Katie L. Lewis

Interpreting Secondary Cardiac Disease Variants in an Exome Cohort

Background—Massively parallel sequencing to identify rare variants is widely practiced in medical research and in the clinic. Genome and exome sequencing can identify the genetic cause of a disease (primary results), but it can also identify pathogenic variants underlying diseases that are not being sought (secondary or incidental results). A major controversy has developed surrounding the return of secondary results to research participants. We have piloted a method to analyze exomes to identify participants at risk for cardiac arrhythmias, cardiomyopathies, or sudden death. Methods and Results—Exome sequencing was performed on 870 participants not selected for arrhythmia, cardiomyopathy, or a family history of sudden death. Exome data from 22 cardiac arrhythmia- and 41 cardiomyopathy-associated genes were analyzed using an algorithm that filtered results on genotype quality, frequency, and database information. We identified 1367 variants in the cardiomyopathy genes and 360 variants in the arrhythmia genes. Six participants had pathogenic variants associated with dilated cardiomyopathy (n=1), hypertrophic cardiomyopathy (n=2), left ventricular noncompaction (n=1), or long-QT syndrome (n=2). Two of these participants had evidence of cardiomyopathy and 1 had left ventricular noncompaction on echocardiogram. Three participants with likely pathogenic variants had prolonged QTc. Family history included unexplained sudden death among relatives. Conclusions—Approximately 0.5% of participants in this study had pathogenic variants in known cardiomyopathy or arrhythmia genes. This high frequency may be due to self-selection, false positives, or underestimation of the prevalence of these conditions. We conclude that clinically important cardiomyopathy and dysrhythmia secondary variants can be identified in unselected exomes.

Homozygosity for the V37I Connexin 26 mutation in three unrelated children with sensorineural hearing loss.

Mutations in the Connexin 26 (Cx26) gene have been found to account for approximately 20% of all childhood deafness. This number approaches 50% in documented recessive cases of hearing loss. Two mutations, 35delG and 167delT, account for the majority of reported mutations in this gene, but to date, more than 60 mutations have been described. No other single gene has yet been identified that contributes this significantly to the aetiology of hearing loss. Several mutations in this gene have been found to predominate in specific ethnic populations (167delT in Ashkenazi Jews and 235delC in Japanese individuals). While the majority of mutations found in Cx26 result in frame shifts and premature terminations, a number of missense mutations have also been identified. The V37I missense mutation has been reported as both a polymorphism and as a potentially disease‐causing missense mutation. The present authors have identified three unrelated individuals with sensorineural hearing loss who are homozygous for this mutation. One individual is of Philippine ancestry, another is from a Chinese and Cambodian background, while the third is of Chinese ancestry, raising the possibility that this mutation may be more frequent among populations in eastern Asia.

Preferences for results delivery from exome sequencing/genome sequencing

Purpose:The aim of this study was to explore the implications of sequencing information and stated preferences for return of results among research participants.Methods:Six focus groups were held with 39 ClinSeq participants. The groups included participants who had received results, those who had not, those affected with cardiovascular disease, and healthy adults. Audio recordings of the sessions were transcribed and coded and analyzed for themes.Results:All participants expressed interest in receiving results that are medically actionable, nonactionable, carrier, and less so variants that cannot be interpreted. Most participants preferred to receive results in person, although several endorsed use of Internet-based resources that they could return to. Participants identified benefits for health management along with satisfying curiosity, making scientific contributions, and partnering in research. Value was seen in gaining control over health risks. Concerns were distress and/or fear that may result. Some participants were opposed to or ambivalent about learning certain types of results, particularly those having to do with diseases that were incurable or that might have implications for the health of their children.Conclusion:There was relative enthusiasm about the value of learning sequencing information, yet it was tempered by concern about negative feeling responses and aversion to learning about incurable conditions.Genet Med 16 6, 442–447.

Elevated basal serum tryptase identifies a multisystem disorder associated with increased TPSAB1 copy number

Elevated basal serum tryptase levels are present in 4–6% of the general population, but the cause and relevance of such increases are unknown. Previously, we described subjects with dominantly inherited elevated basal serum tryptase levels associated with multisystem complaints including cutaneous flushing and pruritus, dysautonomia, functional gastrointestinal symptoms, chronic pain, and connective tissue abnormalities, including joint hypermobility. Here we report the identification of germline duplications and triplications in the TPSAB1 gene encoding α-tryptase that segregate with inherited increases in basal serum tryptase levels in 35 families presenting with associated multisystem complaints. Individuals harboring alleles encoding three copies of α-tryptase had higher basal serum levels of tryptase and were more symptomatic than those with alleles encoding two copies, suggesting a gene-dose effect. Further, we found in two additional cohorts (172 individuals) that elevated basal serum tryptase levels were exclusively associated with duplication of α-tryptase–encoding sequence in TPSAB1, and affected individuals reported symptom complexes seen in our initial familial cohort. Thus, our findings link duplications in TPSAB1 with irritable bowel syndrome, cutaneous complaints, connective tissue abnormalities, and dysautonomia.

Individualized Iterative Phenotyping for Genome-wide Analysis of Loss-of-Function Mutations

Next-generation sequencing provides the opportunity to practice predictive medicine based on identified variants. Putative loss-of-function (pLOF) variants are common in genomes and understanding their contribution to disease is critical for predictive medicine. To this end, we characterized the consequences of pLOF variants in an exome cohort by iterative phenotyping. Exome data were generated on 951 participants from the ClinSeq cohort and filtered for pLOF variants in genes likely to cause a phenotype in heterozygotes. 103 of 951 exomes had such a pLOF variant and 79 participants were evaluated. Of those 79, 34 had findings or family histories that could be attributed to the variant (28 variants in 18 genes), 2 had indeterminate findings (2 variants in 2 genes), and 43 had no findings or a negative family history for the trait (34 variants in 28 genes). The presence of a phenotype was correlated with two mutation attributes: prior report of pathogenicity for the variant (p = 0.0001) and prior report of other mutations in the same exon (p = 0.0001). We conclude that 1/30 unselected individuals harbor a pLOF mutation associated with a phenotype either in themselves or their family. This is more common than has been assumed and has implications for the setting of prior probabilities of affection status for predictive medicine.

Participant use and communication of findings from exome sequencing: a mixed-methods study

Purpose:This study investigated how genome sequencing results affect health behaviors, affect, and communication.Methods:We report on 29 participants who received a sequence result in the ClinSeq study, a cohort of well-educated, postreproductive volunteers. A mixed-methods design was used to explore respondents’ use, communication, and perceived utility of results.Results:Most participants (72%) shared their result with at least one health-care provider, and 31% reported subsequent changes in the health care they received. Participants scored high on the Positive Experiences subscale and low on the Distress subscale of a modified version of the Multidimensional Impact of Cancer Risk Assessment. The majority (93%) shared their result with at least one family member. Participants described deriving personal utility from their results.Conclusion:This article is the first to describe research participants’ reactions to actionable sequencing results. Our findings suggest clinical and personal benefit from receiving sequencing results, both of which may contribute to improved health for the recipients. Given the participants’ largely positive or neutral affective responses and disclosure of their results to physicians and relatives, health-care providers should redirect concern from the potential for distress and attend to motivating patients to follow their medical recommendations.Genet Med 18 6, 577–583.

The role of current affect, anticipated affect and spontaneous self-affirmation in decisions to receive self-threatening genetic risk information

One reason for not seeking personally threatening information may be negative current and anticipated affective responses. We examined whether current (e.g., worry) and anticipated negative affect predicted intentions to seek sequencing results in the context of an actual genomic sequencing trial (ClinSeq®; n = 545) and whether spontaneous self-affirmation mitigated any (negative) association between affect and intentions. Anticipated affective response negatively predicted intentions to obtain and share results pertaining to both medically actionable and non-actionable disease, whereas current affect was only a marginal predictor. The negative association between anticipated affect and intentions to obtain results pertaining to non-actionable disease was weaker in individuals who were higher in spontaneous self-affirmation. These results have implications for the understanding of current and anticipated affect, self-affirmation and consequential decision-making and contribute to a growing body of evidence on the role of affect in medical decisions.

How do research participants perceive "uncertainty" in genome sequencing?

Purpose:The scope of uncertainty in genome sequence information has no rival in health-care delivery. We present data from adults participating in a National Institutes of Health study using this technology, in which perceptions of uncertainty are hypothesized to be key in predicting decisions to learn and act on genome health information.Methods:We conducted six professionally moderated focus groups with 39 randomly selected ClinSeq participants varying on whether they had coronary heart disease and had received prior sequence results. We elicited perceptions of the uncertainties associated with genome sequencing using written prompts.Results:Participants perceived uncertainty as a quality of genome information. The majority of participants characterized uncertainty of sequencing information as “changing, fluid, developing, or ground breaking.” These responses led to anticipation of more optimistic future outcomes. Fewer participants described uncertainty as “questionable, less accurate, limited, or poorly understood.” These perceptions seemed to undermine participants’ faith in genome information, leading to feelings of disillusionment.Conclusion:Our findings suggest that perceptions of uncertainty are related to epistemological beliefs that inform expectations for the information. Interventions that promote realistic expectations of genome sequencing may mitigate negative responses to uncertainty.Genet Med 16 12, 977–980.

Characterizing Participants in the ClinSeq Genome Sequencing Cohort as Early Adopters of a New Health Technology.

Genome sequencing is a novel clinical tool that has the potential to identify genetic origins of disease. However, the complexities of this new technology are significant and little is known about its integration into clinical care, and its potential adoption by patients. Expectations of its promise for personalized medicine are high and it is important to properly match expectations to the realities of the test. The NIH ClinSeq cohort study pilots the integration of genome sequencing into clinical research and care to assess the technical, medical and socio-behavioral aspects of implementing this technology. Over 950 adults ages 45-65 have been enrolled and clinically phenotyped. As an initial study, we describe the personality traits of ClinSeq participants, and explore how these traits compare to those that characterize early adopters of other new technologies. Our analysis was conducted on responses from 630 members of the cohort who completed a baseline survey on health cognitions, affect, health-related behaviors and personality traits, prior to receipt of any genome sequencing results. The majority of participants were white (90.5%), had at least a college degree (86.5%), and had at least one biological child (74.6%). Members of this ClinSeq sample were found to be high in dispositional optimism and resilience. Their high SES paralleled that of other early adopters of new technology. These attributes may contribute to participants’ expectations for favorable outcomes and willingness to take higher risks when compared to the general population. These characteristics may distinguish those who are most likely to pursue genome sequencing and be indicative of their psychological resources to manage returned results.

Information avoidance tendencies, threat management resources, and interest in genetic sequencing feedback.

BackgroundInformation avoidance is a defensive strategy that undermines receipt of potentially beneficial but threatening health information and may especially occur when threat management resources are unavailable.PurposeWe examined whether individual differences in information avoidance predicted intentions to receive genetic sequencing results for preventable and unpreventable (i.e., more threatening) disease and, secondarily, whether threat management resources of self-affirmation or optimism mitigated any effects.MethodsParticipants (N = 493) in an NIH study (ClinSeq®) piloting the use of genome sequencing reported intentions to receive (optional) sequencing results and completed individual difference measures of information avoidance, self-affirmation, and optimism.ResultsInformation avoidance tendencies corresponded with lower intentions to learn results, particularly for unpreventable diseases. The association was weaker among individuals higher in self-affirmation or optimism, but only for results regarding preventable diseases.ConclusionsInformation avoidance tendencies may influence decisions to receive threatening health information; threat management resources hold promise for mitigating this association.