the risk of false positives (as well as false negatives) from DTC genetic tests, and discuss whether these cases represent the start of a worrying trend, where publicly funded clinicians and clinical scientists increasingly need to spend time and money investigating genetic results of dubious validity.

Targeting the delivery of dietary plant bioactives to those who would benefit most: from science to practical applications

Background

A healthy diet and optimal lifestyle choices are amongst the most important actions for the prevention of cardiometabolic diseases. Despite this, it appears difficult to convince consumers to select more nutritious foods. Furthermore, the development and production of healthier foods do not always lead to economic profits for the agro-food sector. Most dietary recommendations for the general population represent a “one-size-fits-all approach” which does not necessarily ensure that everyone has adequate exposure to health-promoting constituents of foods. Indeed, we now know that individuals show a high variability in responses when exposed to specific nutrients, foods, or diets.

Purpose

This review aims to highlight our current understanding of inter-individual variability in response to dietary bioactives, based on the integration of findings of the COST Action POSITIVe. We also evaluate opportunities for translation of scientific knowledge on inter-individual variability in response to dietary bioactives, once it becomes available, into practical applications for stakeholders, such as the agro-food industry. The potential impact from such applications will form an important impetus for the food industry to develop and market new high quality and healthy foods for specific groups of consumers in the future. This may contribute to a decrease in the burden of diet-related chronic diseases.

Individual differences in ADME (Absorption, Digestion, Metabolism and Excretion) is believed to underpin much of the inter-individual variation in responses.

Recent developments in the area of food metabolome databases and fast improvements in innovative metabotyping technologies hold great promise for improved profiling of dietary intake, exposure to individual ingredients, foods and dietary patterns, as well as our ability to identify individual responsiveness.

The food industry needs well-defined population clusters or targets in order to be able to design “personalized products”.

There are indeed excellent industrial opportunities for foods that modulate gut microbiota, and thereby enable the delivery of food bioactive metabolites.

It is currently not clear whether knowledge on individual nutrient needs, based on genetic or metagenomic data, would affect long-term dietary and health behaviours.

Data to support the development of dietary recommendations may need to be generated by new n-of-1-based study designs in the future.

First Responder to Genomic Information: A Guide for Primary Care Providers

With rapid advances in genetics and genomics, the commercialization and access to new applications has become more widespread and omnipresent throughout biomedical research. Thus, increasingly, more patients will have personal genomic information they may share with primary care providers (PCPs) to better understand the clinical significance of the data. To be able to respond to patient inquiries about genomic data, variant interpretation, disease risk, and other issues, PCPs will need to be able to increase or refresh their awareness about genetics and genomics, and identify reliable resources to use or refer patients. While provider educational efforts have increased, with the rapid advances in the field, ongoing efforts will be needed to prepare PCPs to manage patient needs, integrate results into care, and refer as indicated.

Data Work: Meaning-Making in the Era of Data-Rich Medicine

In the era of data-rich medicine, an increasing number of domains of people’s lives are datafied and rendered usable for health care purposes. Yet, deriving insights for clinical practice and individual life choices and deciding what data or information should be used for this purpose pose difficult challenges that require tremendous time, resources, and skill. Thus, big data not only promises new clinical insights but also generates new—and heretofore largely unarticulated—forms of work for patients, families, and health care providers alike. Building on science studies, medical informatics, Anselm Strauss and colleagues’ concept of patient work, and subsequent elaborations of articulation work, in this article, we analyze the forms of work engendered by the need to make data and information actionable for the treatment decisions and lives of individual patients. We outline three areas of data work, which we characterize as the work of supporting digital data practices, the work of interpretation and contextualization, and the work of inclusion and interaction. This is a first step toward naming and making visible these forms of work in order that they can be adequately seen, rewarded, and assessed in the future. We argue that making data work visible is also necessary to ensure that the insights of big and diverse datasets can be applied in meaningful and equitable ways for better health care.

Third-Party Genetic Interpretation Tools: A Mixed-Methods Study of Consumer Motivation and Behavior

In an effort to meet ethical obligations and/or participant expectations, researchers may consider offering "raw" or uninterpreted genetic data for result return. It is therefore important to understand the motivations, behaviors, and perspectives of individuals who might choose to access raw data before such return becomes routine. In the direct-to-consumer (DTC) context, where raw data are often made available to customers, the use of third-party interpretation tools has raised concerns about genotype accuracy, data privacy, reliability of interpretation, and consumption of limited health care resources. However, relatively little is known about why individuals access raw data or what they do with the information received from third-party interpretation. Accordingly, we conducted a survey on raw data access and third-party tool usage among 1,137 DTC customers recruited through social media. Most survey respondents (89%) reported downloading their raw data. Among downloaders, 94% used at least one tool, most commonly Promethease (63%) or GEDmatch (84%). More than half (56%) used both health-related and non-health-related tools and differed significantly from those who used only one tool type in terms of demographics, participation in research, DTC tests ordered, and testing motivations. Exploratory interviews were conducted with 10 respondents and illustrated how social networking, initial lack of interesting findings, and general curiosity contributed to use of multiple tool types. These results suggest that even when initially motivated by ancestry and genealogy, consumers frequently also pursue health information in a largely unregulated and expanding suite of third-party tools, raising both challenges and opportunities for the professional genetics community.

Mind the gap: resources required to receive, process and interpret research-returned whole genome data

Most genotype-phenotype studies have historically lacked population diversity, impacting the generalizability of findings and thereby limiting the ability to equitably implement precision medicine. This well-documented problem has generated much interest in the ascertainment of new cohorts with an emphasis on multiple dimensions of diversity, including race/ethnicity, gender, age, socioeconomic status, disability, and geography. The most well known of these new cohort efforts is arguably All of Us, formerly known as the Precision Medicine Cohort Initiative Program. All of Us intends to ascertain at least one million participants in the United States representative of the multiple dimensions of diversity. As an incentive to participate, All of Us is offering the return of research results, including whole genome sequencing data, as well as the opportunity to contribute to the scientific process as non-scientists. The scale and scope of the proposed return of research results are unprecedented. Here, we briefly review possible return of genetic data models, including the likely data file formats and modes of data transfer or access. We also review the resources required to access and interpret the genetic or genomic data once received by the average participant, highlighting the nuanced anticipated barriers that will challenge both the digitally, computationally literate and illiterate participant alike. This inventory of resources required to receive, process, and interpret return of research results exposes the potential for access disparities and warns the scientific community to mind the gap so that all participants have equal access and understanding of the benefits of human genetic research.

Potential use of clinical polygenic risk scores in psychiatry - ethical implications and communicating high polygenic risk

Psychiatric disorders present distinct clinical challenges which are partly attributable to their multifactorial aetiology and the absence of laboratory tests that can be used to confirm diagnosis or predict risk. Psychiatric disorders are highly heritable, but also polygenic, with genetic risk conferred by interactions between thousands of variants of small effect that can be summarized in a polygenic risk score. We discuss four areas in which the use of polygenic risk scores in psychiatric research and clinical contexts could have ethical implications. First, there is concern that clinical use of polygenic risk scores may exacerbate existing health inequities. Second, research findings regarding polygenic risk could be misinterpreted in stigmatising or discriminatory ways. Third, there are concerns associated with testing minors as well as eugenics concerns elicited by prenatal polygenic risk testing. Fourth, potential challenges that could arise with the feedback and interpretation of high polygenic risk for a psychiatric disorder would require consideration. While there would be extensive overlap with the challenges of feeding back genetic findings in general, the potential clinical use of polygenic risk scoring warrants discussion in its own right, given the recency of this possibility. To this end, we discuss how lay interpretations of risk and genetic information could intersect. Consideration of these factors would be necessary for ensuring effective and constructive communication and interpretation of polygenic risk information which, in turn, could have implications for the uptake of any therapeutic recommendations. Recent advances in polygenic risk scoring have major implications for its clinical potential, however, care should be taken to ensure that communication of polygenic risk does not feed into problematic assumptions regarding mental disorders or support reductive interpretations.

Health Information Counselors: A New Profession for the Age of Big Data

Health care is increasingly data driven. Concurrently, there are concerns that health professionals lack the time and training to guide patients through the growing medical "data jungle." In the age of big data, ever wider domains of people's lives are "datafied," which renders ever more information-at least in principle-usable for health care purposes. Turning data into meaningful information for clinical practice-and deciding what data or information should not be used for this purpose-requires a significant amount of time, resources, and skill. The authors argue that academic medicine should lead the way in navigating the use of complex, highly personal data in clinical practice. To make data actionable for both clinicians and patients, the authors propose that the best way to navigate the interface between patients and providers in the era of data-rich medicine would be the creation of a new profession entirely: health information counselors (HICs). HICs would have broad knowledge of various kinds of health data and data quality evaluation techniques, as well as analytic skills in statistics and data interpretation. Trained also in interpersonal communication, health management, insurance systems, and medico-legal aspects of data privacy, HICs would know enough about clinical medicine to advise on the relevance of any kind of data for prevention, diagnosis, and treatment. The creation of this new specialty would help patients and health care professionals to make more informed choices about how increasing amounts of health data and information can or should inform health care.

Genes wide open: Data sharing and the social gradient of genomic privacy

This study reports on 13 semistructured in-depth interviews to qualitatively explore the experiences of individuals who publicly shared their direct-to-consumer genetic testing results on the platform openSNP. In particular, we focused on interviewees' understanding of privacy. Participants reported that the likelihood and the magnitude of privacy harms depend on gender, ethnicity, sexual orientation, the stigma associated with certain clinical conditions, the existence of adequate legislation, and the nature of national health care systems. Some participants expressed the view that those who enjoy higher socioeconomic status or are better protected by their country's legislation have a responsibility to share their genetic data. Our study shows that people who share their genetic data publicly online-far from being insensitive to privacy risks-have a complex understanding of the social, relational, and contextual nature of genetic privacy.

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.

False-positive results released by direct-to-consumer genetic tests highlight the importance of clinical confirmation testing for appropriate patient care

Purpose

There is increasing demand from the public for direct-to-consumer (DTC) genetic tests, and the US Food and Drug Administration limits the type of health-related claims DTC tests can market. Some DTC companies provide raw genotyping data to customers if requested, and these raw data may include variants occurring in genes recommended by the American College of Medical Genetics and Genomics to be reported as incidental/secondary findings. The purpose of this study was to review the outcome of requests for clinical confirmation of DTC results that were received by our laboratory and to analyze variant classification concordance.

Methods

We identified 49 patient samples received for further testing that had previously identified genetic variants reported in DTC raw data. For each case identified, information pertaining to the outcome of clinical confirmation testing as well as classification of the DTC variant was collected and analyzed.

Results

Our analyses indicated that 40% of variants in a variety of genes reported in DTC raw data were false positives. In addition, some variants designated with the “increased risk” classification in DTC raw data or by a third-party interpretation service were classified as benign at Ambry Genetics as well as several other clinical laboratories, and are noted to be common variants in publicly available population frequency databases.

Conclusion

Our results demonstrate the importance of confirming DTC raw data variants in a clinical laboratory that is well versed in both complex variant detection and classification.

APPLaUD: access for patients and participants to individual level uninterpreted genomic data

BACKGROUND

There is a growing support for the stance that patients and research participants should have better and easier access to their raw (uninterpreted) genomic sequence data in both clinical and research contexts.

MAIN BODY

We review legal frameworks and literature on the benefits, risks, and practical barriers of providing individuals access to their data. We also survey genomic sequencing initiatives that provide or plan to provide individual access. Many patients and research participants expect to be able to access their health and genomic data. Individuals have a legal right to access their genomic data in some countries and contexts. Moreover, increasing numbers of participatory research projects, direct-to-consumer genetic testing companies, and now major national sequencing initiatives grant individuals access to their genomic sequence data upon request.

CONCLUSION

Drawing on current practice and regulatory analysis, we outline legal, ethical, and practical guidance for genomic sequencing initiatives seeking to offer interested patients and participants access to their raw genomic data.

Raw Genomic Data: Storage, Access, and Sharing

Patients are increasingly being encouraged and supported to access and control their own medical and genomic data. We argue that well-established and transparent raw genomic data retention and returning policies are imperative to enable patients to practice their rights to access and control raw data.