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PURPOSE: Clinical next-generation sequencing is an effective approach for identifying pathogenic sequence variants that are medically actionable for participants and families but are not associated with the participant's primary diagnosis. These variants are called secondary findings (SFs). According to the literature, there is no report of the types and frequencies of SFs in a large pediatric cohort which includes substantial African-American participants. We sought to investigate the types (including American College of Medical Genetics and Genomics [ACMG] and non-ACMG recommended gene lists), frequencies, and rates of SFs, as well as the effects of SF disclosure on the participants and families of a large pediatric cohort at the Center for Applied Genomics at The Children's Hospital of Philadelphia (CHOP). METHODS: We systematically identified pathogenic (P) and likely pathogenic (LP) variants in established disease-causing genes, adhering to ACMG v3.2 secondary finding guidelines and beyond. For non-ACMG secondary findings, akin to incidental findings in clinical settings, we utilized a set of criteria focusing on pediatric onset, high penetrance, moderate to severe phenotypes, and the clinical actionability of the variants. This criteria-based approach was applied rather than using a fixed gene list to ensure that the variants identified are likely to impact participant health significantly. To identify and categorize these variants, we employed a clinical-grade variant classification standard per ACMG/AMP recommendations; additionally, we conducted a detailed literature search to ensure a comprehensive exploration of potential secondary findings relevant to pediatric participants. RESULTS: We report a distinctive distribution of 1,464 P/LP SF variants in 16,713 participants. There were 427 unique variants in ACMG genes and 265 in non-ACMG genes. The most frequently mutated genes among the ACMG and non-ACMG gene lists were TTR (41.6%) and CHEK2 (7.16%), respectively. Overall, variants of possible medical importance were found in 8.76% of participants in both ACMG (5.81%) and non-ACMG (2.95%) genes.
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Novel gene-disease discoveries, rapid advancements in technology, and improved bioinformatics tools all have the potential to yield additional molecular diagnoses through the reanalysis of exome sequencing data. Collaborations between clinical laboratories, ordering physicians, and researchers are also driving factors that can contribute to these new insights. Automation in ongoing natural history collection, evolving phenotype updates, advancements in processing next-generation sequencing data, and up-to-date variant-gene-disease databases are increasingly needed for systematic exome reanalysis. Here, we review some of the advantages and challenges for clinician-initiated and laboratory-initiated exome reanalysis, and we propose a model for the future that could potentially maximize the clinical utility of exome reanalysis by integrating information from electronic medical records and knowledge databases into routine clinical workflows.
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Exoma , Laboratorios Clínicos , Biología Computacional , Exoma/genética , Humanos , Fenotipo , Secuenciación del ExomaAsunto(s)
Genética Médica , Pruebas Genéticas , Genoma Humano , Genómica , Células Germinativas , Humanos , Estados UnidosRESUMEN
Leukodystrophies are a heterogeneous group of heritable disorders characterized by abnormal brain white matter signal on magnetic resonance imaging (MRI) and primary involvement of the cellular components of myelin. Previous estimates suggest the incidence of leukodystrophies as a whole to be 1 in 7,000 individuals, however the frequency of specific diagnoses relative to others has not been described. Next generation sequencing approaches offer the opportunity to redefine our understanding of the relative frequency of different leukodystrophies. We assessed the relative frequency of all 30 leukodystrophies (associated with 55 genes) in more than 49,000 exomes. We identified a relatively high frequency of disorders previously thought of as very rare, including Aicardi Goutières Syndrome, TUBB4A-related leukodystrophy, Peroxisomal biogenesis disorders, POLR3-related Leukodystrophy, Vanishing White Matter, and Pelizaeus-Merzbacher Disease. Despite the relative frequency of these conditions, carrier-screening laboratories regularly test only 20 of the 55 leukodystrophy-related genes, and do not test at all, or test only one or a few, genes for some of the higher frequency disorders. Relative frequency of leukodystrophies previously considered very rare suggests these disorders may benefit from expanded carrier screening.
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Enfermedades Autoinmunes del Sistema Nervioso/genética , Enfermedades Desmielinizantes/genética , Malformaciones del Sistema Nervioso/genética , Enfermedad de Pelizaeus-Merzbacher/genética , ARN Polimerasa III/genética , Tubulina (Proteína)/genética , Enfermedades Autoinmunes del Sistema Nervioso/patología , Enfermedades Desmielinizantes/epidemiología , Enfermedades Desmielinizantes/patología , Exoma/genética , Femenino , Predisposición Genética a la Enfermedad , Heterocigoto , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Enfermedades por Almacenamiento Lisosomal/epidemiología , Enfermedades por Almacenamiento Lisosomal/genética , Imagen por Resonancia Magnética , Masculino , Vaina de Mielina/genética , Vaina de Mielina/metabolismo , Malformaciones del Sistema Nervioso/patología , Enfermedad de Pelizaeus-Merzbacher/epidemiología , Enfermedad de Pelizaeus-Merzbacher/patología , Sustancia Blanca/diagnóstico por imagen , Sustancia Blanca/patologíaRESUMEN
Pathogenic variants in the CFTR gene are causative of classic cystic fibrosis (CF) as well as some nonclassic CF phenotypes. In 2001, CF became the first target of pan-ethnic universal carrier screening by molecular methods. The American College of Medical Genetics and Genomics (ACMG) recommended a core panel of 23 disease-causing variants as the minimal set to be included in pan-ethnic carrier screening of individuals with no family history of the disease, and these variants were usually assessed using targeted methods. The original recommendation also left open the option for laboratories to offer expanded CFTR variant panels; however, at the time, expanded CFTR variant panels were met with some controversy on the basis of the available technologies and the limited phenotypic knowledge of rare variants. Both of those aspects have now evolved, prompting this update of the ACMG technical standards for CFTR variant testing.
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Regulador de Conductancia de Transmembrana de Fibrosis Quística , Pruebas Genéticas/normas , Genética Médica , Regulador de Conductancia de Transmembrana de Fibrosis Quística/genética , Genómica , Humanos , Mutación , Estados UnidosRESUMEN
BACKGROUND: Clinical care teams providing presymptomatic genetic testing often employ advanced confidentiality practices for documentation and result storage. However, patient requests for increased confidentiality may be in conflict with the legal obligations of medical providers to document patient care activities in the electronic health record (EHR). Huntington disease presents a representative case study for investigating the ways centers currently balance the requirements of EHRs with the privacy demands of patients seeking presymptomatic genetic testing. METHODS: We surveyed 23 HD centers (53% response rate) regarding their use of the EHR for presymptomatic HD testing. RESULTS: Our survey revealed that clinical care teams and laboratories have each developed their own practices, which are cumbersome and often include EHR avoidance. We found that a majority of HD care teams record appointments in the EHR (91%), often using vague notes. Approximately half of the care teams (52%) keep presymptomatic results of out of the EHR. CONCLUSION: As genetic knowledge grows, linking more genes to late-onset conditions, institutions will benefit from having professional recommendations to guide development of policies for EHR documentation of presymptomatic genetic results. Policies must be sensitive to the ethical differences and patient demands for presymptomatic genetic testing compared to those undergoing confirmatory genetic testing.
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Registros Electrónicos de Salud/normas , Privacidad Genética/normas , Pruebas Genéticas/normas , Enfermedad de Huntington/diagnóstico , Servicios de Laboratorio Clínico/estadística & datos numéricos , Registros Electrónicos de Salud/ética , Pruebas Genéticas/ética , Humanos , Enfermedad de Huntington/genética , Encuestas y Cuestionarios , Estados UnidosRESUMEN
Genetic ataxias are associated with mutations in hundreds of genes with high phenotypic overlap complicating the clinical diagnosis. Whole-exome sequencing (WES) has increased the overall diagnostic rate considerably. However, the upper limit of this method remains ill-defined, hindering efforts to address the remaining diagnostic gap. To further assess the role of rare coding variation in ataxic disorders, we reanalyzed our previously published exome cohort of 76 predominantly adult and sporadic-onset patients, expanded the total number of cases to 260, and introduced analyses for copy number variation and repeat expansion in a representative subset. For new cases (n = 184), our resulting clinically relevant detection rate remained stable at 47% with 24% classified as pathogenic. Reanalysis of the previously sequenced 76 patients modestly improved the pathogenic rate by 7%. For the combined cohort (n = 260), the total observed clinical detection rate was 52% with 25% classified as pathogenic. Published studies of similar neurological phenotypes report comparable rates. This consistency across multiple cohorts suggests that, despite continued technical and analytical advancements, an approximately 50% diagnostic rate marks a relative ceiling for current WES-based methods and a more comprehensive genome-wide assessment is needed to identify the missing causative genetic etiologies for cerebellar ataxia and related neurodegenerative diseases.
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Ataxia Cerebelosa/diagnóstico , Ataxia Cerebelosa/genética , Secuenciación del Exoma , Exoma , Enfermedades del Sistema Nervioso/diagnóstico , Enfermedades del Sistema Nervioso/genética , Variaciones en el Número de Copia de ADN , Estudios de Asociación Genética , Ligamiento Genético , Predisposición Genética a la Enfermedad , Humanos , Repeticiones de MicrosatéliteRESUMEN
We identified individuals with variations in ACTL6B, a component of the chromatin remodeling machinery including the BAF complex. Ten individuals harbored bi-allelic mutations and presented with global developmental delay, epileptic encephalopathy, and spasticity, and ten individuals with de novo heterozygous mutations displayed intellectual disability, ambulation deficits, severe language impairment, hypotonia, Rett-like stereotypies, and minor facial dysmorphisms (wide mouth, diastema, bulbous nose). Nine of these ten unrelated individuals had the identical de novo c.1027G>A (p.Gly343Arg) mutation. Human-derived neurons were generated that recaptured ACTL6B expression patterns in development from progenitor cell to post-mitotic neuron, validating the use of this model. Engineered knock-out of ACTL6B in wild-type human neurons resulted in profound deficits in dendrite development, a result recapitulated in two individuals with different bi-allelic mutations, and reversed on clonal genetic repair or exogenous expression of ACTL6B. Whole-transcriptome analyses and whole-genomic profiling of the BAF complex in wild-type and bi-allelic mutant ACTL6B neural progenitor cells and neurons revealed increased genomic binding of the BAF complex in ACTL6B mutants, with corresponding transcriptional changes in several genes including TPPP and FSCN1, suggesting that altered regulation of some cytoskeletal genes contribute to altered dendrite development. Assessment of bi-alleic and heterozygous ACTL6B mutations on an ACTL6B knock-out human background demonstrated that bi-allelic mutations mimic engineered deletion deficits while heterozygous mutations do not, suggesting that the former are loss of function and the latter are gain of function. These results reveal a role for ACTL6B in neurodevelopment and implicate another component of chromatin remodeling machinery in brain disease.
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Actinas/genética , Proteínas Cromosómicas no Histona/genética , Proteínas de Unión al ADN/genética , Dendritas/patología , Epilepsia/etiología , Células Madre Pluripotentes Inducidas/patología , Mutación , Trastornos del Neurodesarrollo/etiología , Neuronas/patología , Adulto , Niño , Preescolar , Cromatina/genética , Cromatina/metabolismo , Dendritas/metabolismo , Epilepsia/patología , Femenino , Humanos , Células Madre Pluripotentes Inducidas/metabolismo , Lactante , Masculino , Trastornos del Neurodesarrollo/patología , Neuronas/metabolismo , Adulto JovenRESUMEN
OBJECTIVE: We report a 35 year-old male with childhood learning disability and early onset dementia who is homozygous for the A431E variant in the PSEN1 gene. Presenilin1 mutations are associated with autosomal dominant Alzheimer's dementia with young and somewhat stereotyped onset. Such variants may cause Alzheimer's dementia through aberrant processing of amyloid precursor protein through effects on γ-secretase activity. γ-secretase is involved in the cleavage of many proteins critical to normal function, including brain development. Therefore, manifestations in persons without normal Presenilin1 function is of interest. METHODS: Clinical evaluation including family history, examination, brain MRI, and genetic analysis. RESULTS: Our patient had mild developmental delay, chronic nighttime behavioral disturbance, and onset of progressive cognitive deficits at age 33. Clinical evaluation demonstrated spastic paraparesis and pseudobulbar affect. Brain MRI revealed cerebral atrophy disproportionate to age. Chronic microhemorrhages within bilateral occipital, temporal, and right frontal lobes were seen. Sanger sequencing confirmed homozygosity for the A431E variant in PSEN1, which is a known pathogenic variant causing autosomal dominant Alzheimer's dementia. CONCLUSIONS: Our report demonstrates that homozygosity for pathogenic Presenilin1 variants is compatible with life, though may cause a more aggressive phenotype with younger age of onset and possibly REM behavior disorder.
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Enfermedad de Alzheimer/genética , Predisposición Genética a la Enfermedad/genética , Homocigoto , Mutación/genética , Presenilina-1/genética , Adulto , Humanos , Masculino , FenotipoRESUMEN
PURPOSE: Clinical laboratories performing exome or genome sequencing (ES/GS) are familiar with the challenges associated with proper consenting for and reporting of medically actionable secondary findings based on recommendations from the American College of Medical Genetics and Genomics (ACMG). Misattributed parentage is another type of unanticipated finding a laboratory may encounter during family-based ES/GS; however, there are currently no professional recommendations related to the proper consenting for and reporting of misattributed parentage encountered during ES/GS. METHODS: We surveyed 10 clinical laboratories offering family-based ES/GS regarding their consent language, discovery, and reporting of misattributed parentage. RESULTS: Many laboratories have already developed their own practices/policies for these issues, which do not necessarily agree with those from other labs. CONCLUSION: There are several other possibilities besides true misattributed parentage that could result in similar laboratory findings, and laboratories often feel they lack sufficient information to make formal conclusions on a report regarding the true genetic relatedness of the submitted samples. However, understanding the genetic relatedness (or lack thereof) of the samples submitted for family-based ES/GS has medical relevance. Therefore, professional recommendations for the appropriate handling of suspected misattributed parentage encountered during ES/GS are needed to help standardize current clinical laboratory practices.
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Pruebas Genéticas/tendencias , Genética Médica/tendencias , Genómica/tendencias , Padres , Servicios de Laboratorio Clínico , Exoma/genética , Femenino , Genoma Humano/genética , Humanos , Hallazgos Incidentales , Consentimiento Informado , Masculino , Encuestas y Cuestionarios , Secuenciación del Exoma/tendencias , Secuenciación Completa del Genoma/tendenciasRESUMEN
ClinVar provides open access to variant classifications shared from many clinical laboratories. Although most classifications are consistent across laboratories, classification differences exist. To facilitate resolution of classification differences on a large scale, clinical laboratories were encouraged to reassess outlier classifications of variants with medically significant differences (MSDs). Outliers were identified by first comparing ClinVar submissions from 41 clinical laboratories to detect variants with MSDs between the laboratories (650 variants). Next, MSDs were filtered for variants with ≥3 classifications (244 variants), of which 87.6% (213 variants) had a majority consensus in ClinVar, thus allowing for identification of outlier classifications in need of reassessment. Laboratories with outlier classifications were sent a custom report and encouraged to reassess variants. Results were returned for 204 (96%) variants, of which 62.3% (127) were resolved. Of those 127, 64.6% (82) were resolved due to reassessment prompted by this study and 35.4% (45) resolved by a previously completed reassessment. This study demonstrates a scalable approach to classification resolution and capitalizes on the value of data sharing within ClinVar. These activities will help the community move toward more consistent variant classifications, which will improve the care of patients with, or at risk for, genetic disorders.
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Bases de Datos Genéticas , Pruebas Genéticas/métodos , Variación Genética/genética , Genoma Humano/genética , HumanosRESUMEN
The OncoKids panel is an amplification-based next-generation sequencing assay designed to detect diagnostic, prognostic, and therapeutic markers across the spectrum of pediatric malignancies, including leukemias, sarcomas, brain tumors, and embryonal tumors. This panel uses low input amounts of DNA (20 ng) and RNA (20 ng) and is compatible with formalin-fixed, paraffin-embedded and frozen tissue, bone marrow, and peripheral blood. The DNA content of this panel covers the full coding regions of 44 cancer predisposition loci, tumor suppressor genes, and oncogenes; hotspots for mutations in 82 genes; and amplification events in 24 genes. The RNA content includes 1421 targeted gene fusions. We describe the validation of this panel by using a large cohort of 192 unique clinical samples that included a wide range of tumor types and alterations. Robust performance was observed for analytical sensitivity, reproducibility, and limit of detection studies. The results from this study support the use of OncoKids for routine clinical testing of a wide variety of pediatric malignancies.