Assessing management practices for variants of uncertain significance among genetic counselors in pediatrics

Increased utilization of genomic sequencing in pediatric medicine has increased the detection of variants of uncertain significance (VUS). Periodic VUS reinterpretation can clarify clinical significance and increase diagnostic yield, highlighting the importance of systematic VUS tracking and reinterpretation. There are currently no standardized guidelines or established best practices for VUS management, and our understanding of how genetic counselors (GCs) track and manage VUS results for pediatric patients is limited. In this exploratory study, GCs in pediatric clinics in North America were surveyed about their VUS management practices. A total of 124 responses were included in the analysis. The majority (n = 115, 92.7%) of GCs reported that VUS management workflows were at the discretion of each individual provider in their workplace. Approximately half (n = 65, 52%) kept track of patient VUS results over time, and GCs with lower patient volumes were more likely to do so (p = 0.04). While 95% (n = 114) of GCs had requested VUS reinterpretation at least once, only 5% (n = 6) requested it routinely. Most (n = 80, 86%) GCs notified patients when a VUS was reclassified, although methods of recontact differed when the reclassification was an upgrade versus a downgrade. GCs who asked patients to stay in touch through periodic recontact or follow-up appointments were more likely to request VUS reinterpretation (p = 0.01). The most frequently reported barriers to requesting reinterpretation regularly were patients being lost to follow-up (n = 39, 33.1%), insufficient bandwidth (n = 27, 22.9%), and lack of standardized guidelines (n = 25, 21.2%). GCs had consistent overall practices around VUS management around investigation, disclosure, reinterpretation, and recontact, but specific methods used differed and were at the discretion of each provider. These results showcase the current landscape of VUS management workflows in pediatrics and the challenges associated with adopting more uniform practices. The study findings can help inform future strategies to develop standardized guidelines surrounding VUS management.

RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS

SPOUT1/CENP-32 encodes a putative SPOUT RNA methyltransferase previously identified as a mitotic chromosome associated protein. SPOUT1/CENP-32 depletion leads to centrosome detachment from the spindle poles and chromosome misalignment. Aided by gene matching platforms, we identified 24 individuals with neurodevelopmental delays from 18 families with bi-allelic variants in SPOUT1/CENP-32 detected by exome/genome sequencing. Zebrafish spout1/cenp-32 mutants showed reduction in larval head size with concomitant apoptosis likely associated with altered cell cycle progression. In vivo complementation assays in zebrafish indicated that SPOUT1/CENP-32 missense variants identified in humans are pathogenic. Crystal structure analysis of SPOUT1/CENP-32 revealed that most disease-associated missense variants mapped to the catalytic domain. Additionally, SPOUT1/CENP-32 recurrent missense variants had reduced methyltransferase activity in vitro and compromised centrosome tethering to the spindle poles in human cells. Thus, SPOUT1/CENP-32 pathogenic variants cause an autosomal recessive neurodevelopmental disorder: SpADMiSS ( SPOUT1 Associated Development delay Microcephaly Seizures Short stature) underpinned by mitotic spindle organization defects and consequent chromosome segregation errors.

Practical considerations for reinterpretation of individual genetic variants

With the growing use of genetic testing in medicine, the question of when genetic findings should be reinterpreted in light of new data has become inescapable. The generation of population and disease-specific data, development of computational tools, and new understandings of the relationship of specific genes to disorders can all trigger changes in variant classification that may have important implications for patients and the clinicians caring for them. This is a particular concern for patients from groups underrepresented in current reference datasets, since they have higher rates of uncertain findings. Here we identify the challenges to implementing a systematic approach to variant reinterpretation and propose solutions. In particular, we address (a) the infrastructure needed to support implementation of systematic variant reinterpretation, (b) the issues around obtaining consent from patients for reinterpretation, (c) the process for triggering reinterpretation, (d) pathways for the flow of reinterpreted data, (e) considerations for how to cover the costs of reinterpretation, and (f) practical issues related to implementation of processes and policies that address these issues, including the importance of a fixed duration during which there is an expectation that variants will be reinterpreted.

Rare pathogenic variants in WNK3 cause X-linked intellectual disability

PURPOSE

WNK3 kinase (PRKWNK3) has been implicated in the development and function of the brain via its regulation of the cation-chloride cotransporters, but the role of WNK3 in human development is unknown.

METHOD

We ascertained exome or genome sequences of individuals with rare familial or sporadic forms of intellectual disability (ID).

RESULTS

We identified a total of 6 different maternally-inherited, hemizygous, 3 loss-of-function or 3 pathogenic missense variants (p.Pro204Arg, p.Leu300Ser, p.Glu607Val) in WNK3 in 14 male individuals from 6 unrelated families. Affected individuals had ID with variable presence of epilepsy and structural brain defects. WNK3 variants cosegregated with the disease in 3 different families with multiple affected individuals. This included 1 large family previously diagnosed with X-linked Prieto syndrome. WNK3 pathogenic missense variants localize to the catalytic domain and impede the inhibitory phosphorylation of the neuronal-specific chloride cotransporter KCC2 at threonine 1007, a site critically regulated during the development of synaptic inhibition.

CONCLUSION

Pathogenic WNK3 variants cause a rare form of human X-linked ID with variable epilepsy and structural brain abnormalities and implicate impaired phospho-regulation of KCC2 as a pathogenic mechanism.

Challenges of variant reinterpretation: Opinions of stakeholders and need for guidelines

PURPOSE

The knowledge used to classify genetic variants is continually evolving, and the classification can change on the basis of newly available data. Although up-to-date variant classification is essential for clinical management, reproductive planning, and identifying at-risk family members, there is no consistent practice across laboratories or clinicians on how or under what circumstances to perform variant reinterpretation.

METHODS

We conducted exploratory focus groups (N = 142) and surveys (N = 1753) with stakeholders involved in the process of variant reinterpretation (laboratory directors, clinical geneticists, genetic counselors, nongenetic providers, and patients/parents) to assess opinions on key issues, including initiation of reinterpretation, variants to report, termination of the responsibility to reinterpret, and concerns about consent, cost, and liability.

RESULTS

Stakeholders widely agreed that there should be no fixed termination point to the responsibility to reinterpret a previously reported genetic variant. There were significant concerns about liability and lack of agreement about many logistical aspects of variant reinterpretation.

CONCLUSION

Our findings suggest a need to (1) develop consensus and (2) create transparency and awareness about the roles and responsibilities of parties involved in variant reinterpretation. These data provide a foundation for developing guidelines on variant reinterpretation that can aid in the development of a low-cost, scalable, and accessible approach.

The Challenge of Genetic Variants of Uncertain Clinical Significance : A Narrative Review

Genomic tests expand diagnostic and screening opportunities but also identify genetic variants of uncertain clinical significance (VUSs). Only a minority of VUSs are likely to prove pathogenic when later reassessed, but resolution of the uncertainty is rarely timely. That uncertainty adds complexity to clinical decision making and can result in harms and costs to patients and the health care system, including the time-consuming analysis required to interpret a VUS and the potential for unnecessary treatment and adverse psychological effects. Current efforts to improve variant interpretation will help reduce the scope of the problem, but the high prevalence of rare and novel variants in the human genome points to VUSs as an ongoing challenge. Additional strategies can help mitigate the potential harms of VUSs, including testing protocols that limit identification or reporting of VUSs, subclassification of VUSs according to the likelihood of pathogenicity, routine family-based evaluation of variants, and enhanced counseling efforts. All involve tradeoffs, and the appropriate balance of measures is likely to vary for different test uses and clinical settings. Cross-specialty deliberation and public input could contribute to systematic and broadly supported policies for managing VUSs.

The clinical and molecular spectrum of QRICH1 associated neurodevelopmental disorder

De novo variants in QRICH1 (Glutamine-rich protein 1) has recently been reported in 11 individuals with intellectual disability (ID). The function of QRICH1 is largely unknown but it is likely to play a key role in the unfolded response of endoplasmic reticulum stress through transcriptional control of proteostasis. In this study, we present 27 additional individuals and delineate the clinical and molecular spectrum of the individuals (n = 38) with QRICH1 variants. The main clinical features were mild to moderate developmental delay/ID (71%), nonspecific facial dysmorphism (92%) and hypotonia (39%). Additional findings included poor weight gain (29%), short stature (29%), autism spectrum disorder (29%), seizures (24%) and scoliosis (18%). Minor structural brain abnormalities were reported in 52% of the individuals with brain imaging. Truncating or splice variants were found in 28 individuals and 10 had missense variants. Four variants were inherited from mildly affected parents. This study confirms that heterozygous QRICH1 variants cause a neurodevelopmental disorder including short stature and expands the phenotypic spectrum to include poor weight gain, scoliosis, hypotonia, minor structural brain anomalies, and seizures. Inherited variants from mildly affected parents are reported for the first time, suggesting variable expressivity.

Reimbursement for genetic variant reinterpretation: five questions payers should ask

Reaching the goals set by the Health Care Payment and Learning Action Network requires an unyielding and unrelenting focus on encouraging providers to adopt advanced alternative payment models (APMs). Many of these models will continue to be voluntary because they either are in early stages or have not yet proven their effectiveness. The models that have proven their effectiveness should become permanent, comprising the new way that providers are paid in the Medicare program. Either way, getting today's high performers into those programs and keeping them engaged to continue to innovate and set new benchmarks is as important as attracting and improving the performance of poorer performers. That will require a shift in Medicare's policy on pricing and evaluating APMs.

Is there a duty to reinterpret genetic data? The ethical dimensions

The evolving evidence base for the interpretation of variants identified in genetic and genomic testing has presented the genetics community with the challenge of variant reinterpretation. In particular, it is unclear whether an ethical duty of periodic reinterpretation should exist, who should bear that duty, and what its dimensions should be. Based on an analysis of the ethical arguments for and against a duty to reinterpret, we conclude that a duty should be recognized. Most importantly, by virtue of ordering and conducting tests likely to produce data on variants that cannot be definitively interpreted today, the health-care system incurs a duty to reinterpret when more reliable data become available. We identify four elements of the proposed ethical duty: data storage, initiation of reinterpretation, conduct of reinterpretation, and patient recontact, and we identify the parties best situated to implement each component. We also consider the reasonable extent and duration of a duty, and the role of the patient's consent in the process, although we acknowledge that some details regarding procedures and funding still need to be addressed. The likelihood of substantial patient benefit from a systematic approach to reinterpretation suggests the importance for the genetics community to reach consensus on this issue.

Impact of patient education videos on genetic counseling outcomes after exome sequencing

OBJECTIVE

Growing use of clinical exome sequencing (CES) has led to an increased burden of genomic education. Self-guided educational tools can minimize the educational burden for genetic counselors (GCs). The effectiveness of these tools must be evaluated.

METHODS

Parents of patients offered CES were randomized to watch educational videos before their visit or to receive routine care. Parents and GCs were surveyed about their experiences following the sessions. The responses of the video (n = 102) and no-video (n = 105) groups were compared.

RESULTS

GCs reported no significant differences between parents in the video and no-video groups on genetics knowledge or CES knowledge. In contrast, parents' scores on genetics knowledge questions were lower in the video than no-video group (p = 0.007). Most parents reported the videos were informative, and the groups did not differ in satisfaction with GCs or decisions to have CES.

CONCLUSION

GCs and parents perceived the videos to be beneficial. However, lower scores on genetics knowledge questions highlight the need for careful development of educational tools.

PRACTICE IMPLICATIONS

Educational tools should be developed and assessed for effectiveness with the input of all stakeholders before widespread implementation. Better measures of the effectiveness of these educational tools are needed.

Impact of metabolic disorders on the relation between overweight/obesity and incident myocardial infarction and ischaemic stroke in fertile women: a nationwide cohort study

AIMS

Whether overweight is a risk factor for cardiovascular disease in the absence of metabolic disorders remains under debate and is largely unexamined in young women. We evaluated the risk of myocardial infarction and ischaemic stroke in fertile women conditional on time-dependent presence of metabolic disorders.

MATERIALS AND METHODS

From nationwide registers we identified all normal weight (body mass index [BMI] ≥ 18.5 to <25 kg m(-2) and overweight (BMI ≥ 25 kg m(-2)) Danish women giving birth from 2004 to 2009. Using multivariable Poisson regression models adjusted for age, calendar year and smoking, the risk of the composite outcome of myocardial infarction and ischaemic stroke was assessed with metabolic disorders (i.e. hypertensive conditions, abnormal glucose metabolism and/or dyslipidaemia) included as time-dependent variables.

RESULTS

The population comprised 261,489 women with median age of 30.5 years (interquartile range = [27.3, 33.8]). Median follow-up was 5.6 years (interquartile range = [4.0, 6.8]). Compared with normal weight women without metabolic disorders (with an incidence rate [IR] of 17.0 [95% confidence interval {CI} = 14.5-20.0] events per 100,000 person-years), overweight women without metabolic disorders had no significantly increased risk, IR 22.6 (CI = 18.3-27.8), adjusted incidence rate ratio (IRR), 1.26 (CI = 0.97-1.65). For women with metabolic disorders, IR was 30.2 (CI = 18.8-48.6) and adjusted IRR 1.77 (CI = 1.07-2.93) in normal weight, while IR was 87.1 (CI = 67.6-112.2) and IRR 4.24 (CI = 5 3.11-5.79) in overweight.

CONCLUSIONS

The risk of myocardial infarction and ischaemic stroke was more strongly associated with the presence of metabolic disorders than with overweight per se in fertile women. Targeting prevention of metabolic disorders might be beneficial to reduce cardiovascular disease in overweight/obese young women.

Morphologic observations after percutaneous transluminal balloon angioplasty of early and late aortocoronary saphenous vein bypass grafts

Clinical and morphologic observations from two patients undergoing percutaneous transluminal angioplasty of stenotic aortocoronary saphenous vein bypass grafts early (3 months) and late (56 months) after graft insertion are described. Each patient had one or more clinically successful graft dilations resulting in an angiographic increase in luminal diameter and a decrease in mean trans-stenotic gradient, and each had restenosis of the graft at the site of previous angioplasty within 2 months of dilation. Both operatively excised grafts had diffuse but variable amounts of intimal fibrous thickening and severe narrowing at the previous angioplasty site. The early graft had no evidence of dilation injury, and the intimal thickening consisted solely of fibrocollagenous tissue free of calcific deposits. In contrast, the late graft had a healing intimal dissection at the angioplasty site, and the intimal thickening consisted of atherosclerotic plaque with calcific deposits. Angiographic and morphologic correlations suggest that the mechanism of saphenous vein angioplasty early (less than or equal to 1 year) after insertion is by graft "stretching," while late (greater than 1 year) after insertion it is by atherosclerotic plaque "fracture" similar to that observed in atherosclerotic coronary arteries subjected to angioplasty procedures.

Conservative management of phantom-limb and amputation-stump pain

The causes of pain in the amputation stump or in the so-called phantom limb are far from clear and a wide variety of methods of treatment have been used with varying degrees of success. Surgical techniques do not always give lasting relief and it is suggested that conservative methods such as vibration therapy and various forms of electrical stimulation may prove more helpful.

Tar gel-phototherapy for psoriasis. Combined therapy with suberythemogenic doses of fluorescent sunlamp ultraviolet radiation

To determine the efficacy of suberythemogenic ultraviolet phototherapy in conjunction with administration of a tar gel (SEUV TG), patients with widespread psoriasis were treated by application of a tar gel preparation followed after 12 hours by suberythemogenic doses of fluorescent sunlamp irradiation. In paired comparison studies, therapeutic effects of the following treatments were evaluated: SEUV-TG, a more conventional erythemogenic tar gel phototherapy regimen (modified Goeckerman), the tar gel alone, and SEUV irradiation following application of gel vehicle. Response to therapy was monitored with a severity score system. In patients with psoriasis responsive to phototherapy, smaller quantities of UV energy administered in combination with a tar gel were at least as effective as larger erythemogenic doses. Production of erythema with fluorescent sunlamp radiation does not appear to be necessary to improve psoriasis. Both UV radiation and tar gel have beneficial effects on psoriasis, but the combination is superior.

Vicarious eyelid conditioning

This study attempted to demonstrate that elicited electromyographic (EMG) reactions in observers may become conditioned to environmental events during the observation of a modeling sequence. Observers were shown a videotape of a model in a simulated direct eyelid discriminative conditioning situation involving adaptation, acquisition, and extinction trials. Various EMG measures were obtained in order to determine the occurrence of vicarious instigation and conditioning. The results demonstrated vicarious EMG eyelid responses. Also, the motor reactions were found to be localized to specific muscular activity rather than a result of general arousal. Some theoretical and clinical implications of these findings are discussed.

Vicarious eyelid conditioning

This study attempted to demonstrate that elicited electromyographic (EMG) reactions in observers may become conditioned to environmental events during the observation of a modeling sequence. Observers were shown a videotape of a model in a simulated direct eyelid discriminative conditioning situation involving adaptation, acquisition, and extinction trials. Various EMG measures were obtained in order to determine the occurrence of vicarious instigation and conditioning. The results demonstrated vicarious EMG eyelid responses. Also, the motor reactions were found to be localized to specific muscular activity rather than a result of general arousal. Some theoretical and clinical implications of these findings are discussed.

Some effects of a model's performance on an observer's electromyographic activity

It is suggested that motor reactions may be elicited in an observer as a consequence of his exposure to a model and that such reactions may become conditioned to environmental events. An experiment is reported in which observers showed greater EMG activity in the arm while watching models arm wrestle than while watching a model stutter, and greater lip EMG activity while watching a model stutter than while watching arm wrestling. Some evidence for conditioning was found in the arm activity of males watching wrestling.