Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 71
Filter
3.
Am J Hum Genet ; 111(1): 96-118, 2024 Jan 04.
Article in English | MEDLINE | ID: mdl-38181735

ABSTRACT

PPFIA3 encodes the protein-tyrosine phosphatase, receptor-type, F-polypeptide-interacting-protein-alpha-3 (PPFIA3), which is a member of the LAR-protein-tyrosine phosphatase-interacting-protein (liprin) family involved in synapse formation and function, synaptic vesicle transport, and presynaptic active zone assembly. The protein structure and function are evolutionarily well conserved, but human diseases related to PPFIA3 dysfunction are not yet reported in OMIM. Here, we report 20 individuals with rare PPFIA3 variants (19 heterozygous and 1 compound heterozygous) presenting with developmental delay, intellectual disability, hypotonia, dysmorphisms, microcephaly or macrocephaly, autistic features, and epilepsy with reduced penetrance. Seventeen unique PPFIA3 variants were detected in 18 families. To determine the pathogenicity of PPFIA3 variants in vivo, we generated transgenic fruit flies producing either human wild-type (WT) PPFIA3 or five missense variants using GAL4-UAS targeted gene expression systems. In the fly overexpression assays, we found that the PPFIA3 variants in the region encoding the N-terminal coiled-coil domain exhibited stronger phenotypes compared to those affecting the C-terminal region. In the loss-of-function fly assay, we show that the homozygous loss of fly Liprin-α leads to embryonic lethality. This lethality is partially rescued by the expression of human PPFIA3 WT, suggesting human PPFIA3 function is partially conserved in the fly. However, two of the tested variants failed to rescue the lethality at the larval stage and one variant failed to rescue lethality at the adult stage. Altogether, the human and fruit fly data reveal that the rare PPFIA3 variants are dominant-negative loss-of-function alleles that perturb multiple developmental processes and synapse formation.


Subject(s)
Drosophila Proteins , Intellectual Disability , Neurodevelopmental Disorders , Adult , Animals , Humans , Alleles , Animals, Genetically Modified , Drosophila , Drosophila Proteins/genetics , Intellectual Disability/genetics , Intracellular Signaling Peptides and Proteins , Neurodevelopmental Disorders/genetics , Protein Tyrosine Phosphatases
4.
Bioinformation ; 19(4): 375-379, 2023.
Article in English | MEDLINE | ID: mdl-37822815

ABSTRACT

Diabetic nephropathy/diabetic kidney disease (DKD) is one of the leading causes of renal failure. Early identification of the development or progression of diabetic nephropathy using appropriate screening and diagnostic tools is very important in order to provide timely and proper management. Inflammation plays a crucial role in development and progression of diabetic nephropathy. The aim of this study was to evaluate the relationship of inflammatory markers (neutrophil-to-lymphocyte ratio-NLR) as an early indicator to prevent the progression of diabetic kidney disease. A total of 158 patients with type 2 diabetes mellitus were distributed into three groups according urinary albumin-to-creatinine ratio. Levels of inflammatory markers neutrophil-to-lymphocyte ratio was recorded and compared among the three groups. Significant differences were detected between the groups in terms of neutrophil-to-lymphocyte ratio (p = 0.000).Characteristic curve analysis of inflammatory markers and microalbuminuria prediction demonstrated an area under curve (AUC) of 0.869 for neutrophil-to-lymphocyte ratio (p = 0.000). A NLR cut-off point of 2.2 has 72.3 % sensitivity and 78.1 % specificity, which suggested sufficient accuracy. Increased neutrophil-to-lymphocyte ratio was significantly correlated with diabetic nephropathy progression and increased neutrophil-to-lymphocyte ratio can be considered as an early indicator and a prognostic risk marker of diabetic nephropathy.

5.
Brain ; 146(11): 4766-4783, 2023 11 02.
Article in English | MEDLINE | ID: mdl-37437211

ABSTRACT

KPTN-related disorder is an autosomal recessive disorder associated with germline variants in KPTN (previously known as kaptin), a component of the mTOR regulatory complex KICSTOR. To gain further insights into the pathogenesis of KPTN-related disorder, we analysed mouse knockout and human stem cell KPTN loss-of-function models. Kptn -/- mice display many of the key KPTN-related disorder phenotypes, including brain overgrowth, behavioural abnormalities, and cognitive deficits. By assessment of affected individuals, we have identified widespread cognitive deficits (n = 6) and postnatal onset of brain overgrowth (n = 19). By analysing head size data from their parents (n = 24), we have identified a previously unrecognized KPTN dosage-sensitivity, resulting in increased head circumference in heterozygous carriers of pathogenic KPTN variants. Molecular and structural analysis of Kptn-/- mice revealed pathological changes, including differences in brain size, shape and cell numbers primarily due to abnormal postnatal brain development. Both the mouse and differentiated induced pluripotent stem cell models of the disorder display transcriptional and biochemical evidence for altered mTOR pathway signalling, supporting the role of KPTN in regulating mTORC1. By treatment in our KPTN mouse model, we found that the increased mTOR signalling downstream of KPTN is rapamycin sensitive, highlighting possible therapeutic avenues with currently available mTOR inhibitors. These findings place KPTN-related disorder in the broader group of mTORC1-related disorders affecting brain structure, cognitive function and network integrity.


Subject(s)
Signal Transduction , TOR Serine-Threonine Kinases , Humans , Animals , Mice , Signal Transduction/genetics , TOR Serine-Threonine Kinases/metabolism , Brain/metabolism , Mechanistic Target of Rapamycin Complex 1/metabolism , Cognition , Microfilament Proteins/genetics
6.
Nat Commun ; 14(1): 4109, 2023 07 11.
Article in English | MEDLINE | ID: mdl-37433783

ABSTRACT

Genetic variants in chromatin regulators are frequently found in neurodevelopmental disorders, but their effect in disease etiology is rarely determined. Here, we uncover and functionally define pathogenic variants in the chromatin modifier EZH1 as the cause of dominant and recessive neurodevelopmental disorders in 19 individuals. EZH1 encodes one of the two alternative histone H3 lysine 27 methyltransferases of the PRC2 complex. Unlike the other PRC2 subunits, which are involved in cancers and developmental syndromes, the implication of EZH1 in human development and disease is largely unknown. Using cellular and biochemical studies, we demonstrate that recessive variants impair EZH1 expression causing loss of function effects, while dominant variants are missense mutations that affect evolutionarily conserved aminoacids, likely impacting EZH1 structure or function. Accordingly, we found increased methyltransferase activity leading to gain of function of two EZH1 missense variants. Furthermore, we show that EZH1 is necessary and sufficient for differentiation of neural progenitor cells in the developing chick embryo neural tube. Finally, using human pluripotent stem cell-derived neural cultures and forebrain organoids, we demonstrate that EZH1 variants perturb cortical neuron differentiation. Overall, our work reveals a critical role of EZH1 in neurogenesis regulation and provides molecular diagnosis for previously undefined neurodevelopmental disorders.


Subject(s)
Neurodevelopmental Disorders , Neurogenesis , Polycomb Repressive Complex 2 , Animals , Chick Embryo , Humans , Cell Differentiation/genetics , Cell Nucleus , Chromatin/genetics , Methyltransferases , Neurodevelopmental Disorders/genetics , Neurogenesis/genetics , Polycomb Repressive Complex 2/genetics
7.
Nat Genet ; 54(10): 1534-1543, 2022 Oct.
Article in English | MEDLINE | ID: mdl-36195757

ABSTRACT

Sleep apnea is a common disorder that represents a global public health burden. KCNK3 encodes TASK-1, a K+ channel implicated in the control of breathing, but its link with sleep apnea remains poorly understood. Here we describe a new developmental disorder with associated sleep apnea (developmental delay with sleep apnea, or DDSA) caused by rare de novo gain-of-function mutations in KCNK3. The mutations cluster around the 'X-gate', a gating motif that controls channel opening, and produce overactive channels that no longer respond to inhibition by G-protein-coupled receptor pathways. However, despite their defective X-gating, these mutant channels can still be inhibited by a range of known TASK channel inhibitors. These results not only highlight an important new role for TASK-1 K+ channels and their link with sleep apnea but also identify possible therapeutic strategies.


Subject(s)
Gain of Function Mutation , Sleep Apnea Syndromes , Child , Developmental Disabilities , Humans , Mutation/genetics , Nerve Tissue Proteins , Potassium Channels, Tandem Pore Domain , Sleep Apnea Syndromes/genetics
8.
Am J Med Genet A ; 188(12): 3492-3504, 2022 12.
Article in English | MEDLINE | ID: mdl-36135330

ABSTRACT

Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a life-threatening birth defect that often occurs with other major birth defects (EA/TEF+). Despite advances in genetic testing, a molecular diagnosis can only be made in a minority of EA/TEF+ cases. Here, we analyzed clinical exome sequencing data and data from the DECIPHER database to determine the efficacy of exome sequencing in cases of EA/TEF+ and to identify phenotypic expansions involving EA/TEF. Among 67 individuals with EA/TEF+ referred for clinical exome sequencing, a definitive or probable diagnosis was made in 11 cases for an efficacy rate of 16% (11/67). This efficacy rate is significantly lower than that reported for other major birth defects, suggesting that polygenic, multifactorial, epigenetic, and/or environmental factors may play a particularly important role in EA/TEF pathogenesis. Our cohort included individuals with pathogenic or likely pathogenic variants that affect TCF4 and its downstream target NRXN1, and FANCA, FANCB, and FANCC, which are associated with Fanconi anemia. These cases, previously published case reports, and comparisons to other EA/TEF genes made using a machine learning algorithm, provide evidence in support of a potential pathogenic role for these genes in the development of EA/TEF.


Subject(s)
Esophageal Atresia , Tracheoesophageal Fistula , Humans , Tracheoesophageal Fistula/diagnosis , Tracheoesophageal Fistula/genetics , Tracheoesophageal Fistula/complications , Esophageal Atresia/diagnosis , Esophageal Atresia/genetics , Esophageal Atresia/complications , Exome/genetics , Exome Sequencing
9.
Am J Med Genet A ; 185(8): 2445-2454, 2021 08.
Article in English | MEDLINE | ID: mdl-34032352

ABSTRACT

Smith-Kingsmore Syndrome (SKS) is a rare genetic syndrome associated with megalencephaly, a variable intellectual disability, autism spectrum disorder, and MTOR gain of function variants. Only 30 patients with MTOR missense variants are published, including 14 (47%) with the MTOR c.5395G>A p.(Glu1799Lys) variant. Limited phenotypic data impacts the quality of information delivered to families and the robustness of interpretation of novel MTOR missense variation. This study aims to improve our understanding of the SKS phenotype through the investigation of 16 further patients with the MTOR c.5395G>A p.(Glu1799Lys) variant. Through the careful phenotypic evaluation of these 16 patients and integration with data from 14 previously reported patients, we have defined major (100% patients) and frequent (>15%) SKS clinical characteristics and, using these data, proposed guidance for evidence-based management. In addition, in the absence of functional studies, we suggest that the combination of the SKS major clinical features of megalencephaly (where the head circumference is at least 3SD) and an intellectual disability with a de novo MTOR missense variant (absent from population databases) should be considered diagnostic for SKS.


Subject(s)
Alleles , Genetic Association Studies , Mutation, Missense , Phenotype , TOR Serine-Threonine Kinases/genetics , Adolescent , Amino Acid Substitution , Autism Spectrum Disorder/diagnosis , Autism Spectrum Disorder/genetics , Child , Child, Preschool , Facies , Female , Genetic Loci , Humans , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Male , Megalencephaly/diagnosis , Megalencephaly/genetics , Syndrome
10.
Hum Mutat ; 42(7): 811-817, 2021 07.
Article in English | MEDLINE | ID: mdl-33993607

ABSTRACT

Heterozygous intragenic loss-of-function mutations of ERF, encoding an ETS transcription factor, were previously reported to cause a novel craniosynostosis syndrome, suggesting that ERF is haploinsufficient. We describe six families harboring heterozygous deletions including, or near to, ERF, of which four were characterized by whole-genome sequencing and two by chromosomal microarray. Based on the severity of associated intellectual disability (ID), we identify three categories of ERF-associated deletions. The smallest (32 kb) and only inherited deletion included two additional centromeric genes and was not associated with ID. Three larger deletions (264-314 kb) that included at least five further centromeric genes were associated with moderate ID, suggesting that deletion of one or more of these five genes causes ID. The individual with the most severe ID had a more telomerically extending deletion, including CIC, a known ID gene. Children found to harbor ERF deletions should be referred for craniofacial assessment, to exclude occult raised intracranial pressure.


Subject(s)
Chromosomes, Human, Pair 19 , Intellectual Disability , Child , Chromosome Deletion , Haploinsufficiency , Heterozygote , Humans , Intellectual Disability/genetics , Mutation , Repressor Proteins/genetics
11.
Eur J Hum Genet ; 29(4): 625-636, 2021 04.
Article in English | MEDLINE | ID: mdl-33437032

ABSTRACT

Witteveen-Kolk syndrome (OMIM 613406) is a recently defined neurodevelopmental syndrome caused by heterozygous loss-of-function variants in SIN3A. We define the clinical and neurodevelopmental phenotypes related to SIN3A-haploinsufficiency in 28 unreported patients. Patients with SIN3A variants adversely affecting protein function have mild intellectual disability, growth and feeding difficulties. Involvement of a multidisciplinary team including a geneticist, paediatrician and neurologist should be considered in managing these patients. Patients described here were identified through a combination of clinical evaluation and gene matching strategies (GeneMatcher and Decipher). All patients consented to participate in this study. Mean age of this cohort was 8.2 years (17 males, 11 females). Out of 16 patients ≥ 8 years old assessed, eight (50%) had mild intellectual disability (ID), four had moderate ID (22%), and one had severe ID (6%). Four (25%) did not have any cognitive impairment. Other neurological symptoms such as seizures (4/28) and hypotonia (12/28) were common. Behaviour problems were reported in a minority. In patients ≥2 years, three were diagnosed with Autism Spectrum Disorder (ASD) and four with Attention Deficit Hyperactivity Disorder (ADHD). We report 27 novel variants and one previously reported variant. 24 were truncating variants; three were missense variants and one large in-frame gain including exons 10-12.


Subject(s)
Craniofacial Abnormalities/genetics , Developmental Disabilities/genetics , Intellectual Disability/genetics , Phenotype , Sin3 Histone Deacetylase and Corepressor Complex/genetics , Adolescent , Child , Child, Preschool , Craniofacial Abnormalities/pathology , Developmental Disabilities/pathology , Female , Humans , Infant , Intellectual Disability/pathology , Male , Mutation , Syndrome
12.
Genet Med ; 23(5): 881-887, 2021 05.
Article in English | MEDLINE | ID: mdl-33473207

ABSTRACT

PURPOSE: Neurodevelopmental disorders (NDDs) encompass a spectrum of genetically heterogeneous disorders with features that commonly include developmental delay, intellectual disability, and autism spectrum disorders. We sought to delineate the molecular and phenotypic spectrum of a novel neurodevelopmental disorder caused by variants in the GNAI1 gene. METHODS: Through large cohort trio-based exome sequencing and international data-sharing, we identified 24 unrelated individuals with NDD phenotypes and a variant in GNAI1, which encodes the inhibitory Gαi1 subunit of heterotrimeric G-proteins. We collected detailed genotype and phenotype information for each affected individual. RESULTS: We identified 16 unique variants in GNAI1 in 24 affected individuals; 23 occurred de novo and 1 was inherited from a mosaic parent. Most affected individuals have a severe neurodevelopmental disorder. Core features include global developmental delay, intellectual disability, hypotonia, and epilepsy. CONCLUSION: This collaboration establishes GNAI1 variants as a cause of NDDs. GNAI1-related NDD is most often characterized by severe to profound delays, hypotonia, epilepsy that ranges from self-limiting to intractable, behavior problems, and variable mild dysmorphic features.


Subject(s)
Intellectual Disability , Neurodevelopmental Disorders , Child , Developmental Disabilities/genetics , Humans , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Muscle Hypotonia/diagnosis , Muscle Hypotonia/genetics , Neurodevelopmental Disorders/diagnosis , Neurodevelopmental Disorders/genetics , Seizures/genetics , Exome Sequencing
13.
Ann Neurol ; 88(2): 348-362, 2020 08.
Article in English | MEDLINE | ID: mdl-32515017

ABSTRACT

OBJECTIVE: Pathogenic variants in SCN3A, encoding the voltage-gated sodium channel subunit Nav1.3, cause severe childhood onset epilepsy and malformation of cortical development. Here, we define the spectrum of clinical, genetic, and neuroimaging features of SCN3A-related neurodevelopmental disorder. METHODS: Patients were ascertained via an international collaborative network. We compared sodium channels containing wild-type versus variant Nav1.3 subunits coexpressed with ß1 and ß2 subunits using whole-cell voltage clamp electrophysiological recordings in a heterologous mammalian system (HEK-293T cells). RESULTS: Of 22 patients with pathogenic SCN3A variants, most had treatment-resistant epilepsy beginning in the first year of life (16/21, 76%; median onset, 2 weeks), with severe or profound developmental delay (15/20, 75%). Many, but not all (15/19, 79%), exhibited malformations of cortical development. Pathogenic variants clustered in transmembrane segments 4 to 6 of domains II to IV. Most pathogenic missense variants tested (10/11, 91%) displayed gain of channel function, with increased persistent current and/or a leftward shift in the voltage dependence of activation, and all variants associated with malformation of cortical development exhibited gain of channel function. One variant (p.Ile1468Arg) exhibited mixed effects, with gain and partial loss of function. Two variants demonstrated loss of channel function. INTERPRETATION: Our study defines SCN3A-related neurodevelopmental disorder along a spectrum of severity, but typically including epilepsy and severe or profound developmental delay/intellectual disability. Malformations of cortical development are a characteristic feature of this unusual channelopathy syndrome, present in >75% of affected individuals. Gain of function at the channel level in developing neurons is likely an important mechanism of disease pathogenesis. ANN NEUROL 2020;88:348-362.


Subject(s)
Brain/diagnostic imaging , Epilepsy/diagnostic imaging , Epilepsy/genetics , NAV1.3 Voltage-Gated Sodium Channel/genetics , Neurodevelopmental Disorders/diagnostic imaging , Neurodevelopmental Disorders/genetics , Sodium Channels/genetics , Adolescent , Adult , Child , Child, Preschool , Female , Fetus/diagnostic imaging , Genetic Variation/genetics , HEK293 Cells , Humans , Infant , Male
14.
Mol Genet Genomic Med ; 8(9): e1354, 2020 09.
Article in English | MEDLINE | ID: mdl-32578940

ABSTRACT

BACKGROUND: Type 2 Stickler syndrome is usually a dominant disorder resulting from pathogenic variants in COL11A1 encoding the alpha 1 chain of type XI collagen. Typical molecular changes result in either substitution of an obligate glycine within the Gly-Xaa-Yaa amino acid sequence repeat region of the molecule, mRNA missplicing or deletions/duplications that typically leaves the message in-frame. Clinical features include myopia, retinal detachment, craniofacial, joint, and hearing problems. Fibrochondrogenesis is also a COL11A1 related disorder, but here disease-associated variants are recessive and may be either null alleles or substitutions of glycine, and the condition is usually lethal in infancy. METHODS: The patient was assessed in the NHS England Stickler syndrome diagnostic service. DNA from the patient and family were analyzed with Next Generation Sequencing on a panel of genes known to cause Stickler Syndrome. The effect of sequence variants was assessed using minigene analysis. Allele-specific RT-PCR was performed. RESULTS: This patient had clinical type 2 Stickler syndrome but with severe hearing loss and severe ocular features including retinal atrophy and retinal tears in childhood. We identified a de novo in frame deletion of COL11A1 (c.4109_4126del) consistent with dominantly inherited Stickler syndrome but also a second inherited variant (c.1245+2T>C), on the other allele, affecting normal splicing of COL11A1 exon 9. CONCLUSION: Exon 9 of COL11A1 is alternatively expressed and disease causing changes affecting only this exon modify the phenotype resulting from biallelic COL11A1 disease-associated variants and, instead of fibrochondrogenesis, produce a form of Stickler syndrome with severe hearing loss. Disease phenotypes from de novo pathogenic variants can be modified by inherited recessive variants on the other allele. This highlights the need for functional and family analysis to confirm the mode of inheritance in COL11A1-related disorders, particularly for those variants that may alter normal pre-mRNA splicing.


Subject(s)
Arthritis/genetics , Collagen Type XI/genetics , Connective Tissue Diseases/genetics , Hearing Loss, Sensorineural/genetics , Retinal Detachment/genetics , Adolescent , Arthritis/pathology , Connective Tissue Diseases/pathology , Female , Gene Deletion , Genes, Dominant , Hearing Loss, Sensorineural/pathology , Humans , Phenotype , RNA Splicing , Retinal Detachment/pathology
15.
Arch Dis Child ; 105(4): 384-389, 2020 04.
Article in English | MEDLINE | ID: mdl-31481360

ABSTRACT

INTRODUCTION: Fetal anticonvulsant syndrome (FACS) describes the pattern of physical and developmental problems seen in those children exposed to certain antiepileptic drugs (AEDs) in utero. The diagnosis of FACS is a clinical one and so excluding alternative diagnoses such as genetic disorders is essential. METHODS: We reviewed the pathogenicity of reported variants identified on exome sequencing in the Deciphering Developmental Disorders (DDD) Study in 42 children exposed to AEDs in utero, but where a diagnosis other than FACS was suspected. In addition, we analysed chromosome microarray data from 10 patients with FACS seen in a Regional Genetics Service. RESULTS: Seven children (17%) from the DDD Study had a copy number variant or pathogenic variant in a developmental disorder gene which was considered to explain or partially explain their phenotype. Across the AED exposure types, variants were found in 2/15 (13%) valproate exposed cases and 3/14 (21%) carbamazepine exposed cases. No pathogenic copy number variants were identified in our local sample (n=10). CONCLUSIONS: This study is the first of its kind to analyse the exomes of children with developmental disorders who were exposed to AEDs in utero. Though we acknowledge that the results are subject to bias, a significant number of children were identified with alternate diagnoses which had an impact on counselling and management. We suggest that consideration is given to performing whole exome sequencing as part of the diagnostic work-up for children exposed to AEDs in utero.


Subject(s)
Anticonvulsants/adverse effects , Developmental Disabilities/chemically induced , Epilepsy/drug therapy , Exome Sequencing , Prenatal Exposure Delayed Effects/chemically induced , Valproic Acid/adverse effects , Abnormalities, Drug-Induced , Anticonvulsants/therapeutic use , Child , Child, Preschool , Female , Humans , Male , Phenotype , Pregnancy , Pregnancy Complications , Prenatal Exposure Delayed Effects/genetics , Retrospective Studies , Valproic Acid/therapeutic use
16.
Genet Med ; 22(1): 124-131, 2020 01.
Article in English | MEDLINE | ID: mdl-31316167

ABSTRACT

PURPOSE: Congenital contractural arachnodactyly (CCA) is an autosomal dominant connective tissue disorder manifesting joint contractures, arachnodactyly, crumpled ears, and kyphoscoliosis as main features. Due to its rarity, rather aspecific clinical presentation, and overlap with other conditions including Marfan syndrome, the diagnosis is challenging, but important for prognosis and clinical management. CCA is caused by pathogenic variants in FBN2, encoding fibrillin-2, but locus heterogeneity has been suggested. We designed a clinical scoring system and diagnostic criteria to support the diagnostic process and guide molecular genetic testing. METHODS: In this retrospective study, we assessed 167 probands referred for FBN2 analysis and classified them into a FBN2-positive (n = 44) and FBN2-negative group (n = 123) following molecular analysis. We developed a 20-point weighted clinical scoring system based on the prevalence of ten main clinical characteristics of CCA in both groups. RESULTS: The total score was significantly different between the groups (P < 0.001) and was indicative for classifying patients into unlikely CCA (total score <7) and likely CCA (total score ≥7) groups. CONCLUSIONS: Our clinical score is helpful for clinical guidance for patients suspected to have CCA, and provides a quantitative tool for phenotyping in research settings.


Subject(s)
Arachnodactyly/diagnosis , Contracture/diagnosis , Fibrillin-2/genetics , Sequence Analysis, DNA/methods , Arachnodactyly/genetics , Child , Contracture/genetics , Diagnosis, Differential , Early Diagnosis , Female , Genetic Testing , Humans , Male , Marfan Syndrome/diagnosis , Marfan Syndrome/genetics , Phenotype , Retrospective Studies , Sensitivity and Specificity
17.
Lancet ; 393(10173): 747-757, 2019 02 23.
Article in English | MEDLINE | ID: mdl-30712880

ABSTRACT

BACKGROUND: Fetal structural anomalies, which are detected by ultrasonography, have a range of genetic causes, including chromosomal aneuploidy, copy number variations (CNVs; which are detectable by chromosomal microarrays), and pathogenic sequence variants in developmental genes. Testing for aneuploidy and CNVs is routine during the investigation of fetal structural anomalies, but there is little information on the clinical usefulness of genome-wide next-generation sequencing in the prenatal setting. We therefore aimed to evaluate the proportion of fetuses with structural abnormalities that had identifiable variants in genes associated with developmental disorders when assessed with whole-exome sequencing (WES). METHODS: In this prospective cohort study, two groups in Birmingham and London recruited patients from 34 fetal medicine units in England and Scotland. We used whole-exome sequencing (WES) to evaluate the presence of genetic variants in developmental disorder genes (diagnostic genetic variants) in a cohort of fetuses with structural anomalies and samples from their parents, after exclusion of aneuploidy and large CNVs. Women were eligible for inclusion if they were undergoing invasive testing for identified nuchal translucency or structural anomalies in their fetus, as detected by ultrasound after 11 weeks of gestation. The partners of these women also had to consent to participate. Sequencing results were interpreted with a targeted virtual gene panel for developmental disorders that comprised 1628 genes. Genetic results related to fetal structural anomaly phenotypes were then validated and reported postnatally. The primary endpoint, which was assessed in all fetuses, was the detection of diagnostic genetic variants considered to have caused the fetal developmental anomaly. FINDINGS: The cohort was recruited between Oct 22, 2014, and June 29, 2017, and clinical data were collected until March 31, 2018. After exclusion of fetuses with aneuploidy and CNVs, 610 fetuses with structural anomalies and 1202 matched parental samples (analysed as 596 fetus-parental trios, including two sets of twins, and 14 fetus-parent dyads) were analysed by WES. After bioinformatic filtering and prioritisation according to allele frequency and effect on protein and inheritance pattern, 321 genetic variants (representing 255 potential diagnoses) were selected as potentially pathogenic genetic variants (diagnostic genetic variants), and these variants were reviewed by a multidisciplinary clinical review panel. A diagnostic genetic variant was identified in 52 (8·5%; 95% CI 6·4-11·0) of 610 fetuses assessed and an additional 24 (3·9%) fetuses had a variant of uncertain significance that had potential clinical usefulness. Detection of diagnostic genetic variants enabled us to distinguish between syndromic and non-syndromic fetal anomalies (eg, congenital heart disease only vs a syndrome with congenital heart disease and learning disability). Diagnostic genetic variants were present in 22 (15·4%) of 143 fetuses with multisystem anomalies (ie, more than one fetal structural anomaly), nine (11·1%) of 81 fetuses with cardiac anomalies, and ten (15·4%) of 65 fetuses with skeletal anomalies; these phenotypes were most commonly associated with diagnostic variants. However, diagnostic genetic variants were least common in fetuses with isolated increased nuchal translucency (≥4·0 mm) in the first trimester (in three [3·2%] of 93 fetuses). INTERPRETATION: WES facilitates genetic diagnosis of fetal structural anomalies, which enables more accurate predictions of fetal prognosis and risk of recurrence in future pregnancies. However, the overall detection of diagnostic genetic variants in a prospectively ascertained cohort with a broad range of fetal structural anomalies is lower than that suggested by previous smaller-scale studies of fewer phenotypes. WES improved the identification of genetic disorders in fetuses with structural abnormalities; however, before clinical implementation, careful consideration should be given to case selection to maximise clinical usefulness. FUNDING: UK Department of Health and Social Care and The Wellcome Trust.


Subject(s)
Abnormal Karyotype/statistics & numerical data , Congenital Abnormalities/genetics , Exome Sequencing/statistics & numerical data , Fetal Development/genetics , Fetus/abnormalities , Abnormal Karyotype/embryology , Abortion, Eugenic/statistics & numerical data , Abortion, Spontaneous/epidemiology , Congenital Abnormalities/diagnosis , Congenital Abnormalities/epidemiology , DNA Copy Number Variations/genetics , Female , Fetus/diagnostic imaging , Humans , Infant, Newborn , Live Birth/epidemiology , Male , Nuchal Translucency Measurement , Parents , Perinatal Death/etiology , Pregnancy , Prospective Studies , Stillbirth/epidemiology , Exome Sequencing/methods
18.
Genet Med ; 21(7): 1667-1671, 2019 Jul.
Article in English | MEDLINE | ID: mdl-30783266

ABSTRACT

The article has been corrected to account for one patient being investigated through genome sequencing rather than exome sequencing as originally published; thus amendments to the Abstract and Methods have been made as well as addition of the relevant authors and acknowledgment.

19.
Am J Med Genet A ; 179(4): 615-627, 2019 04.
Article in English | MEDLINE | ID: mdl-30758909

ABSTRACT

Mutations in the ERF gene, coding for ETS2 repressor factor, a member of the ETS family of transcription factors cause a recently recognized syndromic form of craniosynostosis (CRS4) with facial dysmorphism, Chiari-1 malformation, speech and language delay, and learning difficulties and/or behavioral problems. The overall prevalence of ERF mutations in patients with syndromic craniosynostosis is around 2%, and 0.7% in clinically nonsyndromic craniosynostosis. Here, we present findings from 16 unrelated probands with ERF-related craniosynostosis, with additional data from 20 family members sharing the mutations. Most of the probands exhibited multisutural (including pan-) synostosis but a pattern involving the sagittal and lambdoid sutures (Mercedes-Benz pattern) predominated. Importantly the craniosynostosis was often postnatal in onset, insidious and progressive with subtle effects on head morphology resulting in a median age at presentation of 42 months among the probands and, in some instances, permanent visual impairment due to unsuspected raised intracranial pressure (ICP). Facial dysmorphism (exhibited by all of the probands and many of the affected relatives) took the form of orbital hypertelorism, mild exorbitism and malar hypoplasia resembling Crouzon syndrome but, importantly, a Class I occlusal relationship. Speech delay, poor gross and/or fine motor control, hyperactivity and poor concentration were common. Cranial vault surgery for raised ICP and/or Chiari-1 malformation was expected when multisutural synostosis was observed. Variable expressivity and nonpenetrance among genetically affected relatives was encountered. These observations form the most complete phenotypic and developmental profile of this recently identified craniosynostosis syndrome yet described and have important implications for surgical intervention and follow-up.


Subject(s)
Craniosynostoses/genetics , Craniosynostoses/pathology , Mutation , Repressor Proteins/genetics , Adolescent , Adult , Age of Onset , Child , Child, Preschool , Female , Humans , Infant , Infant, Newborn , Male , Phenotype , Syndrome , Young Adult
20.
Genet Med ; 21(6): 1308-1318, 2019 06.
Article in English | MEDLINE | ID: mdl-30356099

ABSTRACT

PURPOSE: Germline WWOX pathogenic variants have been associated with disorder of sex differentiation (DSD), spinocerebellar ataxia (SCA), and WWOX-related epileptic encephalopathy (WOREE syndrome). We review clinical and molecular data on WWOX-related disorders, further describing WOREE syndrome and phenotype/genotype correlations. METHODS: We report clinical and molecular findings in 20 additional patients from 18 unrelated families with WOREE syndrome and biallelic pathogenic variants in the WWOX gene. Different molecular screening approaches were used (quantitative polymerase chain reaction/multiplex ligation-dependent probe amplification [qPCR/MLPA], array comparative genomic hybridization [array-CGH], Sanger sequencing, epilepsy gene panel, exome sequencing), genome sequencing. RESULTS: Two copy-number variations (CNVs) or two single-nucleotide variations (SNVs) were found respectively in four and nine families, with compound heterozygosity for one SNV and one CNV in five families. Eight novel missense pathogenic variants have been described. By aggregating our patients with all cases reported in the literature, 37 patients from 27 families with WOREE syndrome are known. This review suggests WOREE syndrome is a very severe epileptic encephalopathy characterized by absence of language development and acquisition of walking, early-onset drug-resistant seizures, ophthalmological involvement, and a high likelihood of premature death. The most severe clinical presentation seems to be associated with null genotypes. CONCLUSION: Germline pathogenic variants in WWOX are clearly associated with a severe early-onset epileptic encephalopathy. We report here the largest cohort of individuals with WOREE syndrome.


Subject(s)
Epileptic Syndromes/genetics , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/physiology , WW Domain-Containing Oxidoreductase/genetics , WW Domain-Containing Oxidoreductase/physiology , Adolescent , Child , Child, Preschool , DNA Copy Number Variations/genetics , Epilepsy/genetics , Female , Genetic Association Studies/methods , Humans , Infant , Male , Mutation/genetics , Mutation, Missense/genetics , Syndrome , Tumor Suppressor Proteins/metabolism , WW Domain-Containing Oxidoreductase/metabolism
SELECTION OF CITATIONS
SEARCH DETAIL
...