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Defects in the mRNA export scaffold protein GANP, encoded by the MCM3AP gene, cause autosomal recessive early-onset peripheral neuropathy with or without intellectual disability. We extend here the phenotypic range associated with MCM3AP variants, by describing a severely hypotonic child and a sibling pair with a progressive encephalopathic syndrome. In addition, our analysis of skin fibroblasts from affected individuals from seven unrelated families indicates that disease variants result in depletion of GANP except when they alter critical residues in the Sac3 mRNA binding domain. GANP depletion was associated with more severe phenotypes compared with the Sac3 variants. Patient fibroblasts showed transcriptome alterations that suggested intron content-dependent regulation of gene expression. For example, all differentially expressed intronless genes were downregulated, including ATXN7L3B, which couples mRNA export to transcription activation by association with the TREX-2 and SAGA complexes. Our results provide insight into the molecular basis behind genotype-phenotype correlations in MCM3AP-associated disease and suggest mechanisms by which GANP defects might alter RNA metabolism.
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Acetiltransferasas/genética , Flavoproteínas/genética , Péptidos y Proteínas de Señalización Intracelular/genética , Enfermedades del Sistema Nervioso/genética , Proteínas Nucleares/genética , Monoéster Fosfórico Hidrolasas/genética , Factores de Transcripción/genética , Acetiltransferasas/química , Acetiltransferasas/ultraestructura , Edad de Inicio , Antígenos de Superficie/genética , Núcleo Celular/genética , Niño , Preescolar , Exodesoxirribonucleasas/genética , Femenino , Regulación de la Expresión Génica/genética , Glicoproteínas/genética , Humanos , Discapacidad Intelectual/genética , Discapacidad Intelectual/patología , Péptidos y Proteínas de Señalización Intracelular/química , Intrones/genética , Masculino , Enfermedades del Sistema Nervioso/patología , Proteínas Nucleares/ultraestructura , Enfermedades del Sistema Nervioso Periférico/genética , Enfermedades del Sistema Nervioso Periférico/patología , Fenotipo , Fosfoproteínas/genética , Conformación Proteica , Transporte de ARN/genética , ARN Mensajero/genéticaRESUMEN
PURPOSE: This study aimed to correlate the indications and diagnostic yield of exome sequencing (ES) in adult patients across various clinical settings. The secondary aim was to examine the clinical utility of ES in adult patients. METHODS: Data on demographics, clinical indications, results, management changes, and cascade testing were collected for 250 consecutive patients who underwent ES through an adult genetics department between 2016 and 2021. Data were analyzed using descriptive and inferential statistics. Testing in which traditional gene panels were in standard use, such as in heritable cancers, was excluded. RESULTS: The average age at testing was 43 years (range = 17-80 years). A molecular diagnosis was identified in 29% of patients. Older age at symptom onset did not pre-exclude a substantial diagnostic yield. Patients with syndromic intellectual disability and multiple system disorders had the highest yield. In >50% of patients with an exome diagnosis, the results changed management. Cascade testing occured in at least one family member for 30% of patients with a diagnosis. Diagnostic results had reproductive implications for 26% of patients and 31% of patients' relatives. CONCLUSION: ES has a robust diagnostic yield and clear clinical utility in adult patients across a range of ages and phenotypes.
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Exoma , Discapacidad Intelectual , Adulto , Exoma/genética , Pruebas Genéticas/métodos , Humanos , Discapacidad Intelectual/diagnóstico , Discapacidad Intelectual/genética , Fenotipo , Secuenciación del Exoma/métodosRESUMEN
BACKGROUND: In the clinical setting, identification of the genetic cause in patients with early-onset dementia (EOD) is challenging due to multiple types of genetic tests required to arrive at a diagnosis. Whole-genome sequencing (WGS) has the potential to serve as a single diagnostic platform, due to its superior ability to detect common, rare and structural genetic variation. METHODS: WGS analysis was performed in 50 patients with EOD. Point mutations, small insertions/deletions, as well as structural variants (SVs) and short tandem repeats (STRs), were analysed. An Alzheimer's disease (AD)-related polygenic risk score (PRS) was calculated in patients with AD. RESULTS: Clinical genetic diagnosis was achieved in 7 of 50 (14%) of the patients, with a further 8 patients (16%) found to have established risk factors which may have contributed to their EOD. Two pathogenic variants were identified through SV analysis. No expanded STRs were found in this study cohort, but a blinded analysis with a positive control identified a C9orf72 expansion accurately. Approximately 37% (7 of 19) of patients with AD had a PRS equivalent to >90th percentile risk. DISCUSSION: WGS acts as a single genetic test to identify different types of clinically relevant genetic variations in patients with EOD. WGS, if used as a first-line clinical diagnostic test, has the potential to increase the diagnostic yield and reduce time to diagnosis for EOD.
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Mitochondrial disorders causing neurodegeneration in childhood are genetically heterogeneous, and the underlying genetic etiology remains unknown in many affected individuals. We identified biallelic variants in PMPCB in individuals of four families including one family with two affected siblings with neurodegeneration and cerebellar atrophy. PMPCB encodes the catalytic subunit of the essential mitochondrial processing protease (MPP), which is required for maturation of the majority of mitochondrial precursor proteins. Mitochondria isolated from two fibroblast cell lines and induced pluripotent stem cells derived from one affected individual and differentiated neuroepithelial stem cells showed reduced PMPCB levels and accumulation of the processing intermediate of frataxin, a sensitive substrate for MPP dysfunction. Introduction of the identified PMPCB variants into the homologous S. cerevisiae Mas1 protein resulted in a severe growth and MPP processing defect leading to the accumulation of mitochondrial precursor proteins and early impairment of the biogenesis of iron-sulfur clusters, which are indispensable for a broad range of crucial cellular functions. Analysis of biopsy materials of an affected individual revealed changes and decreased activity in iron-sulfur cluster-containing respiratory chain complexes and dysfunction of mitochondrial and cytosolic Fe-S cluster-dependent enzymes. We conclude that biallelic mutations in PMPCB cause defects in MPP proteolytic activity leading to dysregulation of iron-sulfur cluster biogenesis and triggering a complex neurological phenotype of neurodegeneration in early childhood.
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Dominio Catalítico/genética , Metaloendopeptidasas/genética , Mutación/genética , Degeneración Nerviosa/genética , Niño , Preescolar , Dermis/patología , Transporte de Electrón , Femenino , Fibroblastos/metabolismo , Humanos , Células Madre Pluripotentes Inducidas/metabolismo , Proteínas Hierro-Azufre/genética , Imagen por Resonancia Magnética , Masculino , Mitocondrias/metabolismo , Linaje , Proto-Oncogenes Mas , Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/genética , Peptidasa de Procesamiento MitocondrialRESUMEN
LARS2 variants are associated with Perrault syndrome, characterized by premature ovarian failure and hearing loss, and with an infantile lethal multisystem disorder: Hydrops, lactic acidosis, sideroblastic anemia (HLASA) in one individual. Recently we reported LARS2 deafness with (ovario) leukodystrophy. Here we describe five patients with a range of phenotypes, in whom we identified biallelic LARS2 variants: three patients with a HLASA-like phenotype, an individual with Perrault syndrome whose affected siblings also had leukodystrophy, and an individual with a reversible mitochondrial myopathy, lactic acidosis, and developmental delay. Three HLASA cases from two unrelated families were identified. All were males with genital anomalies. Two survived multisystem disease in the neonatal period; both have developmental delay and hearing loss. A 55-year old male with deafness has not displayed neurological symptoms while his female siblings with Perrault syndrome developed leukodystrophy and died in their 30s. Analysis of muscle from a child with a reversible myopathy showed reduced LARS2 and mitochondrial complex I levels, and an unusual form of degeneration. Analysis of recombinant LARS2 variant proteins showed they had reduced aminoacylation efficiency, with HLASA-associated variants having the most severe effect. A broad phenotypic spectrum should be considered in association with LARS2 variants.
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Aminoacil-ARNt Sintetasas/genética , Disgenesia Gonadal 46 XX/genética , Pérdida Auditiva Sensorineural/genética , Miopatías Mitocondriales/genética , Acidosis Láctica/genética , Adulto , Anemia Sideroblástica/genética , Edema/genética , Femenino , Humanos , Lactante , Masculino , Persona de Mediana Edad , Fenotipo , Estructura Terciaria de ProteínaRESUMEN
Serine biosynthesis disorders comprise a spectrum of very rare autosomal recessive inborn errors of metabolism with wide phenotypic variability. Neu-Laxova syndrome represents the most severe expression and is characterized by multiple congenital anomalies and pre- or perinatal lethality. Here, we present the mutation spectrum and a detailed phenotypic analysis in 15 unrelated families with severe types of serine biosynthesis disorders. We identified likely disease-causing variants in the PHGDH and PSAT1 genes, several of which have not been reported previously. Phenotype analysis and a comprehensive review of the literature corroborates the evidence that serine biosynthesis disorders represent a continuum with varying degrees of phenotypic expression and suggest that even gradual differences at the severe end of the spectrum may be correlated with particular genotypes. We postulate that the individual residual enzyme activity of mutant proteins is the major determinant of the phenotypic variability, but further functional studies are needed to explore effects at the enzyme protein level.
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Anomalías Múltiples/genética , Encefalopatías/genética , Retardo del Crecimiento Fetal/genética , Estudios de Asociación Genética , Ictiosis/genética , Deformidades Congénitas de las Extremidades/genética , Microcefalia/genética , Fosfoglicerato-Deshidrogenasa/genética , Transaminasas/genética , Femenino , Feto , Humanos , Recién Nacido , Masculino , Mutación , Serina/biosíntesisRESUMEN
Internationally, the practice of offering additional findings (AFs) when undertaking a clinically indicated genomic test differs. In the USA, the recommendation is to include analysis for AFs alongside diagnostic analysis, unless a patient opts-out, whereas European and Canadian guidelines recommend opt-in models. These guidelines all consider the offer of AFs as an activity concurrent with the offer of diagnostic testing. This paper describes a novel two-step model for managing AFs within the healthcare system in Victoria, Australia and presents the study protocol for its evaluation. Adults who have received results of diagnostic whole exome sequencing undertaken within the healthcare system are invited to attend a genetic counseling appointment to consider reanalysis of their stored genomic data for AFs. The evaluation protocol addresses uptake, decision-making, understanding, counseling challenges, and explores preferences for future models of care. Recruitment commenced in November 2017 and will cease when 200 participants have been approached. When the study is concluded, the evaluation results will contribute to the evidence base guiding approaches to counseling and models of care for AFs.
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Asesoramiento Genético/métodos , Genómica , Adulto , Canadá , Toma de Decisiones , Atención a la Salud , Humanos , Masculino , Guías de Práctica Clínica como Asunto , VictoriaRESUMEN
Defects in mRNA export from the nucleus have been linked to various neurodegenerative disorders. We report mutations in the gene MCM3AP, encoding the germinal center associated nuclear protein (GANP), in nine affected individuals from five unrelated families. The variants were associated with severe childhood onset primarily axonal (four families) or demyelinating (one family) Charcot-Marie-Tooth neuropathy. Mild to moderate intellectual disability was present in seven of nine affected individuals. The affected individuals were either compound heterozygous or homozygous for different MCM3AP variants, which were predicted to cause depletion of GANP or affect conserved amino acids with likely importance for its function. Accordingly, fibroblasts of affected individuals from one family demonstrated severe depletion of GANP. GANP has been described to function as an mRNA export factor, and to suppress TDP-43-mediated motor neuron degeneration in flies. Thus our results suggest defective mRNA export from nucleus as a potential pathogenic mechanism of axonal degeneration in these patients. The identification of MCM3AP variants in affected individuals from multiple centres establishes it as a disease gene for childhood-onset recessively inherited Charcot-Marie-Tooth neuropathy with intellectual disability.
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Acetiltransferasas/genética , Enfermedad de Charcot-Marie-Tooth/genética , Predisposición Genética a la Enfermedad/genética , Discapacidad Intelectual/genética , Péptidos y Proteínas de Señalización Intracelular/genética , Acetiltransferasas/metabolismo , Adolescente , Adulto , Células Cultivadas , Enfermedad de Charcot-Marie-Tooth/complicaciones , Niño , Preescolar , Femenino , Fibroblastos/metabolismo , Humanos , Discapacidad Intelectual/complicaciones , Péptidos y Proteínas de Señalización Intracelular/metabolismo , Masculino , Mutación , Linaje , Adulto JovenRESUMEN
Hereditary haemorrhagic telangiectasia is characterised by abnormal blood vessel formation, producing telangiectasia and arteriovenous malformations in multiple organs. Information regarding possible renal involvement in hereditary haemorrhagic telangiectasia is limited. This study assessed renal structure and function in 11 patients with genetically confirmed diagnosis and known arteriovenous malformations in lung, liver, gastrointestinal tract or brain. All had significant current or past epistaxis. Despite the vascularity of the kidneys, we found no evidence of renal involvement. This observation warrants further consideration.
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Malformaciones Arteriovenosas/diagnóstico , Riñón/anomalías , Telangiectasia Hemorrágica Hereditaria/diagnóstico , Telangiectasia Hemorrágica Hereditaria/genética , Adulto , Malformaciones Arteriovenosas/complicaciones , Malformaciones Arteriovenosas/genética , Femenino , Pruebas Genéticas , Humanos , Riñón/diagnóstico por imagen , Imagen por Resonancia Magnética , Masculino , Persona de Mediana Edad , Mutación/genética , Fenotipo , Factores de Riesgo , Telangiectasia Hemorrágica Hereditaria/complicaciones , UltrasonografíaRESUMEN
Hereditary leiomyomatosis and renal cell cancer (HLRCC) is a rare autosomal dominant condition, which manifests as cutaneous leiomyomas (CL), uterine fibroids and renal cell cancer (RCC). We describe the case of a 53-year-old woman who presented with multiple CL with a novel heterozygous canonical splice site mutation in intron 9 of the fumarate hydratase (FH) gene IVS 9-1 G>C (NM_000143.3:c 1391-1 G>C) that was not detected on initial screening of a mutation hotspot but was picked up on sequencing the remaining exons and splice site junctions. This report highlights the importance of clinical suspicion in the diagnosis of HLRCC in the absence of a family or personal history of cancer and despite initial genetic testing being negative.
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Fumarato Hidratasa/genética , Leiomiomatosis/diagnóstico , Leiomiomatosis/genética , Síndromes Neoplásicos Hereditarios/diagnóstico , Síndromes Neoplásicos Hereditarios/genética , Neoplasias Cutáneas/diagnóstico , Neoplasias Cutáneas/genética , Neoplasias Uterinas/diagnóstico , Neoplasias Uterinas/genética , Femenino , Humanos , Persona de Mediana Edad , MutaciónRESUMEN
PURPOSE: To prospectively evaluate the diagnostic and clinical utility of singleton whole-exome sequencing (WES) as a first-tier test in infants with suspected monogenic disease. METHODS: Singleton WES was performed as a first-tier sequencing test in infants recruited from a single pediatric tertiary center. This occurred in parallel with standard investigations, including single- or multigene panel sequencing when clinically indicated. The diagnosis rate, clinical utility, and impact on management of singleton WES were evaluated. RESULTS: Of 80 enrolled infants, 46 received a molecular genetic diagnosis through singleton WES (57.5%) compared with 11 (13.75%) who underwent standard investigations in the same patient group. Clinical management changed following exome diagnosis in 15 of 46 diagnosed participants (32.6%). Twelve relatives received a genetic diagnosis following cascade testing, and 28 couples were identified as being at high risk of recurrence in future pregnancies. CONCLUSIONS: This prospective study provides strong evidence for increased diagnostic and clinical utility of singleton WES as a first-tier sequencing test for infants with a suspected monogenic disorder. Singleton WES outperformed standard care in terms of diagnosis rate and the benefits of a diagnosis, namely, impact on management of the child and clarification of reproductive risks for the extended family in a timely manner.Genet Med 18 11, 1090-1096.
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Enfermedades Genéticas Congénitas/diagnóstico , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Patología Molecular , Exoma/genética , Enfermedades Genéticas Congénitas/genética , Humanos , Recién NacidoRESUMEN
Terminal osseous dysplasia with pigmentary defects (TOD) is an extremely rare X-linked dominant disorder, which is characterised by cutaneous digital fibromas, pigmentary skin defects and skeletal abnormalities. A single mutation in the last nucleotide of exon 31 of the filamin A gene (FLNA) has recently been identified as a cause of the disease. We describe a case of an 18-month-old girl with the clinical phenotype of TOD and the disease-specific FLNA mutation confirmed by genetic testing. This report highlights the importance of recognising this distinct phenotype that can present to a wide variety of health-care professionals, and reviews the spectrum of filamin A disorders.
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Mutación/genética , Nevo Pigmentado/etiología , Nevo Pigmentado/patología , Nevo Sebáceo de Jadassohn/patología , Proteínas Proto-Oncogénicas p21(ras)/genética , Neoplasias Cutáneas/etiología , Neoplasias Cutáneas/patología , Humanos , Masculino , Nevo Sebáceo de Jadassohn/complicaciones , Nevo Sebáceo de Jadassohn/genética , Adulto JovenRESUMEN
BACKGROUND: Many families and individuals do not meet criteria for a known hereditary cancer syndrome but display unusual clusters of cancers. These families may carry pathogenic variants in cancer predisposition genes and be at higher risk for developing cancer. METHODS: This multi-centre prospective study recruited 195 cancer-affected participants suspected to have a hereditary cancer syndrome for whom previous clinical targeted genetic testing was either not informative or not available. To identify pathogenic disease-causing variants explaining participant presentation, germline whole-genome sequencing (WGS) and a comprehensive cancer virtual gene panel analysis were undertaken. RESULTS: Pathogenic variants consistent with the presenting cancer(s) were identified in 5.1% (10/195) of participants and pathogenic variants considered secondary findings with potential risk management implications were identified in another 9.7% (19/195) of participants. Health economic analysis estimated the marginal cost per case with an actionable variant was significantly lower for upfront WGS with virtual panel ($8744AUD) compared to standard testing followed by WGS ($24,894AUD). Financial analysis suggests that national adoption of diagnostic WGS testing would require a ninefold increase in government annual expenditure compared to conventional testing. CONCLUSIONS: These findings make a case for replacing conventional testing with WGS to deliver clinically important benefits for cancer patients and families. The uptake of such an approach will depend on the perspectives of different payers on affordability.
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Síndromes Neoplásicos Hereditarios , Humanos , Estudios Prospectivos , Oncogenes , Pruebas Genéticas , Células GerminativasRESUMEN
OBJECTIVE: Genomic testing for early-onset dementia is becoming more accessible, along with predictive testing for at-risk relatives; however, complex counselling issues are important to address. The topic of suicide often has stigma associated, and thoughts or experiences may not be volunteered without prompting. Little has been published with consideration to suicide rates in the context of family experiences and their significance in genetic counselling for relatives of people with Huntington disease and frontotemporal dementia. DESIGN: This study included pedigree information for 267 symptomatic individuals with frontotemporal dementia or Huntington disease, provided via genetic counselling clinics. MAIN OUTCOME MEASURES: Descriptive statistics and suicide rate calculations based on family reported pedigree data. RESULTS: The suicide rate was 2996 per 100,000 compared with the population rate of 10 per 100,000. Approximately one in 15 families reported suicide of an affected family member, and file notes indicated that one in five families had experienced suicide, suicidal thoughts or suicide attempts in one or more affected, unaffected or pre-symptomatic relative. CONCLUSION: Health professional awareness of family experiences, including suicide of a relative, is vital in facilitating client decisions about genetic testing, and in providing adequate psychosocial support during the process of genetic testing and adaption to results.
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Demencia Frontotemporal , Enfermedad de Huntington , Atención a la Salud , Demencia Frontotemporal/genética , Asesoramiento Genético/métodos , Asesoramiento Genético/psicología , Humanos , Enfermedad de Huntington/genética , Enfermedad de Huntington/psicología , LinajeRESUMEN
Massively parallel sequencing has markedly improved mendelian diagnostic rates. This study assessed the effects of custom alterations to a diagnostic genomic bioinformatic pipeline in response to clinical need and derived practice recommendations relative to diagnostic rates and efficiency. The Genomic Annotation and Interpretation Application (GAIA) bioinformatics pipeline was designed to detect panel, exome, and genome sample integrity and prioritize gene variants in mendelian disorders. Reanalysis of selected negative cases was performed after improvements to the pipeline. GAIA improvements and their effect on sensitivity are described, including addition of a PubMed search for gene-disease associations not in the Online Mendelian Inheritance of Man database, inclusion of a process for calling low-quality variants (known as QPatch), and gene symbol nomenclature consistency checking. The new pipeline increased the diagnostic rate and reduced staff costs, resulting in a saving of US$844.34 per additional diagnosis. Recommendations for genomic analysis pipeline requirements are summarized. Clinically responsive bioinformatics pipeline improvements increase diagnostic sensitivity and increase cost-effectiveness.
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Secuenciación del Exoma/métodos , Enfermedades Genéticas Congénitas/genética , Pruebas Genéticas/métodos , Genómica/métodos , Mutación de Línea Germinal , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Análisis Costo-Beneficio , Exoma , Pruebas Genéticas/economía , Genoma Humano , Genómica/economía , Secuenciación de Nucleótidos de Alto Rendimiento/economía , Humanos , Mutación INDEL , Fenotipo , Polimorfismo de Nucleótido Simple , Sensibilidad y Especificidad , Secuenciación del Exoma/economíaRESUMEN
Currently there is no secured ongoing funding in Australia for next generation sequencing (NGS) such as exome sequencing (ES) for adult neurological disorders. Studies have focused on paediatric populations in research or highly specialised settings, utilised standard NGS pipelines focusing only on small insertions, deletions and single nucleotide variants, and not explored impacts on management in detail. This prospective multi-site study performed ES and an extended bioinformatics repeat expansion analysis pipeline, on patients with broad phenotypes (ataxia, dementia, dystonia, spastic paraparesis, motor neuron disease, Parkinson's disease and complex/not-otherwise-specified), with symptom onset between 2 and 60 years. Genomic data analysis was phenotype-driven, using virtual gene panels, reported according to American College of Medical Genetics and Genomics guidelines. One-hundred-and-sixty patients (51% female) were included, median age 52 years (range 14-79) and median 9 years of symptoms. 34/160 (21%) patients received a genetic diagnosis. Highest diagnostic rates were in spastic paraparesis (10/25, 40%), complex/not-otherwise-specified (10/38, 26%) and ataxia (7/28, 25%) groups. Findings were considered 'possible/uncertain' in 21/160 patients. Repeat expansion detection identified an unexpected diagnosis of Huntington disease in an ataxic patient with negative ES. Impacts on management, such as more precise and tailored care, were seen in most diagnosed patients (23/34, 68%). ES and a novel bioinformatics analysis pipepline had a substantial diagnostic yield (21%) and management impacts for most diagnosed patients, in heterogeneous, complex, mainly adult-onset neurological disorders in real-world settings in Australia, providing evidence for NGS and complementary multiple, new technologies as valuable diagnostic tools.
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Exoma , Pruebas Genéticas , Adolescente , Adulto , Anciano , Australia , Niño , Biología Computacional , Femenino , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Masculino , Persona de Mediana Edad , Fenotipo , Estudios Prospectivos , Adulto JovenRESUMEN
BACKGROUND: Greenberg dysplasia is a rare, autosomal recessive, prenatal lethal bone dysplasia caused by biallelic pathogenic variants in the lamin B receptor (LBR) gene. Pathogenic variants in LBR are also associated with Pelger-Huët anomaly, an autosomal dominant benign abnormality of the nuclear shape and chromatin organization of blood granulocytes, and Pelger-Huët anomaly with variable skeletal anomalies, a mild, regressing to moderate-severe autosomal recessive condition. Conditions with abnormal sterol metabolism and different genetic basis have clinical and radiographic features similar to Greenberg dysplasia, for example X-linked dominant chondrodysplasia punctata, Conradi-Hünermann type, and CHILD syndrome, and other conditions with unknown genetic etiology display very similar features, for example, dappled diaphyseal dysplasia and Astley-Kendall dysplasia. METHODS: We present a fetus with typical clinical and radiographic features of Greenberg dysplasia, and review the literature. RESULTS: Genetic testing confirmed the diagnosis Greenberg dysplasia: homozygosity for a pathogenic variant in LBR. CONCLUSION: Comparing the clinical and radiographic phenotypes of Greenberg dysplasia, dappled diaphyseal dysplasia, and Astley-Kendall dysplasia, we suggest that these are allelic disorders.
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Condrodisplasia Punctata/genética , Enanismo/genética , Osteocondrodisplasias/genética , Osteogénesis Imperfecta/genética , Fenotipo , Receptores Citoplasmáticos y Nucleares/genética , Adulto , Alelos , Condrodisplasia Punctata/diagnóstico por imagen , Condrodisplasia Punctata/patología , Enanismo/diagnóstico por imagen , Enanismo/patología , Femenino , Feto/patología , Homocigoto , Humanos , Osteocondrodisplasias/diagnóstico por imagen , Osteocondrodisplasias/patología , Osteogénesis Imperfecta/diagnóstico por imagen , Osteogénesis Imperfecta/patología , Embarazo , Receptor de Lamina BRESUMEN
OBJECTIVE: To explore the diagnostic utility and cost effectiveness of whole exome sequencing (WES) in a cohort of individuals with peripheral neuropathy. METHODS: Singleton WES was performed in individuals recruited though one pediatric and one adult tertiary center between February 2014 and December 2015. Initial analysis was restricted to a virtual panel of 55 genes associated with peripheral neuropathies. Patients with uninformative results underwent expanded analysis of the WES data. Data on the cost of prior investigations and assessments performed for diagnostic purposes in each patient was collected. RESULTS: Fifty patients with a peripheral neuropathy were recruited (median age 18 years; range 2-68 years). The median time from initial presentation to study enrollment was 6 years 9 months (range 2 months-62 years), and the average cost of prior investigations and assessments for diagnostic purposes AU$4013 per patient. Eleven individuals received a diagnosis from the virtual panel. Eight individuals received a diagnosis following expanded analysis of the WES data, increasing the overall diagnostic yield to 38%. Two additional individuals were diagnosed with pathogenic copy number variants through SNP microarray. CONCLUSIONS: This study provides evidence that WES has a high diagnostic utility and is cost effective in patients with a peripheral neuropathy. Expanded analysis of WES data significantly improves the diagnostic yield in patients in whom a diagnosis is not found on the initial targeted analysis. This is primarily due to diagnosis of conditions caused by newly discovered genes and the resolution of complex and atypical phenotypes.
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Importance: Optimal use of whole-exome sequencing (WES) in the pediatric setting requires an understanding of who should be considered for testing and when it should be performed to maximize clinical utility and cost-effectiveness. Objectives: To investigate the impact of WES in sequencing-naive children suspected of having a monogenic disorder and evaluate its cost-effectiveness if WES had been available at different time points in their diagnostic trajectory. Design, Setting, and Participants: This prospective study was part of the Melbourne Genomics Health Alliance demonstration project. At the ambulatory outpatient clinics of the Victorian Clinical Genetics Services at the Royal Children's Hospital, Melbourne, Australia, children older than 2 years suspected of having a monogenic disorder were prospectively recruited from May 1 through November 30, 2015, by clinical geneticists after referral from general and subspecialist pediatricians. All children had nondiagnostic microarrays and no prior single-gene or panel sequencing. Exposures: All children underwent singleton WES with targeted phenotype-driven analysis. Main Outcomes and Measures: The study examined the clinical utility of a molecular diagnosis and the cost-effectiveness of alternative diagnostic trajectories, depending on timing of WES. Results: Of 61 children originally assessed, 44 (21 [48%] male and 23 [52%] female) aged 2 to 18 years (mean age at initial presentation, 28 months; range, 0-121 months) were recruited, and a diagnosis was achieved in 23 (52%) by singleton WES. The diagnoses were unexpected in 8 of 23 (35%), and clinical management was altered in 6 of 23 (26%). The mean duration of the diagnostic odyssey was 6 years, with each child having a mean of 19 tests and 4 clinical genetics and 4 nongenetics specialist consultations, and 26 (59%) underwent a procedure while under general anesthetic for diagnostic purposes. Economic analyses of the diagnostic trajectory identified that WES performed at initial tertiary presentation resulted in an incremental cost savings of A$9020 (US$6838) per additional diagnosis (95% CI, A$4304-A$15â¯404 [US$3263-US$11 678]) compared with the standard diagnostic pathway. Even if WES were performed at the first genetics appointment, there would be an incremental cost savings of A$5461 (US$4140) (95% CI, A$1433-A$10â¯557 [US$1086- US$8004]) per additional diagnosis compared with the standard diagnostic pathway. Conclusions and Relevance: Singleton WES in children with suspected monogenic conditions has high diagnostic yield, and cost-effectiveness is maximized by early application in the diagnostic pathway. Pediatricians should consider early referral of children with undiagnosed syndromes to clinical geneticists.