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Autism, schizophrenia, and other clinically distinct neurodevelopmental psychiatric disorders (NPDs) have shared genetic etiologies, including single-gene and multigenic copy number variants (CNVs). Because rare variants are primarily investigated in clinical cohorts, population-based estimates of their prevalence and penetrance are lacking. The authors determined the prevalence, penetrance, and NPD risk of pathogenic single-gene variants in a large health care system population.The authors analyzed linked genomic and electronic health record (EHR) data in a subset of 90,595 participants from Geisinger's MyCode Community Health Initiative, known as the DiscovEHR cohort. Loss-of-function pathogenic variants in 94 high-confidence NPD genes were identified through exome sequencing, and NPD penetrance was calculated using preselected EHR diagnosis codes. NPD risk was estimated using a case-control comparison of DiscovEHR participants with and without NPD diagnoses. Results from single-gene variant analyses were also compared with those from 31 previously reported pathogenic NPD CNVs.Pathogenic variants were identified in 0.34% of the DiscovEHR cohort and demonstrated a 34.3% penetrance for NPDs. Similar to CNVs, sequence variants collectively conferred a substantial risk for several NPD diagnoses, including autism, schizophrenia, and bipolar disorder. Significant NPD risk remained after participants with intellectual disability were excluded from the analysis, confirming the association with major psychiatric disorders in individuals without severe cognitive deficits.Collectively, rare single-gene variants and CNVs were found in1% of individuals in a large health care system population and play an important contributory role in mental health disorders. Diagnostic genetic testing for pathogenic variants among symptomatic individuals with NPDs could improve clinical outcomes through early intervention and anticipatory therapeutic support.

ImportanceExome sequencing is a first-tier diagnostic test for individuals with neurodevelopmental disorders, including intellectual disability/developmental delay and autism spectrum disorder; however, this recommendation does not include cerebral palsy.ObjectiveTo evaluate if the diagnostic yield of exome or genome sequencing in cerebral palsy is similar to that of other neurodevelopmental disorders.Data SourcesThe study team searched PubMed for studies published between 2013 and 2022 using cerebral palsy and genetic testing terms. Data were analyzed during March 2022.Study SelectionStudies performing exome or genome sequencing in at least 10 participants with cerebral palsy were included. Studies with fewer than 10 individuals and studies reporting variants detected by other genetic tests were excluded. Consensus review was performed. The initial search identified 148 studies, of which 13 met inclusion criteria.Data Extraction and SynthesisData were extracted by 2 investigators and pooled using a random-effects meta-analysis. Incidence rates with corresponding 95% CIs and prediction intervals were calculated. Publication bias was evaluated by the Egger test. Variability between included studies was assessed via heterogeneity tests using the I2 statistic.Main Outcomes and MeasuresThe primary outcome was the pooled diagnostic yield (rate of pathogenic/likely pathogenic variants) across studies. Subgroup analyses were performed based on population age and on the use of exclusion criteria for patient selection.ResultsThirteen studies were included consisting of 2612 individuals with cerebral palsy. The overall diagnostic yield was 31.1% (95% CI, 24.2%-38.6%; I2 = 91%). The yield was higher in pediatric populations (34.8%; 95% CI, 28.3%-41.5%) than adult populations (26.9%; 95% CI, 1.2%-68.8%) and higher among studies that used exclusion criteria for patient selection (42.1%; 95% CI, 36.0%-48.2%) than those that did not (20.7%; 95% CI, 12.3%-30.5%).Conclusions and RelevanceIn this systematic review and meta-analysis, the genetic diagnostic yield in cerebral palsy was similar to that of other neurodevelopmental disorders for which exome sequencing is recommended as standard of care. Data from this meta-analysis provide evidence to support the inclusion of cerebral palsy in the current recommendation of exome sequencing in the diagnostic evaluation of individuals with neurodevelopmental disorders.

Recurrent 16p11.2 duplications produce a wide range of clinical outcomes with varying effects on cognition and social functioning. Family-based studies of copy number variants (CNVs) have revealed significant contributions of genomic background on variable expressivity. In this study, we measured the phenotypic effect of 16p11.2 duplications and quantified the modulating effect of familial background on cognitive and social outcomes.Genomic and clinical data were ascertained from 41 probands with a 16p11.2 duplication and their first-degree relatives. Paired comparisons were completed to determine the duplication's effect on expected vs actual performance on standardized tests of intelligence (IQ) and social functioning (Social Responsiveness Scale-2). Intraclass correlations between relatives and probands were also calculated.Cognitive and social functioning were significantly lower among individuals with 16p11.2 duplications than their CNV-negative relatives, whereas intraclass correlations between the groups remained high for full-scale IQ and Social Responsiveness Scale-2 scores.The 16p11.2 duplication confers deleterious effects on cognition and social functioning, whereas familial background significantly influences phenotypic expression of these traits. Understanding variable expressivity in CNV disorders has implications for anticipatory clinical care, particularly for individuals who receive a genetic diagnosis at an early age, long before the full scope of manifestations becomes evident.

PURPOSE: Penetrance estimates of Birt-Hogg-Dubé (BHD)-associated cutaneous, pulmonary, and kidney manifestations are based on clinically ascertained families. In a healthcare system population, we used a genetics-first approach to estimate the prevalence of pathogenic/likely pathogenic (P/LP) truncating variants in FLCN, which cause BHD, and the penetrance of BHD-related phenotypes. METHODS: Exomes from 135,990 patient-participants in Geisinger’s MyCode® cohort were assessed for P/LP truncating FLCN variants. BHD-related phenotypes were evaluated from electronic health records. Association between P/LP FLCN variants and BHD-related phenotypes was assessed by Firth’s logistic regression. RESULTS: P/LP truncating FLCN variants were identified in 35 individuals (1 in 3,234 unrelated individuals), 68.6% of whom had BHD-related phenotype(s) including: cystic lung disease (65.7%), pneumothoraces (17.1%), cutaneous manifestations (8.6%), and kidney cancer (2.9%). Four (11.4%) had prior clinical BHD diagnoses. CONCLUSION: In this healthcare population, the frequency of P/LP truncating FLCN variants is 60 times higher than the previously reported prevalence. Although most variant-positive individuals had BHD-related phenotypes, a minority were previously clinically diagnosed, likely because cutaneous manifestations, pneumothoraces, and kidney cancer were observed at lower frequencies than in clinical cohorts. Improved clinical recognition of cystic lung disease and education concerning its association with FLCN variants could prompt evaluation for BHD.

PurposeCurrent penetrance estimates of Birt-Hogg-Dubé (BHD)-associated cutaneous, pulmonary, and renal manifestations are based on clinically ascertained families. In a healthcare system population, we used a genetics-first approach to estimate the prevalence of pathogenic/likely pathogenic (P/LP) variants in the FLCN gene, which cause BHD, and the penetrance of BHD-related phenotypes.MethodsExomes from 135,990 patient-participants in Geisinger’s MyCode® cohort were assessed for P/LP FLCN variants. BHD-related phenotypes were evaluated from electronic health records. Association between FLCN P/LP variants and BHD-related phenotypes were assessed by Firth’s logistic regression.ResultsP/LP FLCN variants were identified in 35 (1 in 3,234) individuals, 68.6% of whom had BHD-related phenotype(s) including: cystic lung disease (65.7%); pneumothoraces (17.1%); cutaneous manifestations (8.6%); and renal cancer (2.9%). Only four (11.4%) were clinically diagnosed with BHD.ConclusionIn this healthcare population, the frequency of P/LP FLCN variants is 60 times higher than the previously reported prevalence. Although most variant-positive individuals had BHD-related phenotypes in the EHR, a minority were clinically diagnosed with BHD, likely because cutaneous manifestations, pneumothoraces, and renal cancer were observed at lower frequencies than clinical cohorts. Improved clinical recognition of cystic lung disease and education concerning its association with FLCN variants could prompt evaluation for BHD.

PURPOSE: Recurrent pathogenic copy number variants (pCNVs) have large-effect impacts on brain function and represent important etiologies of neurodevelopmental psychiatric disorders (NPDs), including autism and schizophrenia. Patterns of health care utilization in adults with pCNVs have gone largely unstudied and are likely to differ in significant ways from those of children. METHODS: We compared the prevalence of NPDs and electronic health record-based medical conditions in 928 adults with 26 pCNVs to a demographically-matched cohort of pCNV-negative controls from >135,000 patient-participants in Geisinger’s MyCode Community Health Initiative. We also evaluated 3 quantitative health care utilization measures (outpatient, inpatient, and emergency department (ED) visits) in both groups. RESULTS: Adults with pCNVs (24.9%) were more likely than controls (16.0%) to have a documented NPD. They had significantly higher rates of several chronic diseases, including diabetes (29.3% in participants with pCNVs vs. 20.4% in participants without pCNVs) and dementia (2.2% in participants with pCNVs vs. 1.0% in participants without pCNVs), and twice as many annual emergency department visits. CONCLUSION: These findings highlight the potential for genetic information – specifically, pCNVs - to inform the study of health care outcomes and utilization in adults. If, as our findings suggest, adults with pCNVs have poorer health and require disproportionate health care resources, early genetic diagnosis paired with patient-centered interventions may help to anticipate problems, improve outcomes, and reduce the associated economic burden.

ImportanceAn increased risk of venous thromboembolism (VTE) has been reported in men with an additional sex chromosome. The association between other sex chromosome aneuploidies and VTE is not well characterized.ObjectiveTo determine if sex chromosome aneuploidy is associated with VTE.Design, Setting, and ParticipantsRetrospective cohort study of sex chromosome aneuploidy and VTE, performed by analyzing X- and Y-chromosome dosage and VTE incidence in 642 544 individuals from 2 population-scale biobanks: the US Geisinger MyCode Community Health Initiative (N = 154 519) and the UK Biobank (N = 488 025); analysis was limited to participants self-identified as White because of inadequate sample sizes for other race and ethnicity groups. A total of 108 461 unrelated MyCode participants with electronic health record follow-up ranging from September 1996 to December 2020 and 418 725 unrelated British and Irish UK Biobank participants who attended the baseline assessment between March 2006 and October 2010, with follow-up extending to November 2020, were included in analyses of VTE.ExposuresSex chromosome aneuploidies.Main Outcomes and MeasuresIndividuals with 1 primary inpatient VTE diagnosis, 2 primary outpatient VTE diagnoses, or a self-reported VTE diagnosis were defined as VTE cases. P values were adjusted for multiple comparisons.ResultsIdentification of sex chromosome aneuploidy was undertaken among 642 544 individuals aged 18 to 90 years. Identification of a diagnosis of VTE was undertaken among 108 461 unrelated MyCode participants (65 565 [60.5%] female; mean age at last visit, 58.0 [SD, 17.6] years; median follow-up, 15.3 [IQR, 9.7] years) and among 418 725 unrelated UK Biobank participants (224 695 [53.7%] female; mean age at baseline interview, 56.9 [SD, 8.0] years; median follow-up, 12.0 [IQR, 1.6] years). Among MyCode participants, during 10 years of follow-up, 17 incident VTE events per 1353 person-years were detected among those with supernumerary sex chromosome aneuploidy (1.3% per person-year) compared with 2060 per 816 682 person-years among those with 46,XX or 46,XY (0.25% per person-year) (hazard ratio, 5.4 [95% CI, 3.4-8.7]; 10-year risk difference, 8.8% [95% CI, 4.2%-14.0%]; P P Conclusions and RelevanceAdults with supernumerary sex chromosome aneuploidies compared with 2 sex chromosomes had a small but statistically significant increased risk of VTE. Further research is needed to understand the clinical implications of this association.

With widespread adoption of fragile X carrier screening in pregnant women, the number of expectant couples receiving news of an unanticipated Fragile X Mental Retardation 1 (FMR1) gene expansion has increased. The most common abnormal result from maternal FMR1 testing involves an intermediate allele, also known as a gray zone result, which requires genetic counseling but poses minimal risk for an adverse developmental outcome. By contrast, the finding of a maternal FMR1 premutation or full mutation during pregnancy has important implications for the woman herself, her unborn child, and her extended family. These multiple levels of impact, in addition to the complex inheritance pattern and variable expressivity of fragile X-associated disorders, cause significant stress for newly identified expectant couples and pose unique challenges for genetic counselors in the prenatal setting. © 2016 John Wiley & Sons, Ltd.

Purpose of Review Psychiatry is steadily moving toward a new conceptualization of brain disorders that blurs long-held diagnostic distinctions among neurodevelopmental and psychiatric conditions, including autism. Genomic discoveries are driving these changing perceptions, yet there has so far been minimal impact on traditional genetic counseling practices that continue to view autism through the lens of a dichotomous, all-or-none risk model. Recent Findings High rates of comorbidity exist across autism spectrum disorder, schizophrenia, intellectual disability, and other brain-based disorders. Recent epidemiological studies have shown that co-occurrence of neurodevelopmental and psychiatric disorders is the rule, rather than the exception, in affected individuals and within families. Moreover, studies of chromosomal microarray analysis and whole exome sequencing have now detected many of the same pathogenic copy number and sequence-level variants across cohorts with different clinical presentations. Summary Going forward, the genetic counseling field will need to significantly adapt its approaches to pedigree interpretation, variant analysis, and patient education to more precisely describe both the chance and the nature of autism recurrence in terms of a continuum of brain dysfunction. These efforts will have implications for multiple practice areas and require philosophical changes for experienced practitioners and for the training of new genetic counselors. Resetting entrenched dichotomous notions about autism and other brain-based manifestations of genetic conditions will require a strategic educational effort on the part of the genetic counseling profession.

Shift happens: family background influences clinical variability in genetic neurodevelopmental disorders

The objectives of the study were to assess the attitudes and experiences of clinicians involved in a consortium of clinics serving people with fragile X-associated disorders to gauge satisfaction with the consortium and its efforts to improve quality of life for patients and the community. An internet survey was sent to 26 fragile X (FX) clinic directors participating in the Fragile X Clinical and Research Consortium (FXCRC). Respondents were asked to complete 19 questions on consortium performance and outcomes relevant for their own clinic. The response rate was 84% (22/26), with two surveys providing incomplete data. Assistance with clinic establishment, opportunities for research collaborations, and access to colleagues and information were highly valued. Approximately 76% of clinicians reported improvements in patient care and 60% reported an increase in patient services. There was a 57% increase in participation in a FX-related clinical trial among clinics since joining the FXCRC (24% vs. 81%). Overall, respondents reported primarily positive experiences from participation in the FXCRC. Common suggestions for improvement included additional financial support and increased utilization of collected patient data for research purposes. Additionally, a Clinic Services Checklist was administered annually to examine changes in services offered over time. There were several important changes regarding the provision of services by clinics, often with multiple clinics changing with respect to a service. In conclusion, the FXCRC has led to the establishment and sustainment of fragile X clinics in the U.S., fostered cooperation among fragile X clinicians, and provided clinics with a platform to share recommendations and best practices to maximize quality of life for their patients and the overall fragile X community. The results from the survey and checklist also provide suggestions to strengthen the FXCRC and enhance future collaborations among FXCRC members. © 2016 Wiley Periodicals, Inc.

Since its establishment over 40 years ago, the genetic counseling profession has grown to an estimated ~4,000 professionals in North America. While the profession has maintained the Master’s degree as the entry-level and terminal degree, many other allied health professions have added advanced training pathways, such as the clinical doctorate (ClinD) either as an optional post-professional degree or required entry-level degree. Discussions regarding advanced degrees have also occurred within the genetic counseling profession, dating back to as early as the 1980s. In 2011, the Genetic Counseling Advanced Degree Task Force (GCADTF) was convened to explore the issue again, with the goal of “[engaging] all of the professional leadership organizations in the field of genetic counseling in a decision-making process about whether the profession should move to a Clinical Doctorate”. As part of their work, the GCADTF surveyed practicing genetic counselors (n = 4,321) and genetic counseling students (n = 522) in the US and Canada regarding their interest in moving to the ClinD as the entry-level degree. This survey also included questions about other options for advanced training to generate data to inform future discussions around this very important professional issue. Herein, we describe the results of the survey, with particular attention to genetic counselor preferences for additional advanced education/certification opportunities and recommendations for future discussion.

Purpose: The chromosome 22q11.2 deletion has been identified in the majority of patients with DiGeorge syndrome, velocardiofacial syndrome, and conotruncal anomaly face syndrome and in some patients with the autosomal dominant Opitz G/BBB syndrome and Cayler cardiofacial syndrome. In addition, 22q11.2 deletion studies are becoming part of a standardized diagnostic workup for some isolated defects such as conotruncal cardiac anomalies and velopharyngeal incompetence. However, there is little information available on the clinical findings of unselected patients. For example, those individuals identified during prenatal diagnosis, as part of a generalized screening protocol, or following the diagnosis in a relative. This information will be invaluable in defining the variability of the disorder and in observing long-term outcome in the absence of targeted remediations. This study allows one to examine the first unselected cohort of patients and serves to highlight the importance of deletion testing in parents of affected probands. Methods: Thirty individuals with a 22q11.2 deletion were identified following the diagnosis in a relative. Nineteen were adults ascertained only following the diagnosis in their child, 10 were children identified following the diagnosis in their sibling, and one was a child diagnosed prenatally following the diagnosis in her parent. Results: Sixty percent of patients had no visceral anomalies. In fact, only 6 of the 19 adults (32%) and 6 of the 11 children (55%) had major findings which would have brought them to medical attention. Deletion sizing demonstrated the same large 3–4MB deletion in most families despite wide inter and intrafamilial variability and there was no difference in clinical findings based on the parent of origin. Thus, no genotype-phenotype correlations could be made. Conclusion: We report the first unselected cohort of patients with the 22q11.2 deletion identified through an affected relative. Analysis of this series of 30 patients, many with very mild manifestations of the deletion, allows one to examine the outcome in individuals who lacked specific remediations for this disorder. It emphasizes the importance of broadening the index of suspicion in order to provide appropriate recurrence risk counseling, cognitive remediation, and medical management. Further, it underscores the lack of familial concordance and the current lack of genotype-phenotype correlations in this disorder, and it raises the possibility that the deletion is more common than previously reported.

We surveyed 439 professionals in the field of autism to assess their knowledge and perceptions about fragile X syndrome (FXS) and related issues. Almost half had worked with at least one child diagnosed with FXS, yet most lacked basic knowledge about the condition, underestimated its significance in the etiology of autism spectrum disorders, and rarely accessed fragile X–specific resources. A majority perceived etiology to be an important variable in therapeutic response while three quarters felt that professionals in the field of autism should play an active role in referring children for etiological evaluation. Despite these opinions, most respondents either rarely or never inquired about etiology when working with a new client. The survey results underscore the need for training and education so that autism professionals can become effective partners in diagnostic genetic referral and in research and implementation of syndrome-specific interventions.

We present the results of ophthalmologic assessment in 10 patients with interstitial chromosome deletions of 17p11.2, otherwise known as the Smith-Magenis syndrome (SMS). The most common abnormalities noted were strabismus, Brushfield spots, high myopia, and retinal detachments. We have previously reported high myopia and retinal detachments in 6 patients with SMS (Finucane et al.: Am J Hum Genet 49:262A, 1991). We present additional details on these individuals, as well as findings in 4 newly reported patients. Ocular pathology appears to be very common in SMS, significantly contributing to disability in people with this syndrome. The combination of high myopia, self-injurious head-banging, aggression, and hyperactivity among these patients makes them particularly susceptible to retinal detachments. Detailed ophthalmologic assessment should be included in the clinical work-up and monitoring of all patients with SMS resulting from deletion 17p11.2.

Various theories have been postulated to account for the unusual inheritance pattern observed in the fragile X syndrome. The recent finding of a secondary amplification of the fragile X mutation in the offspring of carrier females [Oberle et al., 1991; Yu et al., 1991] is consistent with a maternal imprinting process. Laird [1987] has proposed that the fragile X mutation blocks complete reactivation of a previously inactivated fragile X chromosome. We have tested whether or not such a localized block extends as far distal as the red/green color-vision complex at Xq28. We found no evidence of color-vision defects among 25 male subjects with the fragile X syndrome. A fragile X positive woman also had normal color vision, despite being an obligate carrier of her father's gene for red/green color blindness. We conclude that the fragile X gene does not affect the function of neighboring color-vision genes, nor does it affect their ability to compensate adequately for inherited color deficiency on the homologous X chromosome in females.

The Na + / myo -inositol cotransporter (SLC5A3) gene, located on the long arm of human chromosome 21, may play a key role in osmoregulation including the regulation of levels of the “idiogenic osmole,” myo -inositol, in brain cells. To determine whether the levels of myo -inositol are increased in the basal ganglia of children with Down syndrome, we performed in vivo brain hydrogen 1–nuclear magnetic resonance or 1 H-magnetic resonance spectroscopy and measured plasma osmolality in a cohort of children with trisomy 21. Myo -inositol is elevated in the corpus striatum of infants and children with Down syndrome, even in the absence of hypertonic stress. (J Pediatr 1999;135:94-7)

We describe a 14-year-old boy with physical and behavioral manifestations of the Smith-Magenis syndrome. Low level mosaicism (11%) for deletion 17p11.2 was found in peripheral blood lymphocytes. The deletion was also observed in 100% of metaphases examined from skin fibroblast cultures. We confirm that the Smith-Magenis syndrome is associated with a highly recognizable phenotype. Because evidence of the abnormal cell line may be minimal or absent in peripheral blood, fibroblast studies are indicated for patients in whom mosaicism for deletion 17p11.2 is suspected clinically. © 1993 Wiley-Liss, Inc.

We present 2 unrelated children with a distinct pattern of anomalies, including mental retardation, hearing impairment, unusual facial appearance, and skeletal defects. Both children have severe behavior disturbance and hyperactivity. The characteristic facial findings include a broad mouth, broad nasal bridge, mildly anteverted nares with a fleshy nasal tip, and deep nasolabial folds. Skeletal findings include mild to moderate short stature, dysharmonic maturation of epiphyseal ossification centers in the hands, and mild scoliosis. © 1992 Wiley-Liss, Inc.