CLIA-tested genetic variants on commercial SNP arrays: potential for incidental findings in genome-wide association studies

Clinical Strategies in Gene Screening Counseling for the Healthy General Population

The burgeoning interest in precision medicine has propelled an increase in the use of genome tests for screening purposes within the healthy population. Gene screening tests aim to pre-emptively identify those individuals who may be genetically predisposed to certain diseases. However, as genetic screening becomes more commonplace, it is essential to acknowledge the unique challenges it poses. A prevalent issue in this regard is the occurrence of falsepositive results, which can lead to unnecessary additional tests or treatments, and psychological distress. Additionally, the interpretation of genomic variants is based on current research evidence, and can accordingly change as new research findings emerge, potentially altering the clinical significance of these variants. Conversely, a further prominent concern regards false assurances in genetic testing, as genetic tests can yield false-negative results, potentially posing a significant clinical risk. Moreover, the results obtained for the same disease can vary among different genetic testing services, due to differences in the types of variants assessed, the scope of tests, analytical methods, and the algorithms used for predicting diseases. Consequently, whereas genetic testing holds significant promise for the future of medicine, it poses unique challenges. If conducted without a full understanding of its implications, genetic testing may fail to achieve its purpose potentially hindering effective health management. Therefore, to ensure a comprehensive understanding of the implications of genetic testing within the general population, sufficient discussion and careful consideration should be given to counseling based on gene test results.

Computational identification of non-synonymous polymorphisms within regions corresponding to protein interaction sites

BACKGROUND

Protein-protein interactions (PPI) play an important role in function of all organisms and enable understanding of underlying metabolic processes. Computational predictions of PPIs are an important aspect in proteomics, as experimental methods may result in high degree of false positive results and are more expensive. Although there are many databases collecting predicted PPIs, exploration of genetics information underlying PPI interactions has not been investigated thoroughly. The aim of the present study was to identify genomic locations corresponding to regions involved in predicted PPIs and to collect non-synonymous polymorphisms (nsSNPs) located within those regions; which we termed PPI-SNPs.

METHODS

Predicted PPIs were obtained from PiSITE database (http://pisite.hgc.jp). Non-synonymous SNPs mapped on protein structural data (PDBs) were obtained from the UCSC server. Polymorphism locations on protein structures were mapped to predicted PPI regions. DAVID tool was used for pathway enrichment and gene cluster analysis (https://david.ncifcrf.gov/).

RESULTS

We collected 544 polymorphisms located within predicted PPI sites that map to 197 genes. We identified 9 SNPs, previously associated with diseases, but not yet associated with PPI sites. We also found examples in which polymorphisms located within predicted PPI regions are also occurring within previously experimentally validated PPIs and within experimentally determined functional domains.

CONCLUSIONS

Our study provides the first catalog of nsSNPs located within predicted PPIs. These prioritized SNPs present the basis for planning experimental validation of SNPs that cause gain or loss of PPIs. Our implementation is expandable, as datasets used are constantly updated.

Evidence for extensive pleiotropy among pharmacogenes

AIM

We sought to identify potential pleiotropy involving pharmacogenes.

METHODS

We tested 184 functional variants in 34 pharmacogenes for associations using a custom grouping of International Classification and Disease, Ninth Revision billing codes extracted from deidentified electronic health records of 6892 patients.

RESULTS

We replicated several associations including ABCG2 (rs2231142) and gout (p = 1.73 × 10(-7); odds ratio [OR]: 1.73; 95% CI: 1.40-2.12); and SLCO1B1 (rs4149056) and jaundice (p = 2.50 × 10(-4); OR: 1.67; 95% CI: 1.27-2.20).

CONCLUSION

In this systematic screen for phenotypic associations with functional variants, several novel genotype-phenotype combinations also achieved phenome-wide significance, including SLC15A2 rs1143672 and renal osteodystrophy (p = 2.67 × 10(-) (6); OR: 0.61; 95% CI: 0.49-0.75).

Internet-Based Direct-to-Consumer Genetic Testing: A Systematic Review

Background

Direct-to-consumer genetic tests (DTC-GT) are easily purchased through the Internet, independent of a physician referral or approval for testing, allowing the retrieval of genetic information outside the clinical context. There is a broad debate about the testing validity, their impact on individuals, and what people know and perceive about them.

Objective

The aim of this review was to collect evidence on DTC-GT from a comprehensive perspective that unravels the complexity of the phenomenon.

Methods

A systematic search was carried out through PubMed, Web of Knowledge, and Embase, in addition to Google Scholar according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist with the key term “Direct-to-consumer genetic test.”

Results

In the final sample, 118 articles were identified. Articles were summarized in five categories according to their focus on (1) knowledge of, attitude toward use of, and perception of DTC-GT (n=37), (2) the impact of genetic risk information on users (n=37), (3) the opinion of health professionals (n=20), (4) the content of websites selling DTC-GT (n=16), and (5) the scientific evidence and clinical utility of the tests (n=14). Most of the articles analyzed the attitude, knowledge, and perception of DTC-GT, highlighting an interest in using DTC-GT, along with the need for a health care professional to help interpret the results. The articles investigating the content analysis of the websites selling these tests are in agreement that the information provided by the companies about genetic testing is not completely comprehensive for the consumer. Given that risk information can modify consumers’ health behavior, there are surprisingly few studies carried out on actual consumers and they do not confirm the overall concerns on the possible impact of DTC-GT. Data from studies that investigate the quality of the tests offered confirm that they are not informative, have little predictive power, and do not measure genetic risk appropriately.

Conclusions

The impact of DTC-GT on consumers’ health perceptions and behaviors is an emerging concern. However, negative effects on consumers or health benefits have yet to be observed. Nevertheless, since the online market of DTC-GT is expected to grow, it is important to remain aware of a possible impact.

Practical barriers and ethical challenges in genetic data sharing

The underlying ethos of dbGaP is that access to these data by secondary data analysts facilitates advancement of science. NIH has required that genome-wide association study data be deposited in the Database of Genotypes and Phenotypes (dbGaP) since 2003. In 2013, a proposed updated policy extended this requirement to next-generation sequencing data. However, recent literature and anecdotal reports suggest lingering logistical and ethical concerns about subject identifiability, informed consent, publication embargo enforcement, and difficulty in accessing dbGaP data. We surveyed the International Genetic Epidemiology Society (IGES) membership about their experiences. One hundred and seventy five (175) individuals completed the survey, a response rate of 27%. Of respondents who received data from dbGaP (43%), only 32% perceived the application process as easy but most (75%) received data within five months. Remaining challenges include difficulty in identifying an institutional signing official and an overlong application process. Only 24% of respondents had contributed data to dbGaP. Of these, 31% reported local IRB restrictions on data release; an additional 15% had to reconsent study participants before depositing data. The majority of respondents (56%) disagreed that the publication embargo period was sufficient. In response, we recommend longer embargo periods and use of varied data-sharing models rather than a one-size-fits-all approach.

Three clinical experiences with SNP array results consistent with parental incest: a narrative with lessons learned

Single nucleotide polymorphism microarrays have the ability to reveal parental consanguinity which may or may not be known to healthcare providers. Consanguinity can have significant implications for the health of patients and for individual and family psychosocial well-being. These results often present ethical and legal dilemmas that can have important ramifications. Unexpected consanguinity can be confounding to healthcare professionals who may be unprepared to handle these results or to communicate them to families or other appropriate representatives. There are few published accounts of experiences with consanguinity and SNP arrays. In this paper we discuss three cases where molecular evidence of parental incest was identified by SNP microarray. We hope to further highlight consanguinity as a potential incidental finding, how the cases were handled by the clinical team, and what resources were found to be most helpful. This paper aims to contribute further to professional discourse on incidental findings with genomic technology and how they were addressed clinically. These experiences may provide some guidance on how others can prepare for these findings and help improve practice. As genetic and genomic testing is utilized more by non-genetics providers, we also hope to inform about the importance of engaging with geneticists and genetic counselors when addressing these findings.

Funding considerations for the disclosure of genetic incidental findings in biobank research

The use of biobanks in biomedical research has grown considerably in recent years. As a result of the increasing analysis of tissue samples stored in biobanks, there has also been an increase in the probability of discovering-in addition to the research target-incidental findings (IF). We identified 23 laws, policies and guidelines from international, regional and national organizations that provide guidance or identify the need for the disclosure of IF to research participants. We analyzed these instruments to determine their contemplation of the funding considerations for the disclosure of IF, examining their guidance for who discloses and the extent of researcher responsibilities. We found that the available normative documents provide little guidance to researchers and biobanks for how they should address cost and funding concerns associated with IF disclosure. It is therefore essential that the research and policy communities think through the financial implications of imposing an ethical responsibility to disclose IF. Concerted efforts should be made by policymakers, ethicists, researchers, clinicians and research institutions to develop detailed funding recommendations, potentially universal in application, to aid in the disclosure of IF, and we provide recommendations on steps that can be taken to ensure full consideration of these issues.

Experiences and attitudes of genome investigators regarding return of individual genetic test results

PURPOSE

Whether and how to return individual genetic results to study participants is among the most contentious policy issues in contemporary genomic research.

METHODS

We surveyed corresponding authors of genome-wide association studies, identified through the National Human Genome Research Institute's Catalog of Published Genome-Wide Association Studies, to describe the experiences and attitudes of these stakeholders.

RESULTS

Of 357 corresponding authors, 200 (56%) responded. One hundred twenty-six (63%) had been responsible for primary data and sample collection, whereas 74 (37%) had performed secondary analyses. Only 7 (4%) had returned individual results within their index genome-wide association studies. Most (69%) believed that return of results to individual participants was warranted under at least some circumstances. Most respondents identified a desire to benefit participants' health (63%) and respect for participants' desire for information (57%) as major motivations for returning results. Most also identified uncertain clinical utility (76%), the possibility that participants will misunderstand results (74%), the potential for emotional harm (61%), the need to ensure access to trained clinicians (59%), and the potential for loss of confidentiality (51%) as major barriers to return of results.

CONCLUSION

Investigators have limited experience returning individual results from genome-scale research, yet most are motivated to do so in at least some circumstances.

Incidental copy-number variants identified by routine genome testing in a clinical population

PURPOSE

Mutational load of susceptibility variants has not been studied on a genomic scale in a clinical population, nor has the potential to identify these mutations as incidental findings during clinical testing been systematically ascertained.

METHODS

Array comparative genomic hybridization, a method for genome-wide detection of DNA copy-number variants, was performed clinically on DNA from 9,005 individuals. Copy-number variants encompassing or disrupting single genes were identified and analyzed for their potential to confer predisposition to dominant, adult-onset disease. Multigene copy-number variants affecting dominant, adult-onset cancer syndrome genes were also assessed.

RESULTS

In our cohort, 83 single-gene copy-number variants affected 40 unique genes associated with dominant, adult-onset disorders and unrelated to the patients' referring diagnoses (i.e., incidental) were found. Fourteen of these copy-number variants are likely disease-predisposing, 25 are likely benign, and 44 are of unknown clinical consequence. When incidental copy-number variants spanning up to 20 genes were considered, 27 copy-number variants affected 17 unique genes associated with dominant, adult-onset cancer predisposition.

CONCLUSION

Copy-number variants potentially conferring susceptibility to adult-onset disease can be identified as incidental findings during routine genome-wide testing. Some of these mutations may be medically actionable, enabling disease surveillance or prevention; however, most incidentally observed single-gene copy-number variants are currently of unclear significance to the patient.

Individual genetic and genomic research results and the tradition of informed consent: exploring US review board guidance

BACKGROUND

Genomic research is challenging the tradition of informed consent. Genomic researchers in the USA, Canada and parts of Europe are encouraged to use informed consent to address the prospect of disclosing individual research results (IRRs) to study participants. In the USA, no national policy exists to direct this use of informed consent, and it is unclear how local institutional review boards (IRBs) may want researchers to respond.

OBJECTIVE AND METHODS

To explore publicly accessible IRB websites for guidance in this area, using summative content analysis.

FINDINGS

Three types of research results were addressed in 45 informed consent templates and instructions from 20 IRBs based at centres conducting genomic research: (1) IRRs in general, (2) incidental findings (IFs) and (3) a broad and unspecified category of 'significant new findings' (SNFs). IRRs were more frequently referenced than IFs or SNFs. Most documents stated that access to IRRs would not be an option for research participants. These non-disclosure statements were found to coexist in some documents with statements that SNFs would be disclosed to participants if related to their willingness to participate in research. The median readability of template language on IRRs, IFs and SNFs exceeded a ninth-grade level.

CONCLUSION

IRB guidance may downplay the possibility of IFs and contain conflicting messages on IRR non-disclosure and SNF disclosure. IRBs may need to clarify why separate IRR and SNF language should appear in the same consent document. The extent of these issues, nationally and internationally, needs to be determined.

Informed consent and genomic incidental findings: IRB chair perspectives

It is unclear how genomic incidental finding (GIF) prospects should be addressed in informed consent processes. An exploratory study on this topic was conducted with 34 purposively sampled Chairs of institutional review boards (IRBs) at centers conducting genome-wide association studies. Most Chairs (96%) reported no knowledge of local IRB requirements regarding GIFs and informed consent. Chairs suggested consent processes should address the prospect of, and study disclosure policy on, GIFs; GIF management and follow-up; potential clinical significance of GIFs; potential risks of GIF disclosure; an opportunity for participants to opt out of GIF disclosure; and duration of the researcher's duty to disclose GIFs. Chairs were concerned about participant disclosure preferences changing over time; inherent limitations in determining the scope and accuracy of claims about GIFs; and making consent processes longer and more complex. IRB Chair and other stakeholder perspectives can help advance informed consent efforts to accommodate GIF prospects.

Return of individual research results from genome-wide association studies: experience of the Electronic Medical Records and Genomics (eMERGE) Network

PURPOSE

Return of individual genetic results to research participants, including participants in archives and biorepositories, is receiving increased attention. However, few groups have deliberated on specific results or weighed deliberations against relevant local contextual factors.

METHODS

The Electronic Medical Records and Genomics (eMERGE) Network, which includes five biorepositories conducting genome-wide association studies, convened a return of results oversight committee to identify potentially returnable results. Network-wide deliberations were then brought to local constituencies for final decision making.

RESULTS

Defining results that should be considered for return required input from clinicians with relevant expertise and much deliberation. The return of results oversight committee identified two sex chromosomal anomalies, Klinefelter syndrome and Turner syndrome, as well as homozygosity for factor V Leiden, as findings that could warrant reporting. Views about returning findings of HFE gene mutations associated with hemochromatosis were mixed due to low penetrance. Review of electronic medical records suggested that most participants with detected abnormalities were unaware of these findings. Local considerations relevant to return varied and, to date, four sites have elected not to return findings (return was not possible at one site).

CONCLUSION

The eMERGE experience reveals the complexity of return of results decision making and provides a potential deliberative model for adoption in other collaborative contexts.

Disclosing pathogenic genetic variants to research participants: quantifying an emerging ethical responsibility

There is an emerging consensus that when investigators obtain genomic data from research participants, they may incur an ethical responsibility to inform at-risk individuals about clinically significant variants discovered during the course of their research. With whole-exome sequencing becoming commonplace and the falling costs of full-genome sequencing, there will be an increasingly large number of variants identified in research participants that may be of sufficient clinical relevance to share. An explicit approach to triaging and communicating these results has yet to be developed, and even the magnitude of the task is uncertain. To develop an estimate of the number of variants that might qualify for disclosure, we apply recently published recommendations for the return of results to a defined and representative set of variants and then extrapolate these estimates to genome scale. We find that the total number of variants meeting the threshold for recommended disclosure ranges from 3955-12,579 (3.79%-12.06%, 95% CI) in the most conservative estimate to 6998-17,189 (6.69%-16.48%, 95% CI) in an estimate including variants with variable disease expressivity. Additionally, if the growth rate from the previous 4 yr continues, we estimate that the total number of disease-associated variants will grow 37% over the next 4 yr.

Public attitudes toward ancillary information revealed by pharmacogenetic testing under limited information conditions

PURPOSE

Pharmacogenetic testing can inform drug dosing and selection by aiding in estimating a patient's genetic risk of adverse response and/or failure to respond. Some pharmacogenetic tests may generate ancillary clinical information unrelated to the drug treatment question for which testing is done-an informational "side effect." We aimed to assess public interest and concerns about pharmacogenetic tests and ancillary information.

METHODS

We conducted a random-digit-dial phone survey of a sample of the US public.

RESULTS

We achieved an overall response rate of 42% (n = 1139). When the potential for ancillary information was presented, 85% (±2.82%) of respondents expressed interest in pharmacogenetic testing, compared with 82% (±3.02%) before discussion of ancillary information. Most respondents (89% ± 2.27%) indicated that physicians should inform patients that a pharmacogenetic test may reveal ancillary risk information before testing is ordered. Respondents' interest in actually learning of the ancillary risk finding significantly differed based on disease severity, availability of an intervention, and test validity, even after adjusting for age, gender, education, and race.

CONCLUSION

Under the limited information conditions presented in the survey, the potential of ancillary information does not negatively impact public interest in pharmacogenetic testing. Interest in learning ancillary information is well aligned with the public's desire to be informed about potential benefits and risks before testing, promoting patient autonomy.

An extended IUPAC nomenclature code for polymorphic nucleic acids

The International Union of Pure and Applied Chemistry (IUPAC) code specified nearly 25 years ago provides a nomenclature for incompletely specified nucleic acids. However, no system currently exists that allows for the informatics representation of the relative abundance at polymorphic nucleic acids (e.g. single nucleotide polymorphisms) in a single specified character, or a string of characters. Here, I propose such an information code as a natural extension to the IUPAC nomenclature code, and present some potential uses and limitations to such a code. The primary anticipated use of this extended nomenclature code is to assist in the representation of the rapidly growing space of information in human genetic variation.

CONTACT

johnsonad2@nhlbi.nih.gov

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.