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1.
Am J Hum Genet ; 110(2): 215-227, 2023 02 02.
Article in English | MEDLINE | ID: mdl-36586412

ABSTRACT

Neurodevelopmental disorders (NDDs) result from highly penetrant variation in hundreds of different genes, some of which have not yet been identified. Using the MatchMaker Exchange, we assembled a cohort of 27 individuals with rare, protein-altering variation in the transcriptional coregulator ZMYM3, located on the X chromosome. Most (n = 24) individuals were males, 17 of which have a maternally inherited variant; six individuals (4 male, 2 female) harbor de novo variants. Overlapping features included developmental delay, intellectual disability, behavioral abnormalities, and a specific facial gestalt in a subset of males. Variants in almost all individuals (n = 26) are missense, including six that recurrently affect two residues. Four unrelated probands were identified with inherited variation affecting Arg441, a site at which variation has been previously seen in NDD-affected siblings, and two individuals have de novo variation resulting in p.Arg1294Cys (c.3880C>T). All variants affect evolutionarily conserved sites, and most are predicted to damage protein structure or function. ZMYM3 is relatively intolerant to variation in the general population, is widely expressed across human tissues, and encodes a component of the KDM1A-RCOR1 chromatin-modifying complex. ChIP-seq experiments on one variant, p.Arg1274Trp, indicate dramatically reduced genomic occupancy, supporting a hypomorphic effect. While we are unable to perform statistical evaluations to definitively support a causative role for variation in ZMYM3, the totality of the evidence, including 27 affected individuals, recurrent variation at two codons, overlapping phenotypic features, protein-modeling data, evolutionary constraint, and experimentally confirmed functional effects strongly support ZMYM3 as an NDD-associated gene.


Subject(s)
Intellectual Disability , Nervous System Malformations , Neurodevelopmental Disorders , Humans , Male , Female , Neurodevelopmental Disorders/genetics , Intellectual Disability/genetics , Phenotype , Gene Expression Regulation , Face , Nuclear Proteins/genetics , Histone Demethylases/genetics
2.
Am J Epidemiol ; 192(3): 334-341, 2023 02 24.
Article in English | MEDLINE | ID: mdl-36446589

ABSTRACT

NYC FITNESSGRAM, monitored by the New York City (NYC) Department of Education and the NYC Department of Health and Mental Hygiene, functions as the NYC Department of Education's citywide youth fitness surveillance program. Here we present the methods, characteristics, and data used in this surveillance system to monitor physical fitness in public school students (grades kindergarten through 12; initiated in 2006; n = 6,748,265 observations; mean sample of 519,097 observations per year to date) in New York, New York. Youth physical fitness prevalence estimates, longitudinal trends, and spatial analyses may be investigated using continuous fitness composite percentile scores and Cooper Institute for Aerobic Research-defined sex- and age-specific Healthy Fitness Zones. Healthy Fitness Zones are based on individual-child fitness test performance, with standard errors clustered at the school and student levels and adjusted for sociodemographic characteristics. Results may be used to show trends in youth fitness attainment over time and highlight disparities in the fitness prevalence of NYC students. In sum, continuous fitness composite percentile scores offer the opportunity for prospective tracking of shifts in youth physical fitness on a population scale and across subpopulations. NYC FITNESSGRAM can accompany a growing body of surveillance tools demonstrating the potential for population-level surveillance tools to promote global public health.


Subject(s)
Exercise , Physical Fitness , Humans , Adolescent , New York City/epidemiology , Prospective Studies , Students
3.
Genet Med ; 25(7): 100839, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37057675

ABSTRACT

PURPOSE: LHX2 encodes the LIM homeobox 2 transcription factor (LHX2), which is highly expressed in brain and well conserved across species, but it has not been clearly linked to neurodevelopmental disorders (NDDs) to date. METHODS: Through international collaboration, we identified 19 individuals from 18 families with variable neurodevelopmental phenotypes, carrying a small chromosomal deletion, likely gene-disrupting or missense variants in LHX2. Functional consequences of missense variants were investigated in cellular systems. RESULTS: Affected individuals presented with developmental and/or behavioral abnormalities, autism spectrum disorder, variable intellectual disability, and microcephaly. We observed nucleolar accumulation for 2 missense variants located within the DNA-binding HOX domain, impaired interaction with co-factor LDB1 for another variant located in the protein-protein interaction-mediating LIM domain, and impaired transcriptional activation by luciferase assay for 4 missense variants. CONCLUSION: We implicate LHX2 haploinsufficiency by deletion and likely gene-disrupting variants as causative for a variable NDD. Our findings suggest a loss-of-function mechanism also for likely pathogenic LHX2 missense variants. Together, our observations underscore the importance of LHX2 in the nervous system and for variable neurodevelopmental phenotypes.


Subject(s)
Autism Spectrum Disorder , Intellectual Disability , Neurodevelopmental Disorders , Humans , LIM-Homeodomain Proteins/genetics , Autism Spectrum Disorder/genetics , Haploinsufficiency/genetics , Neurodevelopmental Disorders/pathology , Transcription Factors/genetics , Intellectual Disability/genetics , Intellectual Disability/complications
4.
Environ Sci Technol ; 57(46): 17959-17970, 2023 Nov 21.
Article in English | MEDLINE | ID: mdl-36932953

ABSTRACT

Tap water lead testing programs in the U.S. need improved methods for identifying high-risk facilities to optimize limited resources. In this study, machine-learned Bayesian network (BN) models were used to predict building-wide water lead risk in over 4,000 child care facilities in North Carolina according to maximum and 90th percentile lead levels from water lead concentrations at 22,943 taps. The performance of the BN models was compared to common alternative risk factors, or heuristics, used to inform water lead testing programs among child care facilities including building age, water source, and Head Start program status. The BN models identified a range of variables associated with building-wide water lead, with facilities that serve low-income families, rely on groundwater, and have more taps exhibiting greater risk. Models predicting the probability of a single tap exceeding each target concentration performed better than models predicting facilities with clustered high-risk taps. The BN models' Fß-scores outperformed each of the alternative heuristics by 118-213%. This represents up to a 60% increase in the number of high-risk facilities that could be identified and up to a 49% decrease in the number of samples that would need to be collected by using BN model-informed sampling compared to using simple heuristics. Overall, this study demonstrates the value of machine-learning approaches for identifying high water lead risk that could improve lead testing programs nationwide.


Subject(s)
Drinking Water , Lead , Humans , Child , Lead/analysis , Bayes Theorem , Child Care , Water , Decision Making
5.
Am J Hum Genet ; 104(4): 685-700, 2019 04 04.
Article in English | MEDLINE | ID: mdl-30929737

ABSTRACT

Conventional genetic testing of individuals with neurodevelopmental presentations and congenital anomalies (ND/CAs), i.e., the analysis of sequence and copy number variants, leaves a substantial proportion of them unexplained. Some of these cases have been shown to result from DNA methylation defects at a single locus (epi-variants), while others can exhibit syndrome-specific DNA methylation changes across multiple loci (epi-signatures). Here, we investigate the clinical diagnostic utility of genome-wide DNA methylation analysis of peripheral blood in unresolved ND/CAs. We generate a computational model enabling concurrent detection of 14 syndromes using DNA methylation data with full accuracy. We demonstrate the ability of this model in resolving 67 individuals with uncertain clinical diagnoses, some of whom had variants of unknown clinical significance (VUS) in the related genes. We show that the provisional diagnoses can be ruled out in many of the case subjects, some of whom are shown by our model to have other diseases initially not considered. By applying this model to a cohort of 965 ND/CA-affected subjects without a previous diagnostic assumption and a separate assessment of rare epi-variants in this cohort, we identify 15 case subjects with syndromic Mendelian disorders, 12 case subjects with imprinting and trinucleotide repeat expansion disorders, as well as 106 case subjects with rare epi-variants, a portion of which involved genes clinically or functionally linked to the subjects' phenotypes. This study demonstrates that genomic DNA methylation analysis can facilitate the molecular diagnosis of unresolved clinical cases and highlights the potential value of epigenomic testing in the routine clinical assessment of ND/CAs.


Subject(s)
Congenital Abnormalities/genetics , DNA Methylation , Genetic Diseases, Inborn/diagnosis , Genome-Wide Association Study , Cohort Studies , Computer Simulation , Congenital Abnormalities/diagnosis , DNA Copy Number Variations , Epigenomics , Gene Dosage , Genetic Diseases, Inborn/genetics , Genetic Variation , Genomic Imprinting , Humans , Phenotype , Sequence Analysis, DNA , Syndrome , Trinucleotide Repeat Expansion
6.
Am J Public Health ; 112(S7): S695-S705, 2022 09.
Article in English | MEDLINE | ID: mdl-36179303

ABSTRACT

Objectives. To evaluate lead levels in tap water at licensed North Carolina child care facilities. Methods. Between July 2020 and October 2021, we enrolled 4005 facilities in a grant-funded, participatory science testing program. We identified risk factors associated with elevated first-draw lead levels using multiple logistic regression analysis. Results. By sample (n = 22 943), 3% of tap water sources exceeded the 10 parts per billion (ppb) North Carolina hazard level, whereas 25% of tap water sources exceeded 1 ppb, the American Academy of Pediatrics' reference level. By facility, at least 1 tap water source exceeded 1 ppb and 10 ppb at 56% and 12% of facilities, respectively. Well water reliance was the largest risk factor, followed by participation in Head Start programs and building age. We observed large variability between tap water sources within the same facility. Conclusions. Tap water in child care facilities is a potential lead exposure source for children. Given variability among tap water sources, it is imperative to test every source used for drinking and cooking so appropriate action can be taken to protect children's health. (Am J Public Health. 2022;112(S7):S695-S705. https://doi.org/10.2105/AJPH.2022.307003).


Subject(s)
Drinking Water , Lead , Child , Child Care , Humans , Lead/analysis , North Carolina , Water/analysis , Water Supply
7.
Am J Med Genet A ; 185(12): 3793-3803, 2021 12.
Article in English | MEDLINE | ID: mdl-34414661

ABSTRACT

Osteopathia striata with cranial sclerosis (OSCS; OMIM# 300373) is a rare X-linked disorder caused by mutations of the AMER1 gene. OSCS is traditionally considered a skeletal dysplasia, characterized by cranial sclerosis and longitudinal striations in the long bone metaphyses. However, OSCS affects many body systems and varies significantly in phenotypic severity between individuals. This case series focuses on the phenotypic presentation and development of individuals with OSCS. We provide an account of 12 patients with OSCS, ranging from 5 months to 38 years of age. These patients were diagnosed with OSCS after genetic testing confirmed pathogenic mutations in AMER1. Patient consent was obtained for photos and participation. Data were collected regarding perinatal history, dysmorphic features, and review of systems. This case series documents common facial dysmorphology, as well as rare extraskeletal features of OSCS, including two patients with intestinal malrotation and two patients with pyloric stenosis. We share four apparently nonmosaic males with OSCS (one de novo and three maternal variants). We also provide a clinical update on a patient who was previously published by Chénier et al. (2012). American Journal of Medical Genetics Part A, 158, 2946-2952. More research is needed to investigate the links between genotype and phenotype and assess the long-term comorbidities and overall quality of life of individuals with OSCS.


Subject(s)
Adaptor Proteins, Signal Transducing/genetics , Genetic Predisposition to Disease , Osteosclerosis/genetics , Skull/pathology , Tumor Suppressor Proteins/genetics , Adolescent , Adult , Canada , Child , Child, Preschool , Female , Genes, X-Linked , Humans , Infant , Male , Musculoskeletal Abnormalities , Mutation/genetics , Osteosclerosis/diagnosis , Osteosclerosis/pathology , Phenotype , Pregnancy , Quality of Life , Skull/diagnostic imaging , Young Adult
8.
Am J Med Genet A ; 185(9): 2829-2845, 2021 09.
Article in English | MEDLINE | ID: mdl-34056834

ABSTRACT

Mosaic KRAS variants and other RASopathy genes cause oculoectodermal, encephalo-cranio-cutaneous lipomatosis, and Schimmelpenning-Feuerstein-Mims syndromes, and a spectrum of vascular malformations, overgrowth and other associated anomalies, the latter of which are only recently being characterized. We describe eight individuals in total (six unreported cases and two previously reported cases) with somatic KRAS variants and variably associated features. Given the findings of somatic overgrowth (in seven individuals) and vascular or lymphatic malformations (in eight individuals), we suggest mosaic RASopathies (mosaic KRAS variants) be considered in the differential diagnosis for individuals presenting with asymmetric overgrowth and lymphatic or vascular anomalies. We expand the association with embryonal tumors, including the third report of embryonal rhabdomyosarcoma, as well as novel findings of Wilms tumor and nephroblastomatosis in two individuals. Rare or novel findings in our series include the presence of epilepsy, polycystic kidneys, and T-cell deficiency in one individual, and multifocal lytic bone lesions in two individuals. Finally, we describe the first use of targeted therapy with a MEK inhibitor for an individual with a mosaic KRAS variant. The purposes of this report are to expand the phenotypic spectrum of mosaic KRAS-related disorders, and to propose possible mechanisms of pathogenesis, and surveillance of its associated findings.


Subject(s)
Abnormalities, Multiple/pathology , Kidney Neoplasms/pathology , Mosaicism , Mutation , Proto-Oncogene Proteins p21(ras)/genetics , Vascular Malformations/pathology , Wilms Tumor/pathology , Abnormalities, Multiple/genetics , Adolescent , Child , Child, Preschool , Female , Humans , Infant , Infant, Newborn , Kidney Neoplasms/genetics , Male , Phenotype , Vascular Malformations/genetics , Wilms Tumor/genetics
9.
Am J Med Genet A ; 182(1): 162-168, 2020 01.
Article in English | MEDLINE | ID: mdl-31729162

ABSTRACT

Megalencephaly-capillary malformation syndrome (MCAP) is a brain overgrowth disorder characterized by cortical malformations (specifically polymicrogyria), vascular anomalies, and segmental overgrowth secondary to somatic activating mutations in the PI3K-AKT-MTOR pathway (PIK3CA). Cases of growth failure and hypoglycemia have been reported in patients with MCAP, raising the suspicion for unappreciated growth hormone (GH) deficiency. Here we report an observational multicenter study of children with MCAP and GH deficiency. Eleven participants were confirmed to have GH deficiency, all with very low or undetectable circulating concentrations of insulin-like growth factor-1 and insulin-like growth factor binding protein-3. Seven underwent GH stimulation testing and all had insufficient responses with a median GH peak of 3.7 ng/ml (range 1.1-8.6). Growth patterns revealed a drastic decline in length z-scores within the first year of life but then stabilized afterward. Five were treated with GH; one discontinued due to inconsolability. The other four participants continued on GH with improvement in linear growth velocity. Other endocrinopathies were identified in 7 of the 11 participants in this cohort. This study indicates that GH deficiency is associated with MCAP and that children with MCAP and hypoglycemia and/or postnatal growth failure should be evaluated for GH deficiency and other endocrinopathies.


Subject(s)
Capillaries/abnormalities , Class I Phosphatidylinositol 3-Kinases/genetics , Growth Hormone/deficiency , Hypoglycemia/genetics , Vascular Malformations/genetics , Brain/metabolism , Brain/pathology , Capillaries/pathology , Child , Child, Preschool , Female , Genetic Predisposition to Disease , Growth Hormone/genetics , Humans , Hypoglycemia/complications , Hypoglycemia/pathology , Infant , Infant, Newborn , Male , Mutation/genetics , Polymicrogyria/genetics , Polymicrogyria/pathology , Vascular Malformations/complications , Vascular Malformations/pathology
10.
Environ Sci Technol ; 52(13): 7513-7523, 2018 07 03.
Article in English | MEDLINE | ID: mdl-29901991

ABSTRACT

Anthropogenic chemicals have been proposed as potential markers of human fecal contamination in recreational water. However, to date, there are no published studies describing their relationships with illness risks. Using a cohort of swimmers at seven U.S. beaches, we examined potential associations between the presence of chemical markers of human fecal pollution and self-reported gastrointestinal (GI) illness, diarrhea, and respiratory illness. Swimmers were surveyed about their beach activities, water exposure, and baseline symptoms on the day of their beach visit, and about any illness experienced 10-12 days later. Risk differences were estimated using model-based standardization and adjusted for the swimmer's age, beach site, sand contact, rainfall, and water temperature. Sixty-two chemical markers were analyzed from daily water samples at freshwater and marine beaches. Of those, 20 were found consistently. With the possible exception of bisphenol A and cholesterol, no chemicals were consistently associated with increased risks of illness. These two chemicals were suggestively associated with 2% and 1% increased risks of GI illness and diarrhea in both freshwater and marine beaches. Additional research using the more sensitive analytic methods currently available for a wider suite of analytes is needed to support the use of chemical biomarkers to quantify illness risk and identify fecal pollution sources.


Subject(s)
Bathing Beaches , Water Microbiology , Biomarkers , Feces , Humans , Self Report
11.
J Med Genet ; 54(5): 313-323, 2017 05.
Article in English | MEDLINE | ID: mdl-28039329

ABSTRACT

BACKGROUND: Increased heart rate and a prolonged QT interval are important risk factors for cardiovascular morbidity and mortality, and can be influenced by the use of various medications, including tricyclic/tetracyclic antidepressants (TCAs). We aim to identify genetic loci that modify the association between TCA use and RR and QT intervals. METHODS AND RESULTS: We conducted race/ethnic-specific genome-wide interaction analyses (with HapMap phase II imputed reference panel imputation) of TCAs and resting RR and QT intervals in cohorts of European (n=45 706; n=1417 TCA users), African (n=10 235; n=296 TCA users) and Hispanic/Latino (n=13 808; n=147 TCA users) ancestry, adjusted for clinical covariates. Among the populations of European ancestry, two genome-wide significant loci were identified for RR interval: rs6737205 in BRE (ß=56.3, pinteraction=3.9e-9) and rs9830388 in UBE2E2 (ß=25.2, pinteraction=1.7e-8). In Hispanic/Latino cohorts, rs2291477 in TGFBR3 significantly modified the association between TCAs and QT intervals (ß=9.3, pinteraction=2.55e-8). In the meta-analyses of the other ethnicities, these loci either were excluded from the meta-analyses (as part of quality control), or their effects did not reach the level of nominal statistical significance (pinteraction>0.05). No new variants were identified in these ethnicities. No additional loci were identified after inverse-variance-weighted meta-analysis of the three ancestries. CONCLUSIONS: Among Europeans, TCA interactions with variants in BRE and UBE2E2 were identified in relation to RR intervals. Among Hispanic/Latinos, variants in TGFBR3 modified the relation between TCAs and QT intervals. Future studies are required to confirm our results.


Subject(s)
Aging/physiology , Antidepressive Agents, Tricyclic/pharmacology , Electrocardiography , Genome-Wide Association Study , Heart/physiopathology , Pharmacogenetics , Aged , Female , Genetic Loci , Heart/drug effects , Humans , Male , Middle Aged
12.
Environ Health ; 16(1): 103, 2017 10 02.
Article in English | MEDLINE | ID: mdl-28969670

ABSTRACT

BACKGROUND: Fecal indicator bacteria used to assess illness risks in recreational waters (e.g., Escherichia coli, Enterococci) cannot discriminate among pollution sources. To address this limitation, human-associated Bacteroides markers have been proposed, but the risk of illness associated with the presence of these markers in recreational waters is unclear. Our objective was to estimate associations between human-associated Bacteroides markers in water and self-reported illness among swimmers at 6 U.S. beaches spanning 2003-2007. METHODS: We used data from a prospectively-enrolled cohort of 12,060 swimmers surveyed about beach activities and water exposure on the day of their beach visit. Ten to twelve days later, participants reported gastroinestinal, diarrheal, and respiratory illnesses experienced since the visit. Daily water samples were analyzed for the presence of human-associated Bacteroides genetic markers: HF183, BsteriF1, BuniF2, HumM2. We used model-based standardization to estimate risk differences (RD) and 95% confidence intervals (CI). We assessed whether the presence of Bacteroides markers were modifiers of the association between general Enterococcus and illness among swimmers using interaction contrast. RESULTS: Overall we observed inconsistent associations between the presence of Bacteroides markers and illness. There was a pattern of increased risks of gastrointestinal (RD = 1.9%; 95% CI: 0.1%, 3.7%), diarrheal (RD = 1.3%; 95% CI: -0.2%, 2.7%), and respiratory illnesses (RD = 1.1%; 95% CI: -0.2%, 2.5%) associated with BsteriF1. There was no evidence that Bacteroides markers acted as modifiers of Enterococcus and illness. Patterns were similar when stratified by water matrix. CONCLUSIONS: Quantitative measures of fecal pollution using Bacteroides, rather than presence-absence indicators, may be necessary to accurately assess human risk specific to the presence of human fecal pollution.


Subject(s)
Bacteroides/isolation & purification , Bathing Beaches , Diarrhea/epidemiology , Feces/microbiology , Gastrointestinal Diseases/epidemiology , Respiratory Tract Diseases/epidemiology , Alabama/epidemiology , Cohort Studies , Diarrhea/microbiology , Environmental Biomarkers , Gastrointestinal Diseases/microbiology , Great Lakes Region/epidemiology , Incidence , North Carolina/epidemiology , Respiratory Tract Diseases/microbiology , Self Report , Swimming
13.
Mol Genet Metab ; 116(3): 146-51, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26361991

ABSTRACT

Untreated profound biotinidase deficiency results in a wide range of clinical features, including optic atrophy, cutaneous abnormalities, hearing loss and developmental delay. Ontario, Canada incorporated this treatable deficiency in newborn screening over the past 8years. This study elucidates the molecular, biochemical, and clinical findings from the pilot project. Information from initial screens, serum biotinidase activity level assays, molecular testing, and family history for 246 positive newborns screens were analyzed. A mutation spectrum was created for the province of Ontario, including common mutations such as D444H, D444H/A171T, Q456H, C33fs, and R157H. Individuals with partial deficiency were separated into 3 groups: D444H homozygotes (Group 1); compound heterozygotes for D444H with another profound allele (Group 2); compound heterozygotes with two non-D444H alleles (Group 3). Biochemical phenotype-genotype associations in partial deficiency showed a significant difference in serum biotinidase activity in between any given two groups. Three children with partial deficiency discontinued biotin for varied lengths of time. Two of whom became symptomatic with abnormal gait, alopecia, skin rashes and developmental delay. A need for more congruency in diagnostic, treatment and educational practices was highlighted across the province. Heterogeneity and variation in clinical presentations and management was observed in patients with the partial deficiency.


Subject(s)
Biotinidase Deficiency/enzymology , Biotinidase Deficiency/genetics , Neonatal Screening , Alleles , Amidohydrolases/genetics , Biotin/therapeutic use , Biotinidase/blood , Biotinidase/genetics , Biotinidase Deficiency/diagnosis , Biotinidase Deficiency/epidemiology , Child , Child, Preschool , Disease Management , Female , Genetic Association Studies , Hearing Loss/etiology , Heterozygote , Homozygote , Humans , Infant , Infant, Newborn , Male , Mutation , Ontario/epidemiology , Pilot Projects
14.
Can J Neurol Sci ; 41(5): 626-31, 2014 Sep.
Article in English | MEDLINE | ID: mdl-25373814

ABSTRACT

BACKGROUND: Multiple sulfatase deficiency (MSD) is a rare autosomal recessive inborn error of lysosomal metabolism. The clinical phenotypic spectrum encompasses overlapping features of variable severity and is suggestive of individual single sulfatase deficiencies (i.e., metachromatic leukodystrophy, mucopolysaccharidosis, and X-linked ichthyosis). CASE REPORT: We describe a 3-year-old male with severe hypotonia, developmental regression and progressive neurodegeneration, coarse facial features, nystagmus (from ocular albinism), and dysmyelinating motor sensory neuropathy. Ethics approval was obtained from the Western University Ontario. RESULTS: Extensive investigative work-up identified deficiencies of multiple sulfatases: heparan sulfate sulfamidase: 6.5 nmoles/mg/protein/17 hour (reference 25.0-75.0), iduronate-2-sulfate sulfatase: 9 nmol/mg/protein/4 hour (reference 31-110), and arylsulfatase A: 3.8 nmoles/hr/mg protein (reference 22-50). The identification of compound heterozygous pathogenic mutations in the SUMF1 gene c.836 C>T (p.A279V) and c.1045C>T (p.R349W) confirmed the diagnosis of MSD. CONCLUSION: The complex clinical manifestations of MSD and the unrelated coexistence of ocular albinism as in our case can delay diagnosis. Genetic counselling should be provided to all affected families.


Subject(s)
Albinism, Ocular/complications , Albinism, Ocular/diagnosis , Multiple Sulfatase Deficiency Disease/complications , Multiple Sulfatase Deficiency Disease/diagnosis , Albinism, Ocular/genetics , Child, Preschool , Diagnosis, Differential , Humans , Male , Multiple Sulfatase Deficiency Disease/genetics
15.
HGG Adv ; 5(2): 100273, 2024 Apr 11.
Article in English | MEDLINE | ID: mdl-38297832

ABSTRACT

Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 14 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism, reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated an overall milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, and some had alternative symptomatologies with rational biological links to SMC3. Analyses of tumor and model system transcriptomic data and epigenetic data in a subset of cases suggest that SMC3 pLoF variants reduce SMC3 expression but do not strongly support clustering with functional genomic signatures of typical CdLS. Our finding of substantial population-scale LoF intolerance in concert with variable growth and developmental features in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multilayered genomic data paired with careful phenotyping.


Subject(s)
De Lange Syndrome , Intellectual Disability , Humans , Cell Cycle Proteins/genetics , Chondroitin Sulfate Proteoglycans/genetics , Chromosomal Proteins, Non-Histone/genetics , De Lange Syndrome/genetics , Heterozygote , Intellectual Disability/genetics , Mutation , Phenotype
16.
medRxiv ; 2023 Sep 28.
Article in English | MEDLINE | ID: mdl-37808847

ABSTRACT

Heterozygous missense variants and in-frame indels in SMC3 are a cause of Cornelia de Lange syndrome (CdLS), marked by intellectual disability, growth deficiency, and dysmorphism, via an apparent dominant-negative mechanism. However, the spectrum of manifestations associated with SMC3 loss-of-function variants has not been reported, leading to hypotheses of alternative phenotypes or even developmental lethality. We used matchmaking servers, patient registries, and other resources to identify individuals with heterozygous, predicted loss-of-function (pLoF) variants in SMC3, and analyzed population databases to characterize mutational intolerance in this gene. Here, we show that SMC3 behaves as an archetypal haploinsufficient gene: it is highly constrained against pLoF variants, strongly depleted for missense variants, and pLoF variants are associated with a range of developmental phenotypes. Among 13 individuals with SMC3 pLoF variants, phenotypes were variable but coalesced on low growth parameters, developmental delay/intellectual disability, and dysmorphism reminiscent of atypical CdLS. Comparisons to individuals with SMC3 missense/in-frame indel variants demonstrated a milder presentation in pLoF carriers. Furthermore, several individuals harboring pLoF variants in SMC3 were nonpenetrant for growth, developmental, and/or dysmorphic features, some instead having intriguing symptomatologies with rational biological links to SMC3 including bone marrow failure, acute myeloid leukemia, and Coats retinal vasculopathy. Analyses of transcriptomic and epigenetic data suggest that SMC3 pLoF variants reduce SMC3 expression but do not result in a blood DNA methylation signature clustering with that of CdLS, and that the global transcriptional signature of SMC3 loss is model-dependent. Our finding of substantial population-scale LoF intolerance in concert with variable penetrance in subjects with SMC3 pLoF variants expands the scope of cohesinopathies, informs on their allelic architecture, and suggests the existence of additional clearly LoF-constrained genes whose disease links will be confirmed only by multi-layered genomic data paired with careful phenotyping.

17.
Case Rep Genet ; 2022: 9393042, 2022.
Article in English | MEDLINE | ID: mdl-35663206

ABSTRACT

We describe the diagnostic odyssey of an eight-year-old female born to consanguineous parents. Our patient presented with global developmental delay, regression, microcephaly, spastic diplegia, and leukodystrophy confirmed on brain magnetic resonance imaging (MRI). She was found on whole exome sequencing (WES) to have dual genetic diagnoses. The first was a homozygous pathogenic HERC2 gene partial deletion of exons 43-45 that causes HERC2-related disorder. The second was a homozygous pathogenic variant (c.836 C > T, p.A279 V) in the SUMF1 gene responsible for multiple sulfatase deficiency. This case highlights some of the challenges in diagnosing consanguineous pediatric populations where standard genetic and metabolic testing may not provide answers. Our case further supports the recent American College of Medical Genetics and Genomics (ACMG) recommendation of WES as a first or second-tier test for patients with developmental delay, particularly in a population where the chances of dual diagnosis is high.

18.
Prev Med Rep ; 26: 101704, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35141118

ABSTRACT

The Office of School Health, a joint program of the Departments of Health and Education, administers New York City's (NYC) body mass index (BMI) surveillance system to monitor childhood obesity. We describe the context, importance, and process for creating a multi-agency, school-based BMI surveillance system using BMI collected from annual FITNESSGRAM® physical fitness assessments conducted as part of a larger physical activity and wellness curriculum in NYC public schools. We also summarize our current system and methodology, highlighting the types of data and data sources that comprise the system and partnership between the Departments of Health and Education that enable data sharing. Strategies for addressing threats to data quality, including missing data, biologically implausible values, and imprecise/subjective weight or height equipment are discussed. We also review current and future surveillance data products, and provide recommendations for collecting, analyzing, interpreting, and reporting BMI data for childhood obesity surveillance. Collaboration between Departments of Health and Education as well as attention to safeguards of BMI reporting and data quality threats have enabled NYC to collect high quality BMI data to accurately monitor childhood obesity trends. These findings have implications for youth BMI surveillance systems in the United States and globally.

19.
Eye (Lond) ; 36(11): 2088-2093, 2022 11.
Article in English | MEDLINE | ID: mdl-34531550

ABSTRACT

AIMS/PURPOSE: To investigate Leber congenital amaurosis (LCA) patients' expectations, decision-making processes and gene therapy-related concerns. METHODS: Using a qualitative approach, we explored perceptions of gene therapy and clinical trials among individuals with LCA. Young adults with a clinical diagnosis of LCA were recruited through the Ocular Genetics Programme at the Hospital for Sick Children. Semi-structured interviews were conducted with ten patients and analysed following the principles of qualitative description. RESULTS: Study participants were aware of ongoing gene therapy research trials and actively sought information regarding advances in ophthalmology and vision restoration. The majority of participants would enrol or were enrolled in a gene-replacement therapy trial, while a minority was ambivalent or would not enrol if provided an opportunity. Participants attributed different values to clinical trials, which influenced their willingness to participate. Intrinsic factors related to coping, adaptation to vision loss and resilience also influenced decision-making. DISCUSSION: This study highlights the complex factors involved in gene-therapy-related decision-making and acts as a proponent for adopting patient-centred care strategies when counselling individuals considering gene therapy or clinical trial participation.


Subject(s)
Leber Congenital Amaurosis , Child , Humans , Young Adult , Leber Congenital Amaurosis/genetics , Leber Congenital Amaurosis/therapy , Genetic Therapy , Vision, Ocular , Blindness/genetics , Blindness/therapy
20.
PLoS One ; 16(12): e0262083, 2021.
Article in English | MEDLINE | ID: mdl-34972179

ABSTRACT

FITNESSGRAM® is the most widely used criterion-referenced tool to assess/report on student health-related fitness across the US. Potential weight-related biases with the two most common tests of musculoskeletal fitness-the trunk extension and Back-Saver Sit-and-Reach (sit-and-reach)-have been hypothesized, though have not been studied. To determine the association between musculoskeletal fitness test performance and weight status, we use data from 571,133 New York City public school 4th-12th grade students (85% non-White; 75% qualified for free or reduced-price meals) with valid/complete 2017-18 FITNESSGRAM® data. Adjusted logistic mixed effects models with a random effect for school examined the association between weight status and whether a student was in the Healthy Fitness Zone (HFZ; met sex- and age-specific criterion-referenced standards) for the trunk extension and sit-and-reach. Compared to students with normal weight, the odds of being in the HFZ for trunk extension were lower for students with underweight (OR = 0.77; 95% CI: 0.741, 0.795) and higher for students with overweight (OR = 1.10; 95% CI: 1.081, 1.122) and obesity (OR = 1.11; 95% CI: 1.090, 1.13). The odds of being in the HFZ for sit-and-reach were lower for students with underweight OR = 0.85; 95% CI: 0.826, 0.878), overweight (OR = 0.83; 95% CI: 0.819, 0.844) and obesity (OR = 0.65; 95% CI: 0.641, 0.661). Students with overweight and obesity perform better on the trunk extension, yet worse on the sit-and-reach, compared to students with normal weight. Teachers, administrators, and researchers should be aware of the relationship of BMI with student performance in these assessments.


Subject(s)
Exercise Test , Health Status , Physical Fitness , Schools , Students , Adolescent , Body Mass Index , Child , Exercise , Female , Humans , Male , New York City , Obesity , Overweight , Thinness , Young Adult
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