Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 32
Filter
Add more filters

Country/Region as subject
Publication year range
1.
Am J Hum Genet ; 110(5): 790-808, 2023 05 04.
Article in English | MEDLINE | ID: mdl-37071997

ABSTRACT

SRSF1 (also known as ASF/SF2) is a non-small nuclear ribonucleoprotein (non-snRNP) that belongs to the arginine/serine (R/S) domain family. It recognizes and binds to mRNA, regulating both constitutive and alternative splicing. The complete loss of this proto-oncogene in mice is embryonically lethal. Through international data sharing, we identified 17 individuals (10 females and 7 males) with a neurodevelopmental disorder (NDD) with heterozygous germline SRSF1 variants, mostly de novo, including three frameshift variants, three nonsense variants, seven missense variants, and two microdeletions within region 17q22 encompassing SRSF1. Only in one family, the de novo origin could not be established. All individuals featured a recurrent phenotype including developmental delay and intellectual disability (DD/ID), hypotonia, neurobehavioral problems, with variable skeletal (66.7%) and cardiac (46%) anomalies. To investigate the functional consequences of SRSF1 variants, we performed in silico structural modeling, developed an in vivo splicing assay in Drosophila, and carried out episignature analysis in blood-derived DNA from affected individuals. We found that all loss-of-function and 5 out of 7 missense variants were pathogenic, leading to a loss of SRSF1 splicing activity in Drosophila, correlating with a detectable and specific DNA methylation episignature. In addition, our orthogonal in silico, in vivo, and epigenetics analyses enabled the separation of clearly pathogenic missense variants from those with uncertain significance. Overall, these results indicated that haploinsufficiency of SRSF1 is responsible for a syndromic NDD with ID due to a partial loss of SRSF1-mediated splicing activity.


Subject(s)
Intellectual Disability , Neurodevelopmental Disorders , Child , Female , Male , Developmental Disabilities/genetics , Developmental Disabilities/complications , Haploinsufficiency/genetics , Intellectual Disability/pathology , Mutation, Missense/genetics , Neurodevelopmental Disorders/genetics , Phenotype , Humans
2.
Nature ; 586(7831): 757-762, 2020 10.
Article in English | MEDLINE | ID: mdl-33057194

ABSTRACT

De novo mutations in protein-coding genes are a well-established cause of developmental disorders1. However, genes known to be associated with developmental disorders account for only a minority of the observed excess of such de novo mutations1,2. Here, to identify previously undescribed genes associated with developmental disorders, we integrate healthcare and research exome-sequence data from 31,058 parent-offspring trios of individuals with developmental disorders, and develop a simulation-based statistical test to identify gene-specific enrichment of de novo mutations. We identified 285 genes that were significantly associated with developmental disorders, including 28 that had not previously been robustly associated with developmental disorders. Although we detected more genes associated with developmental disorders, much of the excess of de novo mutations in protein-coding genes remains unaccounted for. Modelling suggests that more than 1,000 genes associated with developmental disorders have not yet been described, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of genes associated with developmental disorders.


Subject(s)
DNA Mutational Analysis , Data Analysis , Databases, Genetic , Datasets as Topic , Delivery of Health Care/statistics & numerical data , Developmental Disabilities/genetics , Genetic Diseases, Inborn/genetics , Cohort Studies , DNA Copy Number Variations/genetics , Developmental Disabilities/diagnosis , Europe , Female , Genetic Diseases, Inborn/diagnosis , Germ-Line Mutation/genetics , Haploinsufficiency/genetics , Humans , Male , Mutation, Missense/genetics , Penetrance , Perinatal Death , Sample Size
3.
Am J Hum Genet ; 108(9): 1551-1557, 2021 09 02.
Article in English | MEDLINE | ID: mdl-34329581

ABSTRACT

Clinical validity assessments of gene-disease associations underpin analysis and reporting in diagnostic genomics, and yet wide variability exists in practice, particularly in use of these assessments for virtual gene panel design and maintenance. Harmonization efforts are hampered by the lack of agreed terminology, agreed gene curation standards, and platforms that can be used to identify and resolve discrepancies at scale. We undertook a systematic comparison of the content of 80 virtual gene panels used in two healthcare systems by multiple diagnostic providers in the United Kingdom and Australia. The process was enabled by a shared curation platform, PanelApp, and resulted in the identification and review of 2,144 discordant gene ratings, demonstrating the utility of sharing structured gene-disease validity assessments and collaborative discordance resolution in establishing national and international consensus.


Subject(s)
Consensus , Data Curation/standards , Genetic Diseases, Inborn/genetics , Genomics/standards , Molecular Sequence Annotation/standards , Australia , Biomarkers/metabolism , Data Curation/methods , Delivery of Health Care , Gene Expression , Gene Ontology , Genetic Diseases, Inborn/diagnosis , Genetic Diseases, Inborn/pathology , Genomics/methods , Humans , Mobile Applications/supply & distribution , Terminology as Topic , United Kingdom
4.
Genet Med ; 26(5): 101077, 2024 05.
Article in English | MEDLINE | ID: mdl-38275146

ABSTRACT

PURPOSE: Gene selection for genomic newborn screening (gNBS) underpins the validity, acceptability, and ethical application of this technology. Existing gNBS gene lists are highly variable despite being based on shared principles of gene-disease validity, treatability, and age of onset. This study aimed to curate a gNBS gene list that builds upon existing efforts and provide a core consensus list of gene-disease pairs assessed by multiple expert groups worldwide. METHODS: Our multidisciplinary expert team curated a gene list using an open platform and multiple existing curated resources. We included severe treatable disorders with age of disease onset <5 years with established gene-disease associations and reliable variant detection. We compared the final list with published lists from 5 other gNBS projects to determine consensus genes and to identify areas of discrepancy. RESULTS: We reviewed 1279 genes and 604 met our inclusion criteria. Metabolic conditions comprised the largest group (25%), followed by immunodeficiencies (21%) and endocrine disorders (15%). We identified 55 consensus genes included by all 6 gNBS research projects. Common reasons for discrepancy included variable definitions of treatability and strength of gene-disease association. CONCLUSION: We have identified a consensus gene list for gNBS that can be used as a basis for systematic harmonization efforts internationally.


Subject(s)
Genetic Testing , Genomics , Neonatal Screening , Humans , Neonatal Screening/methods , Infant, Newborn , Genetic Testing/methods , Genetic Testing/standards , Genomics/methods , Consensus
5.
Genet Med ; 26(5): 101076, 2024 05.
Article in English | MEDLINE | ID: mdl-38258669

ABSTRACT

PURPOSE: Genome sequencing (GS)-specific diagnostic rates in prospective tightly ascertained exome sequencing (ES)-negative intellectual disability (ID) cohorts have not been reported extensively. METHODS: ES, GS, epigenetic signatures, and long-read sequencing diagnoses were assessed in 74 trios with at least moderate ID. RESULTS: The ES diagnostic yield was 42 of 74 (57%). GS diagnoses were made in 9 of 32 (28%) ES-unresolved families. Repeated ES with a contemporary pipeline on the GS-diagnosed families identified 8 of 9 single-nucleotide variations/copy-number variations undetected in older ES, confirming a GS-unique diagnostic rate of 1 in 32 (3%). Episignatures contributed diagnostic information in 9% with GS corroboration in 1 of 32 (3%) and diagnostic clues in 2 of 32 (6%). A genetic etiology for ID was detected in 51 of 74 (69%) families. Twelve candidate disease genes were identified. Contemporary ES followed by GS cost US$4976 (95% CI: $3704; $6969) per diagnosis and first-line GS at a cost of $7062 (95% CI: $6210; $8475) per diagnosis. CONCLUSION: Performing GS only in ID trios would be cost equivalent to ES if GS were available at $2435, about a 60% reduction from current prices. This study demonstrates that first-line GS achieves higher diagnostic rate than contemporary ES but at a higher cost.


Subject(s)
Exome Sequencing , Exome , Intellectual Disability , Humans , Intellectual Disability/genetics , Intellectual Disability/diagnosis , Male , Female , Exome/genetics , Exome Sequencing/economics , Cohort Studies , Genetic Testing/economics , Genetic Testing/methods , Whole Genome Sequencing/economics , Child , Genome, Human/genetics , DNA Copy Number Variations/genetics , Polymorphism, Single Nucleotide/genetics , Child, Preschool
6.
J Med Genet ; 59(8): 748-758, 2022 08.
Article in English | MEDLINE | ID: mdl-34740920

ABSTRACT

BACKGROUND: Clinical exome sequencing typically achieves diagnostic yields of 30%-57.5% in individuals with monogenic rare diseases. Undiagnosed diseases programmes implement strategies to improve diagnostic outcomes for these individuals. AIM: We share the lessons learnt from the first 3 years of the Undiagnosed Diseases Program-Victoria, an Australian programme embedded within a clinical genetics service in the state of Victoria with a focus on paediatric rare diseases. METHODS: We enrolled families who remained without a diagnosis after clinical genomic (panel, exome or genome) sequencing between 2016 and 2018. We used family-based exome sequencing (family ES), family-based genome sequencing (family GS), RNA sequencing (RNA-seq) and high-resolution chromosomal microarray (CMA) with research-based analysis. RESULTS: In 150 families, we achieved a diagnosis or strong candidate in 64 (42.7%) (37 in known genes with a consistent phenotype, 3 in known genes with a novel phenotype and 24 in novel disease genes). Fifty-four diagnoses or strong candidates were made by family ES, six by family GS with RNA-seq, two by high-resolution CMA and two by data reanalysis. CONCLUSION: We share our lessons learnt from the programme. Flexible implementation of multiple strategies allowed for scalability and response to the availability of new technologies. Broad implementation of family ES with research-based analysis showed promising yields post a negative clinical singleton ES. RNA-seq offered multiple benefits in family ES-negative populations. International data sharing strategies were critical in facilitating collaborations to establish novel disease-gene associations. Finally, the integrated approach of a multiskilled, multidisciplinary team was fundamental to having diverse perspectives and strategic decision-making.


Subject(s)
Undiagnosed Diseases , Australia , Exome , Humans , Rare Diseases/diagnosis , Rare Diseases/epidemiology , Rare Diseases/genetics , Exome Sequencing
7.
J Med Genet ; 59(5): 511-516, 2022 05.
Article in English | MEDLINE | ID: mdl-34183358

ABSTRACT

PURPOSE: Binding proteins (G-proteins) mediate signalling pathways involved in diverse cellular functions and comprise Gα and Gßγ units. Human diseases have been reported for all five Gß proteins. A de novo missense variant in GNB2 was recently reported in one individual with developmental delay/intellectual disability (DD/ID) and dysmorphism. We aim to confirm GNB2 as a neurodevelopmental disease gene, and elucidate the GNB2-associated neurodevelopmental phenotype in a patient cohort. METHODS: We discovered a GNB2 variant in the index case via exome sequencing and sought individuals with GNB2 variants via international data-sharing initiatives. In silico modelling of the variants was assessed, along with multiple lines of evidence in keeping with American College of Medical Genetics and Genomics guidelines for interpretation of sequence variants. RESULTS: We identified 12 unrelated individuals with five de novo missense variants in GNB2, four of which are recurrent: p.(Ala73Thr), p.(Gly77Arg), p.(Lys89Glu) and p.(Lys89Thr). All individuals have DD/ID with variable dysmorphism and extraneurologic features. The variants are located at the universally conserved shared interface with the Gα subunit, which modelling suggests weaken this interaction. CONCLUSION: Missense variants in GNB2 cause a congenital neurodevelopmental disorder with variable syndromic features, broadening the spectrum of multisystem phenotypes associated with variants in genes encoding G-proteins.


Subject(s)
Intellectual Disability , Neurodevelopmental Disorders , GTP-Binding Proteins/genetics , Humans , Intellectual Disability/genetics , Mutation, Missense/genetics , Neurodevelopmental Disorders/genetics , Phenotype , Exome Sequencing
8.
Hum Mutat ; 43(4): 487-498, 2022 04.
Article in English | MEDLINE | ID: mdl-35077597

ABSTRACT

A proper interaction between muscle-derived collagen XXV and its motor neuron-derived receptors protein tyrosine phosphatases σ and δ (PTP σ/δ) is indispensable for intramuscular motor innervation. Despite this, thus far, pathogenic recessive variants in the COL25A1 gene had only been detected in a few patients with isolated ocular congenital cranial dysinnervation disorders. Here we describe five patients from three unrelated families with recessive missense and splice site COL25A1 variants presenting with a recognizable phenotype characterized by arthrogryposis multiplex congenita with or without an ocular congenital cranial dysinnervation disorder phenotype. The clinical features of the older patients remained stable over time, without central nervous system involvement. This study extends the phenotypic and genotypic spectrum of COL25A1 related conditions, and further adds to our knowledge of the complex process of intramuscular motor innervation. Our observations indicate a role for collagen XXV in regulating the appropriate innervation not only of extraocular muscles, but also of bulbar, axial, and limb muscles in the human.


Subject(s)
Arthrogryposis , Arthrogryposis/diagnosis , Arthrogryposis/genetics , Face , Humans , Muscle, Skeletal , Mutation , Phenotype
9.
Genet Med ; 24(5): 1037-1044, 2022 05.
Article in English | MEDLINE | ID: mdl-35181209

ABSTRACT

PURPOSE: To evaluate whether the additional cost of providing increasingly faster genomic results in pediatric critical care is outweighed by reductions in health care costs and increases in personal utility. METHODS: Hospital costs and medical files from a cohort of 40 children were analyzed. The health economic impact of rapid and ultra-rapid genomic testing, with and without early initiation, relative to standard genomic testing was evaluated. RESULTS: Shortening the time to results led to substantial economic and personal benefits. Early initiation of ultra-rapid genomic testing was the most cost-beneficial strategy, leading to a cost saving of AU$26,600 per child tested relative to standard genomic testing and a welfare gain of AU$12,000 per child tested. Implementation of early ultra-rapid testing of critically ill children is expected to lead to an annual cost saving of AU$7.3 million for the Australian health system and an aggregate welfare gain of AU$3.3 million, corresponding to a total net benefit of AU$10.6 million. CONCLUSION: Early initiation of ultra-rapid genomic testing can offer substantial economic and personal benefits. Future implementation of rapid genomic testing programs should focus not only on optimizing the laboratory workflow to achieve a fast turnaround time but also on changing clinical practice to expedite test initiation.


Subject(s)
Critical Care , Critical Illness , Australia , Child , Cost-Benefit Analysis , Genetic Testing/methods , Humans , Infant
10.
Am J Med Genet A ; 188(12): 3432-3447, 2022 12.
Article in English | MEDLINE | ID: mdl-36367278

ABSTRACT

Verheij syndrome (VRJS) is a rare craniofacial spliceosomopathy presenting with craniofacial dysmorphism, multiple congenital anomalies and variable neurodevelopmental delay. It is caused by single nucleotide variants (SNVs) in PUF60 or interstitial deletions of the 8q24.3 region. PUF60 encodes a splicing factor which forms part of the spliceosome. To date, 36 patients with a sole diagnosis of VRJS due to disease-causing PUF60 SNVs have been reported in peer-reviewed publications. Although the depth of their phenotyping has varied greatly, they exhibit marked phenotypic heterogeneity. We report 10 additional unrelated patients, including the first described patients of Khmer, Indian, and Vietnamese ethnicities, and the eldest patient to date, with 10 heterozygous PUF60 variants identified through exome sequencing, 8 previously unreported. All patients underwent deep phenotyping identifying variable dysmorphism, growth delay, neurodevelopmental delay, and multiple congenital anomalies, including several unique features. The eldest patient is the only reported individual with a germline variant and neither neurodevelopmental delay nor intellectual disability. In combining these detailed phenotypic data with that of previously reported patients (n = 46), we further refine the known frequencies of features associated with VRJS. These include neurodevelopmental delay/intellectual disability (98%), axial skeletal anomalies (74%), appendicular skeletal anomalies (73%), oral anomalies (68%), short stature (66%), cardiac anomalies (63%), brain malformations (48%), hearing loss (46%), microcephaly (41%), colobomata (38%), and other ocular anomalies (65%). This case series, incorporating three patients from previously unreported ethnic backgrounds, further delineates the broad pleiotropy and mutational spectrum of PUF60 pathogenic variants.


Subject(s)
Abnormalities, Multiple , Intellectual Disability , Microcephaly , RNA Splicing Factors , Repressor Proteins , Humans , Abnormalities, Multiple/diagnosis , Abnormalities, Multiple/genetics , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Microcephaly/diagnosis , Microcephaly/genetics , Phenotype , Repressor Proteins/genetics , RNA Splicing Factors/genetics , Spliceosomes/genetics , Spliceosomes/pathology
11.
Genet Med ; 22(12): 1986-1993, 2020 12.
Article in English | MEDLINE | ID: mdl-32773771

ABSTRACT

PURPOSE: Cost-effectiveness evaluations of first-line genomic sequencing (GS) in the diagnosis of children with genetic conditions are limited by the lack of well-defined comparative cohorts. We sought to evaluate the cost-effectiveness of early GS in pediatric patients with complex monogenic conditions compared with a matched historical cohort. METHODS: Data, including investigation costs, were collected in a prospective cohort of 92 pediatric patients undergoing singleton GS over an 18-month period (2016-2017) with two of the following: a condition with high mortality, multisystem disease involving three or more organs, or severe limitation of daily function. Comparative data were collected in a matched historical cohort who underwent traditional investigations in the years 2012-2013. RESULTS: GS yielded a diagnosis in 42% while traditional investigations yielded a diagnosis in 23% (p = 0.003). A change in management was experienced by 74% of patients diagnosed following GS, compared with 32% diagnosed following traditional investigations. Singleton GS at a cost of AU$3100 resulted in a mean saving per person of AU$3602 (95% confidence interval [CI] AU$2520-4685). Cost savings occurred across all investigation subtypes and were only minimally offset by clinical management costs. CONCLUSION: GS in complex pediatric patients saves significant costs and doubles the diagnostic yield of traditional approaches.


Subject(s)
Exome , Genomics , Child , Chromosome Mapping , Cost-Benefit Analysis , Humans , Prospective Studies
12.
Genet Med ; 20(12): 1554-1563, 2018 12.
Article in English | MEDLINE | ID: mdl-29543227

ABSTRACT

PURPOSE: The purpose of the study was to implement and prospectively evaluate the outcomes of a rapid genomic diagnosis program at two pediatric tertiary centers. METHODS: Rapid singleton whole-exome sequencing (rWES) was performed in acutely unwell pediatric patients with suspected monogenic disorders. Laboratory and clinical barriers to implementation were addressed through continuous multidisciplinary review of process parameters. Diagnostic and clinical utility and cost-effectiveness of rWES were assessed. RESULTS: Of 40 enrolled patients, 21 (52.5%) received a diagnosis, with median time to report of 16 days (range 9-109 days). A result was provided during the first hospital admission in 28 of 36 inpatients (78%). Clinical management changed in 12 of the 21 diagnosed patients (57%), including the provision of lifesaving treatment, avoidance of invasive biopsies, and palliative care guidance. The cost per diagnosis was AU$13,388 (US$10,453). Additional cost savings from avoidance of planned tests and procedures and reduced length of stay are estimated to be around AU$543,178 (US$424,101). The clear relative advantage of rWES, joint clinical and laboratory leadership, and the creation of a multidisciplinary "rapid team" were key to successful implementation. CONCLUSION: Rapid genomic testing in acute pediatrics is not only feasible but also cost-effective, and has high diagnostic and clinical utility. It requires a whole-of-system approach for successful implementation.


Subject(s)
Exome Sequencing/trends , Genetic Testing/trends , Pathology, Molecular/trends , Pediatrics/trends , Cost-Benefit Analysis , Exome/genetics , Female , Genetic Testing/economics , Genome, Human/genetics , Genomics , Humans , Male , Pathology, Molecular/economics , Pediatrics/economics , Exome Sequencing/economics
13.
Genet Med ; 20(9): 1061-1068, 2018 09.
Article in English | MEDLINE | ID: mdl-29215649

ABSTRACT

PURPOSE: The craniosynostoses are characterized by premature fusion of one or more cranial sutures. The relative contribution of previously reported genes to craniosynostosis in large cohorts is unclear. Here we report on the use of a massively parallel sequencing panel in individuals with craniosynostosis without a prior molecular diagnosis. METHODS: A 20-gene panel was designed based on the genes' association with craniosynostosis, and clinically validated through retrospective testing of an Australian and New Zealand cohort of 233 individuals with craniosynostosis in whom previous testing had not identified a causative variant within FGFR1-3 hot-spot regions or the TWIST1 gene. An additional 76 individuals were tested prospectively. RESULTS: Pathogenic or likely pathogenic variants in non-FGFR genes were identified in 43 individuals, with diagnostic yields of 14% and 15% in retrospective and prospective cohorts, respectively. Variants were identified most frequently in TCF12 (N = 22) and EFNB1 (N = 8), typically in individuals with nonsyndromic coronal craniosynostosis or TWIST1-negative clinically suspected Saethre-Chotzen syndrome. Clinically significant variants were also identified in ALX4, EFNA4, ERF, and FGF10. CONCLUSION: These findings support the clinical utility of a massively parallel sequencing panel for craniosynostosis. TCF12 and EFNB1 should be included in genetic testing for nonsyndromic coronal craniosynostosis or clinically suspected Saethre-Chotzen syndrome.


Subject(s)
Basic Helix-Loop-Helix Transcription Factors/genetics , Craniosynostoses/genetics , Ephrin-B1/genetics , Australia , Cohort Studies , Cranial Sutures/pathology , DNA-Binding Proteins/genetics , Female , Fibroblast Growth Factor 10/genetics , Genetic Testing , High-Throughput Nucleotide Sequencing/methods , Humans , Male , New Zealand , Nuclear Proteins/genetics , Prospective Studies , Receptor, Fibroblast Growth Factor, Type 1/genetics , Repressor Proteins/genetics , Retrospective Studies , Transcription Factors/genetics , Twist-Related Protein 1/genetics
14.
Hum Genet ; 135(5): 569-586, 2016 May.
Article in English | MEDLINE | ID: mdl-27071622

ABSTRACT

Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal lung developmental disorder caused by heterozygous point mutations or genomic deletion copy-number variants (CNVs) of FOXF1 or its upstream enhancer involving fetal lung-expressed long noncoding RNA genes LINC01081 and LINC01082. Using custom-designed array comparative genomic hybridization, Sanger sequencing, whole exome sequencing (WES), and bioinformatic analyses, we studied 22 new unrelated families (20 postnatal and two prenatal) with clinically diagnosed ACDMPV. We describe novel deletion CNVs at the FOXF1 locus in 13 unrelated ACDMPV patients. Together with the previously reported cases, all 31 genomic deletions in 16q24.1, pathogenic for ACDMPV, for which parental origin was determined, arose de novo with 30 of them occurring on the maternally inherited chromosome 16, strongly implicating genomic imprinting of the FOXF1 locus in human lungs. Surprisingly, we have also identified four ACDMPV families with the pathogenic variants in the FOXF1 locus that arose on paternal chromosome 16. Interestingly, a combination of the severe cardiac defects, including hypoplastic left heart, and single umbilical artery were observed only in children with deletion CNVs involving FOXF1 and its upstream enhancer. Our data demonstrate that genomic imprinting at 16q24.1 plays an important role in variable ACDMPV manifestation likely through long-range regulation of FOXF1 expression, and may be also responsible for key phenotypic features of maternal uniparental disomy 16. Moreover, in one family, WES revealed a de novo missense variant in ESRP1, potentially implicating FGF signaling in the etiology of ACDMPV.


Subject(s)
Genome, Human , Genomic Imprinting , Persistent Fetal Circulation Syndrome/pathology , Pulmonary Alveoli/abnormalities , Pulmonary Veins/pathology , Chromosomes, Human, Pair 16/genetics , Comparative Genomic Hybridization , Female , Forkhead Transcription Factors/genetics , Genes, Lethal , High-Throughput Nucleotide Sequencing , Humans , Infant, Newborn , Male , Pedigree , Persistent Fetal Circulation Syndrome/genetics , Pulmonary Alveoli/pathology , Sequence Deletion
15.
Genet Med ; 18(11): 1090-1096, 2016 11.
Article in English | MEDLINE | ID: mdl-26938784

ABSTRACT

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.


Subject(s)
Genetic Diseases, Inborn/diagnosis , High-Throughput Nucleotide Sequencing/methods , Pathology, Molecular , Exome/genetics , Genetic Diseases, Inborn/genetics , Humans , Infant, Newborn
16.
Gen Dent ; 64(3): 68-71, 2016.
Article in English | MEDLINE | ID: mdl-27148661

ABSTRACT

Cervicofacial subcutaneous emphysema is a known, rare complication of both dental and surgical procedures. Cervicofacial subcutaneous emphysema arises when air is forced beneath the tissues, leading to swelling, crepitus on palpation, and the potential of the air to spread along the fascial planes. This report presents a case of cervicofacial subcutaneous emphysema in a patient who had undergone surgical extraction of the mandibular right first molar. The dentist in this case used a compressed air-driven handpiece to section the tooth. This forced air, under high pressure, into the subcutaneous tissue spaces. The patient presented with severe hemifacial swelling and crepitus on palpation. Computed tomographic examination revealed air subcutaneously, and a diagnosis of cervicofacial subcutaneous emphysema was made.


Subject(s)
Subcutaneous Emphysema/etiology , Adult , Diagnosis, Differential , Face/diagnostic imaging , Face/pathology , Female , Humans , Molar/surgery , Subcutaneous Emphysema/diagnosis , Subcutaneous Emphysema/diagnostic imaging , Subcutaneous Emphysema/pathology , Tomography, X-Ray Computed , Tooth Extraction/adverse effects
17.
Am J Med Genet A ; 167A(10): 2319-26, 2015 Oct.
Article in English | MEDLINE | ID: mdl-26059276

ABSTRACT

Chromosomal abnormalities are an important factor in the pathogenesis of congenital diaphragmatic hernia (CDH), a relatively common congenital defect associated with high morbidity and mortality. The adoption of array-based platforms for chromosome analysis has resulted in the identification of numerous copy number variants (CNVs) in infants with CDH, highlighting the potential pathogenic role of many novel genes. We identified a retrospective cohort of 28 infants treated for CDH at a single institution who had microarray testing to determine the proportion of microarray abnormalities and whether these were contributory to CDH pathogenesis. Eight patients (29%) had microarray abnormality. Seven (25%) were considered likely contributory to CDH pathogenesis, including two mosaic trisomy 9s, a 9q22.31q22.32 microduplication, two atypical 22q11.21 microdeletions, a 2q35q36.1 microdeletion, and a 15q11.2 microdeletion, offering insights into the genetic mechanisms underlying CDH development.


Subject(s)
Chromosome Deletion , Chromosome Duplication , Chromosomes, Human, Pair 15 , Chromosomes, Human, Pair 22 , Chromosomes, Human, Pair 2 , Hernias, Diaphragmatic, Congenital/genetics , Trisomy/genetics , Chromosomes, Human, Pair 9/genetics , Female , Hernias, Diaphragmatic, Congenital/mortality , Hernias, Diaphragmatic, Congenital/pathology , Hernias, Diaphragmatic, Congenital/surgery , Humans , Infant , Inheritance Patterns , Karyotype , Male , Microarray Analysis , Retrospective Studies , Survival Analysis , Trisomy/pathology
18.
BMJ Open ; 14(4): e081426, 2024 Apr 03.
Article in English | MEDLINE | ID: mdl-38569677

ABSTRACT

INTRODUCTION: Newborn bloodspot screening (NBS) is a highly successful public health programme that uses biochemical and other assays to screen for severe but treatable childhood-onset conditions. Introducing genomic sequencing into NBS programmes increases the range of detectable conditions but raises practical and ethical issues. Evidence from prospectively ascertained cohorts is required to guide policy and future implementation. This study aims to develop, implement and evaluate a genomic NBS (gNBS) pilot programme. METHODS AND ANALYSIS: The BabyScreen+ study will pilot gNBS in three phases. In the preimplementation phase, study materials, including education resources, decision support and data collection tools, will be designed. Focus groups and key informant interviews will also be undertaken to inform delivery of the study and future gNBS programmes. During the implementation phase, we will prospectively recruit birth parents in Victoria, Australia, to screen 1000 newborns for over 600 severe, treatable, childhood-onset conditions. Clinically accredited whole genome sequencing will be performed following standard NBS using the same sample. High chance results will be returned by genetic healthcare professionals, with follow-on genetic and other confirmatory testing and referral to specialist services as required. The postimplementation phase will evaluate the feasibility of gNBS as the primary aim, and assess ethical, implementation, psychosocial and health economic factors to inform future service delivery. ETHICS AND DISSEMINATION: This project received ethics approval from the Royal Children's Hospital Melbourne Research Ethics Committee: HREC/91500/RCHM-2023, HREC/90929/RCHM-2022 and HREC/91392/RCHM-2022. Findings will be disseminated to policy-makers, and through peer-reviewed journals and conferences.


Subject(s)
Genomics , Neonatal Screening , Child , Humans , Infant, Newborn , Pilot Projects , Prospective Studies , Victoria
19.
J Med Genet ; 47(5): 299-311, 2010 May.
Article in English | MEDLINE | ID: mdl-20452996

ABSTRACT

BACKGROUND: Chromosome 17p13.3 contains extensive repetitive sequences and is a recognised region of genomic instability. Haploinsufficiency of PAFAH1B1 (encoding LIS1) causes either isolated lissencephaly sequence or Miller-Dieker syndrome, depending on the size of the deletion. More recently, both microdeletions and microduplications mapping to the Miller-Dieker syndrome telomeric critical region have been identified and associated with distinct but overlapping phenotypes. METHODS: Genome-wide microarray screening was performed on 7678 patients referred with unexplained learning difficulties and/or autism, with or without other congenital abnormalities. Eight and five unrelated individuals, respectively, were identified with microdeletions and microduplications in 17p13.3. RESULTS: Comparisons with six previously reported microdeletion cases identified a 258 kb critical region, encompassing six genes including CRK (encoding Crk) and YWHAE (encoding 14-3-3epsilon). Clinical features included growth retardation, facial dysmorphism and developmental delay. Notably, one individual with only subtle facial features and an interstitial deletion involving CRK but not YWHAE suggested that a genomic region spanning 109 kb, encompassing two genes (TUSC5 and YWHAE), is responsible for the main facial dysmorphism phenotype. Only the microduplication phenotype included autism. The microduplication minimal region of overlap for the new and previously reported cases spans 72 kb encompassing a single gene, YWHAE. These genomic rearrangements were not associated with low-copy repeats and are probably due to diverse molecular mechanisms. CONCLUSIONS: The authors further characterise the 17p13.3 microdeletion and microduplication phenotypic spectrum and describe a smaller critical genomic region allowing identification of candidate genes for the distinctive facial dysmorphism (microdeletions) and autism (microduplications) manifestations.


Subject(s)
Chromosome Aberrations , Chromosomes, Human, Pair 17/genetics , Classical Lissencephalies and Subcortical Band Heterotopias/genetics , Lissencephaly/genetics , Adolescent , Brain/abnormalities , Child , Child, Preschool , Chromosome Deletion , Classical Lissencephalies and Subcortical Band Heterotopias/pathology , Craniofacial Abnormalities/genetics , Female , Humans , Infant , Intellectual Disability/genetics , Lissencephaly/pathology , Male , Oligonucleotide Array Sequence Analysis , Pedigree , Phenotype , Segmental Duplications, Genomic
SELECTION OF CITATIONS
SEARCH DETAIL