Loss of Function of the Cytoplasmic Fe-S Assembly Protein CIAO1 Causes a Neuromuscular Disorder with Compromise of Nucleocytoplasmic Fe-S Enzymes

Cytoplasmic and nuclear iron-sulfur enzymes that are essential for genome maintenance and replication depend on the cytoplasmic iron-sulfur assembly (CIA) machinery for cluster acquisition. Here we report that patients with biallelic loss of function in CIAO1 , a key CIA component, develop proximal and axial muscle weakness, fluctuating creatine kinase elevation and respiratory insufficiency. In addition, they present with CNS symptoms including learning difficulties and neurobehavioral comorbidities, along with iron deposition in deep brain nuclei, macrocytic anemia and gastrointestinal symptoms. Mutational analysis and functional assays revealed reduced stability of the variants compared to wild-type CIAO1. Loss of CIAO1 impaired DNA helicases, polymerases and repair enzymes which rely on the CIA complex to acquire their Fe-S cofactors, with lentiviral restoration reversing all patient-derived cellular abnormalities. Our study identifies CIAO1 as a novel human disease gene and provides insights into the broader implications of the iron-sulfur assembly pathway in human health and disease.

Crucial functions of alpha-actinin 2 in the embryonic heart

Funding Acknowledgements

Type of funding sources: Foundation. Main funding source(s): Wellcome Trust; British Heart Foundation

Background/Introduction

Alpha-actinin is an integral protein of the Z-discs in heart and skeletal muscle cells, with important structural and signalling functions.  Missense variants in alpha-actinin can cause inherited conditions, e.g. myopathies and cardiomyopathies. The underlying disease mechanisms are still unknown.

Purpose

In order to study the disease mechanisms of an alpha-actinin missense variant, which is known to cause Hypertrophic Cardiomyopathy in human patients, a mouse model was generated.

Methods

Mice carrying the alpha-actinin missense variant were generated by CRISPR-Cas9 genome editing. The heterozygous adult mice carrying the alpha-actinin variant were characterised by echocardiography and quantitative PCR. Hearts of homozygous embryos were analysed at E15.5 by high-resolution episcopic microscopy (HREM).

Results

Mice carrying a single copy of the missense variant were viable and had normal appearance. Adult heterozygous mice showed no signs of cardiomyopathy on echocardiography. However, mature male mice displayed molecular signs of cardiomyopathy, such as induction of the fetal gene programme at transcript level.

The attempt to generate adult mice homozygous for the variant failed: 9 breeding pairs produced 18 litters with 83 weaned pups, but no homozygous offspring. Embryonic lethality was confirmed and E15.5 was the latest stage homozygous pups were reliably found to be viable. At this timepoint, genotype distribution was within the expected Mendelian ratios.

HREM of the hearts at this stage revealed increased right ventricular chamber size and decreased left atrial size, when compared to wildtype littermates. Membranous ventricular septal defects were observed in 3 out of 8 homozygous hearts. Further these embryos displayed aortic stenosis and dysplasic leaflets of the pulmonary valve.

Conclusions

Heterozygous adult mice only displayed sub-clinical signs of disease. In contrast, the missense variant is embryonic lethal in the homozygous setting and leads to a range of morphological abnormalities in E15.5 hearts. Future work will identify how altered functions of alpha-actinin cause these changes.

Biallelic variants in the RNA exosome gene EXOSC5 are associated with developmental delays, short stature, cerebellar hypoplasia and motor weakness

The RNA exosome is an essential ribonuclease complex required for processing and/or degradation of both coding and non-coding RNAs. We identified five patients with biallelic variants in EXOSC5, which encodes a structural subunit of the RNA exosome. The clinical features of these patients include failure to thrive, short stature, feeding difficulties, developmental delays that affect motor skills, hypotonia and esotropia. Brain MRI revealed cerebellar hypoplasia and ventriculomegaly. While we ascertained five patients, three patients with distinct variants of EXOSC5 were studied in detail. The first patient had a deletion involving exons 5-6 of EXOSC5 and a missense variant, p.Thr114Ile, that were inherited in trans, the second patient was homozygous for p.Leu206His and the third patient had paternal isodisomy for chromosome 19 and was homozygous for p.Met148Thr. The additional two patients ascertained are siblings who had an early frameshift mutation in EXOSC5 and the p.Thr114Ile missense variant that were inherited in trans. We employed three complementary approaches to explore the requirement for EXOSC5 in brain development and assess consequences of pathogenic EXOSC5 variants. Loss of function for exosc5 in zebrafish results in shortened and curved tails/bodies, reduced eye/head size and edema. We modeled pathogenic EXOSC5 variants in both budding yeast and mammalian cells. Some of these variants cause defects in RNA exosome function as well as altered interactions with other RNA exosome subunits. These findings expand the number of genes encoding RNA exosome subunits linked to human disease while also suggesting that disease mechanism varies depending on the specific pathogenic variant.

Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy

The ALF transcription factor paralogs, AFF1, AFF2, AFF3, and AFF4, are components of the transcriptional super elongation complex that regulates expression of genes involved in neurogenesis and development. We describe an autosomal dominant disorder associated with de novo missense variants in the degron of AFF3, a nine amino acid sequence important for its binding to ubiquitin ligase, or with de novo deletions of this region. The sixteen affected individuals we identified, along with two previously reported individuals, present with a recognizable pattern of anomalies, which we named KINSSHIP syndrome (KI for horseshoe kidney, NS for Nievergelt/Savarirayan type of mesomelic dysplasia, S for seizures, H for hypertrichosis, I for intellectual disability, and P for pulmonary involvement), partially overlapping the AFF4-associated CHOPS syndrome. Whereas homozygous Aff3 knockout mice display skeletal anomalies, kidney defects, brain malformations, and neurological anomalies, knockin animals modeling one of the microdeletions and the most common of the missense variants identified in affected individuals presented with lower mesomelic limb deformities like KINSSHIP-affected individuals and early lethality, respectively. Overexpression of AFF3 in zebrafish resulted in body axis anomalies, providing some support for the pathological effect of increased amount of AFF3. The only partial phenotypic overlap of AFF3- and AFF4-associated syndromes and the previously published transcriptome analyses of ALF transcription factors suggest that these factors are not redundant and each contributes uniquely to proper development.

Uniparental disomy in a population of 32,067 clinical exome trios

Purpose

Data on the clinical prevalence and spectrum of uniparental disomy (UPD) remain limited. Trio exome sequencing (ES) presents a comprehensive method for detection of UPD alongside sequence and copy-number variant analysis.

Methods

We analyzed 32,067 ES trios referred for diagnostic testing to create a profile of UPD events and their disease associations. ES single-nucleotide polymorphism (SNP) and copy-number data were used to identify both whole-chromosome and segmental UPD and to categorize whole-chromosome results as isodisomy, heterodisomy, or mixed.

Results

Ninety-nine whole-chromosome and 13 segmental UPD events were identified. Of these, 29 were associated with an imprinting disorder, and 16 were associated with a positive test result through homozygous sequence variants. Isodisomy was more commonly observed in large chromosomes along with a higher rate of homozygous pathogenic variants, while heterodisomy was more frequent in chromosomes associated with imprinting or trisomy mosaicism (14, 15, 16, 20, 22).

Conclusion

Whole-chromosome UPD was observed in 0.31% of cases, resulting in a diagnostic finding in 0.14%. Only three UPD-positive cases had a diagnostic finding unrelated to the UPD. Thirteen UPD events were identified in cases with prior normal SNP chromosomal microarray results, demonstrating the additional diagnostic value of UPD detection by trio ES.

Author Correction: NEMF mutations that impair ribosome-associated quality control are associated with neuromuscular disease

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

NEMF mutations that impair ribosome-associated quality control are associated with neuromuscular disease

A hallmark of neurodegeneration is defective protein quality control. The E3 ligase Listerin (LTN1/Ltn1) acts in a specialized protein quality control pathway—Ribosome-associated Quality Control (RQC)—by mediating proteolytic targeting of incomplete polypeptides produced by ribosome stalling, and Ltn1 mutation leads to neurodegeneration in mice. Whether neurodegeneration results from defective RQC and whether defective RQC contributes to human disease have remained unknown. Here we show that three independently-generated mouse models with mutations in a different component of the RQC complex, NEMF/Rqc2, develop progressive motor neuron degeneration. Equivalent mutations in yeast Rqc2 selectively interfere with its ability to modify aberrant translation products with C-terminal tails which assist with RQC-mediated protein degradation, suggesting a pathomechanism. Finally, we identify NEMF mutations expected to interfere with function in patients from seven families presenting juvenile neuromuscular disease. These uncover NEMF’s role in translational homeostasis in the nervous system and implicate RQC dysfunction in causing neurodegeneration.

Defective protein quality control is a key feature of neurodegeneration. Here, the authors show that mutations in Nemf/NEMF, a component of the Ribosome-associated Quality Control complex, have a neurodegenerative effect in mice and may underlie neuromuscular disease in seven unrelated families.

Biallelic variants in PPP1R13L cause paediatric dilated cardiomyopathy

Childhood dilated cardiomyopathy (DCM) is a leading cause of heart failure requiring cardiac transplantation and approximately 5% of cases result in sudden death. Knowledge of the underlying genetic cause can aid prognostication and clinical management and enables accurate recurrence risk counselling for the family. Here we used genomic sequencing to identify the causative genetic variant(s) in families with children affected by severe DCM. In an international collaborative effort facilitated by GeneMatcher, biallelic variants in PPP1R13L were identified in seven children with severe DCM from five unrelated families following exome or genome sequencing and inheritance-based variant filtering. PPP1R13L encodes inhibitor of apoptosis-stimulating protein of p53 protein (iASPP). In addition to roles in apoptosis, iASPP acts as a regulator of desmosomes and has been implicated in inflammatory pathways. DCM presented early (mean: 2 years 10 months; range: 3 months-9 years) and was progressive, resulting in death (n = 3) or transplant (n = 3), with one child currently awaiting transplant. Genomic sequencing technologies are valuable for the identification of novel and emerging candidate genes. Biallelic variants in PPP1R13L were previously reported in a single consanguineous family with paediatric DCM. The identification here of a further five families now provides sufficient evidence to support a robust gene-disease association between PPP1R13L and severe paediatric DCM. The PPP1R13L gene should be included in panel-based genetic testing for paediatric DCM.

De Novo Frameshift Variants in the Neuronal Splicing Factor NOVA2 Result in a Common C-Terminal Extension and Cause a Severe Form of Neurodevelopmental Disorder

The neuro-oncological ventral antigen 2 (NOVA2) protein is a major factor regulating neuron-specific alternative splicing (AS), previously associated with an acquired neurologic condition, the paraneoplastic opsoclonus-myoclonus ataxia (POMA). We report here six individuals with de novo frameshift variants in NOVA2 affected with a severe neurodevelopmental disorder characterized by intellectual disability (ID), motor and speech delay, autistic features, hypotonia, feeding difficulties, spasticity or ataxic gait, and abnormal brain MRI. The six variants lead to the same reading frame, adding a common proline rich C-terminal part instead of the last KH RNA binding domain. We detected 41 genes differentially spliced after NOVA2 downregulation in human neural cells. The NOVA2 variant protein shows decreased ability to bind target RNA sequences and to regulate target AS events. It also fails to complement the effect on neurite outgrowth induced by NOVA2 downregulation in vitro and to rescue alterations of retinotectal axonal pathfinding induced by loss of NOVA2 ortholog in zebrafish. Our results suggest a partial loss-of-function mechanism rather than a full heterozygous loss-of-function, although a specific contribution of the novel C-terminal extension cannot be excluded.

Missense variants in TAF1 and developmental phenotypes: challenges of determining pathogenicity

We recently described a new neurodevelopmental syndrome (TAF1/MRXS33 intellectual disability syndrome) (MIM# 300966) caused by pathogenic variants involving the X-linked gene TAF1, which participates in RNA polymerase II transcription. The initial study reported eleven families, and the syndrome was defined as presenting early in life with hypotonia, facial dysmorphia, and developmental delay that evolved into intellectual disability (ID) and/or autism spectrum disorder (ASD). We have now identified an additional 27 families through a genotype-first approach. Familial segregation analysis, clinical phenotyping, and bioinformatics were capitalized on to assess potential variant pathogenicity, and molecular modelling was performed for those variants falling within structurally characterized domains of TAF1. A novel phenotypic clustering approach was also applied, in which the phenotypes of affected individuals were classified using 51 standardized Human Phenotype Ontology (HPO) terms. Phenotypes associated with TAF1 variants show considerable pleiotropy and clinical variability, but prominent among previously unreported effects were brain morphological abnormalities, seizures, hearing loss, and heart malformations. Our allelic series broadens the phenotypic spectrum of TAF1/MRXS33 intellectual disability syndrome and the range of TAF1 molecular defects in humans. It also illustrates the challenges for determining the pathogenicity of inherited missense variants, particularly for genes mapping to chromosome X. This article is protected by copyright. All rights reserved.

Confirmation that variants in TTI2 are responsible for autosomal recessive intellectual disability

TTI2 (MIM 614126) has been described as responsible for autosomal recessive intellectual disability (ID; MRT39, MIM:615541) in only two inbred families. Here, we give an account of two individuals from two unrelated outbred families harbouring compound heterozygous TTI2 pathogenic variants. Together with severe ID, progressive microcephaly, scoliosis and sleeping disorder are the most striking features in the two individuals concerned. TTI2, together with TTI1 and TELO2, encode proteins that constitute the triple T heterotrimeric complex. This TTT complex interacts with the HSP90 and R2TP to form a super-complex that has a chaperone function stabilising and maturing a number of kinases, such as ataxia-telangiectasia mutated and mechanistic target of rapamycin, which are key regulators of cell proliferation and genome maintenance. Pathogenic variants in TTI2 logically result in a phenotype close to that caused by TELO2 variants.

SON haploinsufficiency causes impaired pre-mRNA splicing of CAKUT genes and heterogeneous renal phenotypes

Although genetic testing is increasingly used in clinical nephrology, a large number of patients with congenital abnormalities of the kidney and urinary tract (CAKUT) remain undiagnosed with current gene panels. Therefore, careful curation of novel genetic findings is key to improving diagnostic yields. We recently described a novel intellectual disability syndrome caused by de novo heterozygous loss-of-function mutations in the gene encoding the splicing factor SON. Here, we show that many of these patients, including two previously unreported, exhibit a wide array of kidney abnormalities. Detailed phenotyping of 14 patients with SON haploinsufficiency identified kidney anomalies in 8 patients, including horseshoe kidney, unilateral renal hypoplasia, and renal cysts. Recurrent urinary tract infections, electrolyte disturbances, and hypertension were also observed in some patients. SON knockdown in kidney cell lines leads to abnormal pre-mRNA splicing, resulting in decreased expression of several established CAKUT genes. Furthermore, these molecular events were observed in patient-derived cells with SON haploinsufficiency. Taken together, our data suggest that the wide spectrum of phenotypes in patients with a pathogenic SON mutation is a consequence of impaired pre-mRNA splicing of several CAKUT genes. We propose that genetic testing panels designed to diagnose children with a kidney phenotype should include the SON gene.

Lamin B receptor-related disorder is associated with a spectrum of skeletal dysplasia phenotypes

LBR (Lamin B Receptor) encodes a bifunctional protein important for cholesterol biosynthesis and heterochromatin organization on the inner nuclear membrane. Pathogenic variants in LBR are associated with marked phenotypic variability, ranging from the benign Pelger-Huët anomaly to lethal Greenberg Dysplasia. We performed trio exome sequencing (ES) on two patients with atypical variants of skeletal dysplasia and their unaffected parents. Patient 1 exhibited frontal bossing, mid-face hypoplasia, short stature with rhizomelic limb shortening, and relative macrocephaly at birth. Although remained short, Patient 1 later showed spontaneous improvement in her skeletal findings. Exome sequencing revealed two novel variants in LBR, c.1504C > G (p.Arg502Gly) in exon 12 and c.1748G > T (p.Arg583Leu) in exon 14, which were inherited from her unaffected father and mother, respectively. Sterol analysis revealed an increased level of cholesta‑8,14‑dien‑3β‑ol to 2.9% of total sterols, consistent with a functional deficiency of 3β‑hydroxysterol Δ14‑reductase. Patient 2 presented at birth with short stature and marked rhizomelic limb shortening but later exhibited decreasing severity of shortening of the long bones and improvement in the radiographic skeletal abnormalities although he continued to be significantly short at age 10 years. Exome sequencing revealed that Patient 2 is homozygous for a pathogenic variant c.1534C > T (p.Arg512Trp) in exon 12 of LBR, which was inherited from his unaffected consanguineous parents. This report provides further evidence for a phenotypic spectrum of LBR-associated disorders and expands the genotypic spectrum by describing 3 novel disease-causing variants that have not been previously associated with a disease. Moreover, our data on Patient 1 demonstrate that variants throughout the gene appear to influence both the sterol reductase and nuclear functions of LBR.

Variants in TCF20 in neurodevelopmental disability: description of 27 new patients and review of literature

Purpose:

To define the clinical characteristics of patients with variants in TCF20, we describe 27 patients, 26 of whom were identified via exome sequencing. We compare detailed clinical data with 17 previously reported patients.

Methods:

Patients were ascertained through molecular testing laboratories performing exome sequencing (and other testing) with orthogonal confirmation; collaborating referring clinicians provided detailed clinical information.

Results:

The cohort of 27 patients all had novel variants, and ranged in age from two to 68 years. All had developmental delay/intellectual disability. Autism spectrum disorders/autistic features were reported in 69%, attention disorders or hyperactivity in 67%, craniofacial features (no recognizable facial gestalt) in 67%, structural brain anomalies in 24%, and seizures in 12%. Additional features affecting various organ systems were described in 93%. In a majority of patients, we did not observe previously reported findings of postnatal overgrowth or craniosynostosis, in comparison to earlier reports.

Conclusion:

We provide valuable data regarding the prognosis and clinical manifestations of patients with variants in TCF20.

Variable cardiovascular phenotypes associated with SMAD2 pathogenic variants

SMAD2 is a downstream effector in the TGF-β signaling pathway, which is important for pattern formation and tissue differentiation. Pathogenic variants in SMAD2 have been reported in association with arterial aneurysms and dissections and in large cohorts of subjects with complex congenital heart disease (CHD). We used whole exome sequencing (WES) to investigate the molecular cause of CHD and other congenital anomalies in three probands and of an arterial aneurysm in an additional patient. Patients 1 and 2 presented with complex CHD, developmental delay, seizures, dysmorphic features, short stature, and poor weight gain. Patient 3 was a fetus with complex CHD and heterotaxy. The fourth patient is an adult female with aortic root aneurysm and physical features suggestive of a connective tissue disorder. WES identified pathogenic truncating variants, a splice variant, and a predicted deleterious missense variant in SMAD2. We compare the phenotypes and genotypes in our patients with previously reported cases. Our data suggest two distinct phenotypes associated with pathogenic variants in SMAD2: complex CHD with or without laterality defects and other congenital anomalies, and a late-onset vascular phenotype characterized by arterial aneurysms with connective tissue abnormalities.

A Recurrent De Novo Heterozygous COG4 Substitution Leads to Saul-Wilson Syndrome, Disrupted Vesicular Trafficking, and Altered Proteoglycan Glycosylation

The conserved oligomeric Golgi (COG) complex is involved in intracellular vesicular transport, and is composed of eight subunits distributed in two lobes, lobe A (COG1-4) and lobe B (COG5-8). We describe fourteen individuals with Saul-Wilson syndrome, a rare form of primordial dwarfism with characteristic facial and radiographic features. All affected subjects harbored heterozygous de novo variants in COG4, giving rise to the same recurrent amino acid substitution (p.Gly516Arg). Affected individuals' fibroblasts, whose COG4 mRNA and protein were not decreased, exhibited delayed anterograde vesicular trafficking from the ER to the Golgi and accelerated retrograde vesicular recycling from the Golgi to the ER. This altered steady-state equilibrium led to a decrease in Golgi volume, as well as morphologic abnormalities with collapse of the Golgi stacks. Despite these abnormalities of the Golgi apparatus, protein glycosylation in sera and fibroblasts from affected subjects was not notably altered, but decorin, a proteoglycan secreted into the extracellular matrix, showed altered Golgi-dependent glycosylation. In summary, we define a specific heterozygous COG4 substitution as the molecular basis of Saul-Wilson syndrome, a rare skeletal dysplasia distinct from biallelic COG4-CDG.

TANGO2: expanding the clinical phenotype and spectrum of pathogenic variants

Purpose

TANGO2-related disorders were first described in 2016 and prior to this publication, only 15 individuals with TANGO2-related disorder were described in the literature. Primary features include metabolic crisis with rhabdomyolysis, encephalopathy, intellectual disability, seizures, and cardiac arrhythmias. We assess whether genotype and phenotype of TANGO2-related disorder has expanded since the initial discovery and determine the efficacy of exome sequencing (ES) as a diagnostic tool for detecting variants.

Methods

We present a series of 14 individuals from 11 unrelated families with complex medical and developmental histories, in whom ES or microarray identified compound heterozygous or homozygous variants in TANGO2.

Results

The initial presentation of patients with TANGO2-related disorders can be variable, including primarily neurological presentations. We expand the phenotype and genotype for TANGO2, highlighting the variability of the disorder.

Conclusion

TANGO2-related disorders can have a more diverse clinical presentation than previously anticipated. We illustrate the utility of routine ES data reanalysis whereby discovery of novel disease genes can lead to a diagnosis in previously unsolved cases and the need for additional copy-number variation analysis when ES is performed.

'Maybe I will give some help…. maybe not to help the eyes but different help': an analysis of care and support of children with visual impairment in community settings in Malawi

BACKGROUND

Visual impairment in children is common in low and middle-income settings. Whilst visual impairment (VI) can impact on the development of children, many reach full potential with appropriate early intervention programmes. Although there is increased emphasis on early child development globally, it is not yet clear how to provide specific programmes for children with VI in low and middle-income settings. This study aims to identify facilitators and barriers to the provision of a developmental stimulation programme for children with VI in rural and urban Malawi.

METHODS

We undertook 6 focus groups, 10 home observations and 20 in-depth interviews with carers of children with VI under 6 years in urban and rural Southern Malawi. We utilised topic guides relating to care, play, communication and feeding. Qualitative data were subject to thematic analysis that included placing themes within Bronfenbrenner's ecological framework. We established authenticity of themes through feedback from participants.

RESULTS

We identified themes within Bronfenbrenner's framework at five levels: (1) blindness acting as a barrier to stimulation and communication, health and complex needs all affecting the individual child; (2) understanding of VI, ability to be responsive at the microsystem level of the carer; (3) support from other carers at microsystem level within a mesosystem; (4) support from other professionals (knowledge of, identification and management of children with VI, responsibilities and gender roles, environmental safety and prejudice, stigma and child protection all at the level of the exosystem.

DISCUSSION

This study has revealed the requirements needed in order to produce meaningful and appropriate programmes to support nutrition, care and early stimulation for children with VI in this and similar African settings. This includes supporting carers to understand their child's developmental needs, how to better communicate with, feed and stimulate their child; offering advice sensitive to carers' responsibilities and professional training to better support carers and challenge community stigma.

Management of COPD in Primary Care in North-East Scotland

Introduction

We wished to obtain a snapshot of current service provision and how this could best be developed approximately one year on from the introduction of the National Institute for Clinical Excellence (NICE) guidelines for the management of chronic obstructive pulmonary disease (COPD) and the inclusion of COPD care in the New GMS Contract Quality and Outcomes Framework (QOF).

Methodology

A questionnaire-based survey sent to every general practice (n = 84) in Grampian.

Results

Responses were received from 75 of 84 practices (89%). Questionnaires were returned by both general practitioners (GPs) and practice nurses in 45 practices (54%). All responding practices reported that they had COPD registers. 60/75 (80%) of practices reported having a dedicated COPD clinic; 70/75 (93%) had a spirometer. Areas identified for service development were: quality assuring training in COPD care and spirometry; expanding pulmonary rehabilitation provision (86%), delivering this service locally (54%) and in primary care (75%); standardising referral, assessment and communication about provision of home oxygen; training in pulse oximetry (71%).

Conclusion

This data has important implications for the validity of the quality indicators (QOF) under the new GMS contract. Our respondents identified areas where the new GMS contract QOF could be improved, as well as providing useful suggestions for service development. Respondents recognised that not all clinical services can be effectively delivered by general practice with data supporting the development of intermediate care services for people with COPD.

Shaping dental contract reform: a clinical and cost-effective analysis of incentive-driven commissioning for improved oral health in primary dental care

OBJECTIVE

To evaluate the clinical and cost-effectiveness of a new blended dental contract incentivising improved oral health compared with a traditional dental contract based on units of dental activity (UDAs).

DESIGN

Non-randomised controlled study.

SETTING

Six UK primary care dental practices, three working under a new blended dental contract; three matched practices under a traditional contract.

PARTICIPANTS

550 new adult patients.

INTERVENTIONS

A new blended/incentive-driven primary care dentistry contract and service delivery model versus the traditional contract based on UDAs.

MAIN OUTCOME MEASURES

Primary outcome was as follows: percentage of sites with gingival bleeding on probing. Secondary outcomes were as follows: extracted and filled teeth (%), caries (International Caries Detection and Assessment System (ICDAS)), oral health-related quality of life (Oral Health Impact Profile-14 (OHIP-14)). Incremental cost-effective ratios used OHIP-14 and quality adjusted life years (QALYs) derived from the EQ-5D-3L.

RESULTS

At 24 months, 291/550 (53%) patients returned for final assessment; those lost to follow-up attended 6.46 appointments on average (SD 4.80). The primary outcome favoured patients in the blended contract group. Extractions and fillings were more frequent in this group. Blended contracts were financially attractive for the dental provider but carried a higher cost for the service commissioner. Differences in generic health-related quality of life were negligible. Positive changes over time in oral health-related quality of life in both groups were statistically significant.

CONCLUSIONS

This is the first UK study to assess the clinical and cost-effectiveness of a blended contract in primary care dentistry. Although the primary outcome favoured the blended contract, the results are limited because 47% patients did not attend at 24 months. This is consistent with 39% of adults not being regular attenders and 27% only visiting their dentist when they have a problem. Promotion of appropriate attendance, especially among those with high need, necessitates being factored into recruitment strategies of future studies.

De Novo Mutations in SON Disrupt RNA Splicing of Genes Essential for Brain Development and Metabolism, Causing an Intellectual-Disability Syndrome

The overall understanding of the molecular etiologies of intellectual disability (ID) and developmental delay (DD) is increasing as next-generation sequencing technologies identify genetic variants in individuals with such disorders. However, detailed analyses conclusively confirming these variants, as well as the underlying molecular mechanisms explaining the diseases, are often lacking. Here, we report on an ID syndrome caused by de novo heterozygous loss-of-function (LoF) mutations in SON. The syndrome is characterized by ID and/or DD, malformations of the cerebral cortex, epilepsy, vision problems, musculoskeletal abnormalities, and congenital malformations. Knockdown of son in zebrafish resulted in severe malformation of the spine, brain, and eyes. Importantly, analyses of RNA from affected individuals revealed that genes critical for neuronal migration and cortex organization (TUBG1, FLNA, PNKP, WDR62, PSMD3, and HDAC6) and metabolism (PCK2, PFKL, IDH2, ACY1, and ADA) are significantly downregulated because of the accumulation of mis-spliced transcripts resulting from erroneous SON-mediated RNA splicing. Our data highlight SON as a master regulator governing neurodevelopment and demonstrate the importance of SON-mediated RNA splicing in human development.

Network 1000: the changing needs and circumstances of visually-impaired people: project overview

This article outlines the progress of a newly-commissioned three year study known as Network 1000. It is a three-year project funded through the Community Fund and is being carried out by the University of Birmingham on behalf of Vision 2020. The project’s aim is to create a panel survey of 1000 visually-impaired people to be interviewed regularly over the three-year period, and hopefully beyond, enabling their changing needs and circumstances to be monitored over time. The findings will be used to influence policy-makers and service-providers, and will also be disseminated to a wider audience of people with an interest in visual impairment. Building on the longitudinal nature of the project enables the project team to develop a methodology that is both democratic and inclusive. The underlying research philosophy is one of inclusion and participation and in this respect the people this research affects the most - those who are visually impaired - are involved in all stages of the research process. People with a visual impairment have played a key role in generating the data and the themes that will drive the construction of the main survey instrument. The article is divided into five sections that describe the progress of the project to date: first, it briefly outlines the background to the project; second, it describes the underlying philosophy behind the democratic approach to inclusion and participant involvement; third, it presents preliminary results from generative interviews; fourth, it discusses how the team will recruit participants to the project with particular reference to the two-stage sample design that has been adopted; and finally, it describes how this two-stage approach will be operationalized. The article concludes by outlining the next phase of the project and with a short reflection on the research process to date.

De novo pathogenic variants in CHAMP1 are associated with global developmental delay, intellectual disability, and dysmorphic facial features

We identified five unrelated individuals with significant global developmental delay and intellectual disability (ID), dysmorphic facial features and frequent microcephaly, and de novo predicted loss-of-function variants in chromosome alignment maintaining phosphoprotein 1 (CHAMP1). Our findings are consistent with recently reported de novo mutations in CHAMP1 in five other individuals with similar features. CHAMP1 is a zinc finger protein involved in kinetochore–microtubule attachment and is required for regulating the proper alignment of chromosomes during metaphase in mitosis. Mutations in CHAMP1 may affect cell division and hence brain development and function, resulting in developmental delay and ID.

De novo truncating variants in the AHDC1 gene encoding the AT-hook DNA-binding motif-containing protein 1 are associated with intellectual disability and developmental delay

Whole-exome sequencing (WES) represents a significant breakthrough in clinical genetics, and identifies a genetic etiology in up to 30% of cases of intellectual disability (ID). Using WES, we identified seven unrelated patients with a similar clinical phenotype of severe intellectual disability or neurodevelopmental delay who were all heterozygous for de novo truncating variants in the AT-hook DNA-binding motif–containing protein 1 (AHDC1). The patients were all minimally verbal or nonverbal and had variable neurological problems including spastic quadriplegia, ataxia, nystagmus, seizures, autism, and self-injurious behaviors. Additional common clinical features include dysmorphic facial features and feeding difficulties associated with failure to thrive and short stature. The AHDC1 gene has only one coding exon, and the protein contains conserved regions including AT-hook motifs and a PDZ binding domain. We postulate that all seven variants detected in these patients result in a truncated protein missing critical functional domains, disrupting interactions with other proteins important for brain development. Our study demonstrates that truncating variants in AHDC1 are associated with ID and are primarily associated with a neurodevelopmental phenotype.

Mutations in TBCK, Encoding TBC1-Domain-Containing Kinase, Lead to a Recognizable Syndrome of Intellectual Disability and Hypotonia

Through an international multi-center collaboration, 13 individuals from nine unrelated families and affected by likely pathogenic biallelic variants in TBC1-domain-containing kinase (TBCK) were identified through whole-exome sequencing. All affected individuals were found to share a core phenotype of intellectual disability and hypotonia, and many had seizures and showed brain atrophy and white-matter changes on neuroimaging. Minor non-specific facial dysmorphism was also noted in some individuals, including multiple older children who developed coarse features similar to those of storage disorders. TBCK has been shown to regulate the mammalian target of rapamycin (mTOR) signaling pathway, which is also stimulated by exogenous leucine supplementation. TBCK was absent in cells from affected individuals, and decreased phosphorylation of phospho-ribosomal protein S6 was also observed, a finding suggestive of downregulation of mTOR signaling. Lastly, we demonstrated that activation of the mTOR pathway in response to L-leucine supplementation was retained, suggesting a possible avenue for directed therapies for this condition.

The expanding clinical phenotype of Bosch-Boonstra-Schaaf optic atrophy syndrome: 20 new cases and possible genotype-phenotype correlations

PURPOSE

Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS) is an autosomal-dominant disorder characterized by optic atrophy and intellectual disability caused by loss-of-function mutations in NR2F1. We report 20 new individuals with BBSOAS, exploring the spectrum of clinical phenotypes and assessing potential genotype-phenotype correlations.

METHODS

Clinical features of individuals with pathogenic NR2F1 variants were evaluated by review of medical records. The functional relevance of coding nonsynonymous NR2F1 variants was assessed with a luciferase assay measuring the impact on transcriptional activity. The effects of two start codon variants on protein expression were evaluated by western blot analysis.

RESULTS

We recruited 20 individuals with novel pathogenic NR2F1 variants (seven missense variants, five translation initiation variants, two frameshifting insertions/deletions, one nonframeshifting insertion/deletion, and five whole-gene deletions). All the missense variants were found to impair transcriptional activity. In addition to visual and cognitive deficits, individuals with BBSOAS manifested hypotonia (75%), seizures (40%), autism spectrum disorder (35%), oromotor dysfunction (60%), thinning of the corpus callosum (53%), and hearing defects (20%).

CONCLUSION

BBSOAS encompasses a broad range of clinical phenotypes. Functional studies help determine the severity of novel NR2F1 variants. Some genotype-phenotype correlations seem to exist, with missense mutations in the DNA-binding domain causing the most severe phenotypes.Genet Med 18 11, 1143-1150.

Combined trabeculotomy-trabeculectomy with antimetabolite and releasable suture: outcome with primary congenital glaucoma in a north Indian population

OBJECTIVE

To determine the surgical outcomes of combined trabeculotomy- trabeculectomy with mitomycin-C and releasable suture in children with primary congenital glaucoma (PCG) in a North Indian population.

DESIGN

Retrospective, interventional, consecutive, non-comparative case series.

MATERIALS AND METHODS

The medical records of 137 eyes of 77 patients who underwent combined trabeculotomy- trabeculectomy with 0.2 mg/ml mitomycin C (MMC) either bilaterally (49 patients) or unilaterally (28 patients) between January 2004 and March 2012 were reviewed retrospectively. The main outcome measures were postoperative intraocular pressures, corneal clarity and diameter, duration of follow-up, success rate and complications.

RESULTS

The mean preoperative intraocular pressure reduced from 34 ± 7 mm Hg (range 15- 54 mm Hg) to 17 ± 7 mm Hg (range 5 - 32 mm Hg) with a mean reduction of 44 % (P less than 0.001). The mean follow-up period was 24.4 ± 10.3 months (range 6 - 48 months). Complete success defined as intraocular pressure less than 21 mm Hg without any medication and clinically stable glaucoma at last follow-up was achieved in 113 eyes (83 %) while a 'qualified success' of intraocular pressure less than 21 mm Hg with one medication was achieved in ten eyes (7 %). The Kaplan-Meier survival analysis revealed success rates (at 'n' months) of 90 % (6), 85 % (12), 82 % (24), 80 % (36) and 77 % (48). There were no significant intraoperative or postoperative complications.

CONCLUSION

Primary combined trabeculotomy-trabeculectomy with mitomycin-C and releasable suture offers a viable surgical option in Northern Indian infants with primary congenital glaucoma. The use of 0.2 mg/ml mitomycin C for 2 minutes improves the overall success while the releasable suture decreases the risk of postoperative complications especially associated with the use of antimetabolites.

Major element, trace element, nutrient, and radionuclide mobility in a mining by-product-amended soil

This study investigates the use of a mineral processing by-product, neutralized used acid (NUA), primarily composed of gypsum and Fe-oxyhydroxide, as a soil amendment. A 1489-d turf farm field trial assessed nutrient, trace element, and radionuclide mobility of a soil amended with ∼5% by mass to a depth of 15 cm of NUA. Average PO-P fluxes collected as subsoil leachates were 0.7 and 26.6 kg ha yr for NUA-amended and control sites, respectively, equating to a 97% reduction in PO-P loss after 434 kg P ha was applied. Total nitrogen fluxes in NUA-amended soil leachates were similarly reduced by 82%. Incorporation of NUA conferred major changes in leachate geochemistry with a diverse suite of trace elements depleted within NUA-amended leachates. Gypsum dissolution from NUA resulted in an increase from under- to oversaturation of the soil leachates for a range of Fe- and Ca-minerals including calcite and ferrihydrite, many of which have a well-documented ability to assimilate PO-P and trace elements. Isotopic analysis indicated little Pb addition from NUA. Both Sr and Nd isotope results revealed that NUA and added fertilizer became an important source of Ca to leachate and turf biomass. The NUA-amended soils retained a range of U-Th series radionuclides, with little evidence of transfer to soil leachate or turf biomass. Calculated radioactivity dose rates indicate only a small increment due to NUA amendment. With increased nutrient, trace element, and solute retention, and increased productivity, a range of potential agronomic benefits may be conferred by NUA amendment of soils, in addition to the potential to limit offsite nutrient loss and eutrophication.

Characterization of a recurrent 3.8kb deletion involving exons 17a and 17b within the CFTR gene

BACKGROUND

Large deletions within CFTR have been estimated to constitute 1-2% pathogenic alleles, but the occurrence could be much higher in classical cystic fibrosis (CF) patients with one mutation detectable by the routine screening/sequencing work-up. Currently, evaluation of major CFTR rearrangements is not included in the mutation analysis for the reproductive partner of a CF patient/carrier.

METHODS

Exon sequencing and Multiplex Ligation-dependent Amplification (MLPA) analyses were used to make a molecular diagnosis of two unrelated CF patients. Long PCR, restriction mapping, cloning, and hot start sequencing were employed to accurately annotate the rearrangement junctions.

RESULTS

Both patients had a heterozygous single amino acid deletion mutation identified by sequencing, and a heterozygous deletion of CFTR exons 17a and 17b detected by MLPA. Molecular characterization of the rearrangement breakpoints indicated that the two patients had an identical complex c.2988+1616_c.3367+356del3796ins62 change, flanked by a pair of perfectly inverted repeats of 32 nucleotides.

CONCLUSIONS

The c.2988+1616_c.3367+356del3796ins62 complex rearrangement is a recurrent mutation from patients of different ethnic backgrounds. This mutation can be detected through a simple PCR based analysis.

Abstract 3674: Next generation cancer gene sequencing for clinically actionable mutations

Cancer gene mutations are important diagnostic, prognostic, and predictive biologic markers. Mutation detection in cancer tissues has been a real challenge for researchers as a cancer is often associated with multiple mutations and new mutations may occur as the disease progresses and during treatments. Essentially, all cancer tissues are a mosaic mixture of normal and abnormal cell clones. Therefore, a new technology that can target many mutations simultaneously with high sensitivity is exceedingly desirable. Targeted next generation sequencing permits deep sequencing of hundreds of mutations concurrently. We have used a novel next generation sequencing technology that merges multiplex PCR with ion semiconductor sequencing (AmpliSeq, Life Technology) to sequence a panel of clinically actionable cancer gene mutations on 12 tumor samples including 6 archived FFPE samples, 2 bone marrow samples, and 4 cell lines with known mutations, and a normal blood sample as a control. Each sample was run three times to assay for inter-run variability. The panel contains 739 mutations including clinically actionable mutations such as EGFR mutations in exons 18-21, BRAF V600E, KRAS mutations at codons 12, 13, and 61, and many more. Using this technology we successfully identified all known mutations previously detected using Pyposequencing or Sanger sequencing technologies. The most common somatic mutations were also confirmed by Competitive Allele-Specific TaqMan® PCR (castPCR, Life Technology). To determine the sensitivity of the test, we studied mutation positive FFPE samples with serial dilutions. Our results showed that the test can detect mutations at frequencies as low as 5% with 99% confidence. Analysis of mutation calls in different runs showed little inter-run variation. Other benefits of this novel technology are its fast turn around time, which can be as short as two days, and its low cost. Our experience demonstrates that this technology holds great potential clinical utility including diagnostic and therapeutic applications.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3674. doi:1538-7445.AM2012-3674

Guidelines for evaluating and managing children born with disorders of sexual development

Children born with disorders of sexual differentiation (DSD) pose numerous challenges for the parents, family, and treating physicians. The pediatrician is usually the first medical contact for newborns with DSD or for toddlers and children who present with DSD at a later time. Several years ago, we formed a Gender Medicine Team (GMT) at Baylor College of Medicine and Texas Children's Hospital (TCH) to explore and evaluate the most appropriate management strategies, which had long been a matter of concern and contention. Subsequently, the GMT, composed of experts in the fields of endocrinology, ethics, genetics, gynecology, psychology, pediatric surgery, and urology, formed a Task Force to evaluate the information available from our own experiences and from reviews of the literature. Utilizing the Grading of Recommendation, Assessment, Development and Evaluation (GRADE) system to assess the evidence and recommendations, the Task Force developed a consensus statement for clinical management of DSD and for making appropriate sex assignments.