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2.
Am J Hum Genet ; 105(2): 413-424, 2019 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-31327508

RESUMO

WD40 repeat-containing proteins form a large family of proteins present in all eukaryotes. Here, we identified five pediatric probands with de novo variants in WDR37, which encodes a member of the WD40 repeat protein family. Two probands shared one variant and the others have variants in nearby amino acids outside the WD40 repeats. The probands exhibited shared phenotypes of epilepsy, colobomas, facial dysmorphology reminiscent of CHARGE syndrome, developmental delay and intellectual disability, and cerebellar hypoplasia. The WDR37 protein is highly conserved in vertebrate and invertebrate model organisms and is currently not associated with a human disease. We generated a null allele of the single Drosophila ortholog to gain functional insights and replaced the coding region of the fly gene CG12333/wdr37 with GAL4. These flies are homozygous viable but display severe bang sensitivity, a phenotype associated with seizures in flies. Additionally, the mutant flies fall when climbing the walls of the vials, suggesting a defect in grip strength, and repeat the cycle of climbing and falling. Similar to wall clinging defect, mutant males often lose grip of the female abdomen during copulation. These phenotypes are rescued by using the GAL4 in the CG12333/wdr37 locus to drive the UAS-human reference WDR37 cDNA. The two variants found in three human subjects failed to rescue these phenotypes, suggesting that these alleles severely affect the function of this protein. Taken together, our data suggest that variants in WDR37 underlie a novel syndromic neurological disorder.

3.
Neurology ; 92(11): e1225-e1237, 2019 Mar 12.
Artigo em Inglês | MEDLINE | ID: mdl-30737337

RESUMO

OBJECTIVE: To describe the leukodystrophy caused by pathogenic variants in LARS2 and KARS, encoding mitochondrial leucyl transfer RNA (tRNA) synthase and mitochondrial and cytoplasmic lysyl tRNA synthase, respectively. METHODS: We composed a group of 5 patients with leukodystrophy, in whom whole-genome or whole-exome sequencing revealed pathogenic variants in LARS2 or KARS. Clinical information, brain MRIs, and postmortem brain autopsy data were collected. We assessed aminoacylation activities of purified mutant recombinant mitochondrial leucyl tRNA synthase and performed aminoacylation assays on patients' lymphoblasts and fibroblasts. RESULTS: Patients had a combination of early-onset deafness and later-onset neurologic deterioration caused by progressive brain white matter abnormalities on MRI. Female patients with LARS2 pathogenic variants had premature ovarian failure. In 2 patients, MRI showed additional signs of early-onset vascular abnormalities. In 2 other patients with LARS2 and KARS pathogenic variants, magnetic resonance spectroscopy revealed elevated white matter lactate, suggesting mitochondrial disease. Pathology in one patient with LARS2 pathogenic variants displayed evidence of primary disease of oligodendrocytes and astrocytes with lack of myelin and deficient astrogliosis. Aminoacylation activities of purified recombinant mutant leucyl tRNA synthase showed a 3-fold loss of catalytic efficiency. Aminoacylation assays on patients' lymphoblasts and fibroblasts showed about 50% reduction of enzyme activity. CONCLUSION: This study adds LARS2 and KARS pathogenic variants as gene defects that may underlie deafness, ovarian failure, and leukodystrophy with mitochondrial signature. We discuss the specific MRI characteristics shared by leukodystrophies caused by mitochondrial tRNA synthase defects. We propose to add aminoacylation assays as biochemical diagnostic tools for leukodystrophies.

4.
Lancet Psychiatry ; 6(3): 225-234, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30744997

RESUMO

BACKGROUND: An increased prevalence of common mental disorders and suicide has been reported among physicians worldwide. We aimed to assess which, if any, interventions are effective at reducing or preventing symptoms of common mental health disorders or suicidality in physicians. METHODS: For this systematic review and meta-analysis MEDLINE, EMBASE, PsycINFO, and Cochrane CENTRAL (database inception to March 26, 2018), reference lists of included studies, and additional sources were systematically searched and screened by two independent reviewers. We included randomised controlled studies or controlled before-after studies of interventions to reduce depression, anxiety, or suicidality in physicians, as assessed by a validated outcome measure. Both organisation-level and physician-directed interventions were considered. Our primary outcome was differences in symptoms of common mental health disorders following intervention. We used random-effects modelling for the main meta-analyses and planned subgroup and sensitivity analyses. The study protocol is registered with PROSPERO, number CRD42018091646. FINDINGS: We identified 2992 articles for screening, of which eight were included in the systematic review (n=1023 physicians) and seven in the meta-analysis. Results indicated a moderate effect in favour of the physician-directed interventions for reduction in symptoms of common mental health disorders (standardised mean difference 0·62; 95% CI 0·40-0·83; p<0·0001). Separate analyses showed physician-directed interventions resulted in reductions of symptoms of depression, anxiety, and suicidality. No evidence of significant heterogeneity was found (Q=3·78; p=0·44). INTERPRETATION: Physician-directed interventions are associated with small reductions in symptoms of common mental health disorders among physicians. Research regarding organisational interventions aimed at improving physicians' mental health via modification of the work environment is urgently needed. FUNDING: Health Workforce Programme, Commonwealth Department of Health, Australian Government, iCare Foundation, and NSW Health.


Assuntos
Transtornos Mentais/terapia , Médicos/psicologia , Ideação Suicida , Ansiedade/terapia , Depressão/terapia , Humanos , Suicídio/prevenção & controle
5.
Neurology ; 92(6): e587-e593, 2019 Feb 05.
Artigo em Inglês | MEDLINE | ID: mdl-30635494

RESUMO

OBJECTIVE: To determine the molecular etiology of disease in 4 individuals from 2 unrelated families who presented with proximal muscle weakness and features suggestive of mitochondrial disease. METHODS: Clinical information and neuroimaging were reviewed. Genome sequencing was performed on affected individuals and biological parents. RESULTS: All affected individuals presented with muscle weakness and difficulty walking. In one family, both children had neonatal respiratory distress while the other family had 2 children with episodic deteriorations. In each family, muscle biopsy demonstrated ragged red fibers. MRI was suggestive of a mitochondrial leukoencephalopathy, with extensive deep cerebral white matter T2 hyperintense signal and selective involvement of the middle blade of the corpus callosum. Through genome sequencing, homozygous GFPT1 missense variants were identified in the affected individuals of each family. The variants detected (p.Arg14Leu and p.Thr151Lys) are absent from population databases and predicted to be damaging by in silico prediction tools. Following the genetic diagnosis, nerve conduction studies were performed and demonstrated a decremental response to repetitive nerve stimulation, confirming the diagnosis of myasthenia. Treatment with pyridostigmine was started in one family with favorable response. CONCLUSIONS: GFPT1 encodes a widely expressed protein that controls the flux of glucose into the hexosamine-biosynthesis pathway that produces precursors for glycosylation of proteins. GFPT1 variants and defects in other enzymes of this pathway have previously been associated with congenital myasthenia. These findings identify leukoencephalopathy as a previously unrecognized phenotype in GFPT1-related disease and suggest that mitochondrial dysfunction could contribute to this disorder.

6.
Am J Hum Genet ; 102(5): 816-831, 2018 05 03.
Artigo em Inglês | MEDLINE | ID: mdl-29706353

RESUMO

Despite the increasing diagnostic rate of genomic sequencing, the genetic basis of more than 50% of heritable kidney disease remains unresolved. Kidney organoids differentiated from induced pluripotent stem cells (iPSCs) of individuals affected by inherited renal disease represent a potential, but unvalidated, platform for the functional validation of novel gene variants and investigation of underlying pathogenetic mechanisms. In this study, trio whole-exome sequencing of a prospectively identified nephronophthisis (NPHP) proband and her parents identified compound-heterozygous variants in IFT140, a gene previously associated with NPHP-related ciliopathies. IFT140 plays a key role in retrograde intraflagellar transport, but the precise downstream cellular mechanisms responsible for disease presentation remain unknown. A one-step reprogramming and gene-editing protocol was used to derive both uncorrected proband iPSCs and isogenic gene-corrected iPSCs, which were differentiated to kidney organoids. Proband organoid tubules demonstrated shortened, club-shaped primary cilia, whereas gene correction rescued this phenotype. Differential expression analysis of epithelial cells isolated from organoids suggested downregulation of genes associated with apicobasal polarity, cell-cell junctions, and dynein motor assembly in proband epithelial cells. Matrigel cyst cultures confirmed a polarization defect in proband versus gene-corrected renal epithelium. As such, this study represents a "proof of concept" for using proband-derived iPSCs to model renal disease and illustrates dysfunctional cellular pathways beyond the primary cilium in the setting of IFT140 mutations, which are established for other NPHP genotypes.

7.
Cell Syst ; 6(2): 245-255.e5, 2018 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-29396323

RESUMO

The human transcriptome is so large, diverse, and dynamic that, even after a decade of investigation by RNA sequencing (RNA-seq), we have yet to resolve its true dimensions. RNA-seq suffers from an expression-dependent bias that impedes characterization of low-abundance transcripts. We performed targeted single-molecule and short-read RNA-seq to survey the transcriptional landscape of a single human chromosome (Hsa21) at unprecedented resolution. Our analysis reaches the lower limits of the transcriptome, identifying a fundamental distinction between protein-coding and noncoding gene content: almost every noncoding exon undergoes alternative splicing, producing a seemingly limitless variety of isoforms. Analysis of syntenic regions of the mouse genome shows that few noncoding exons are shared between human and mouse, yet human splicing profiles are recapitulated on Hsa21 in mouse cells, indicative of regulation by a deeply conserved splicing code. We propose that noncoding exons are functionally modular, with alternative splicing generating an enormous repertoire of potential regulatory RNAs and a rich transcriptional reservoir for gene evolution.

8.
RNA ; 24(4): 597-608, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29246928

RESUMO

MicroRNAs (miRNAs) are highly conserved ∼22 nt small noncoding RNAs that bind partially complementary sequences in target transcripts. MicroRNAs regulate both translation and transcript stability, and play important roles in development, cellular homeostasis, and disease. There are limited approaches available to agnostically identify microRNA targets transcriptome-wide, and methods using miRNA mimics, which in principle identify direct miRNA:transcript pairs, have low sensitivity and specificity. Here, we describe a novel method to identify microRNA targets using miR-29b mimics containing 3-cyanovinylcarbazole (CNVK), a photolabile nucleoside analog. We demonstrate that biotin-tagged, CNVK-containing miR-29b (CNVK-miR-29b) mimics are nontoxic in cell culture, associate with endogenous mammalian Argonaute2, are sensitive for known targets and recapitulate endogenous transcript destabilization. Partnering CNVK-miR-29b with ultra-low-input RNA sequencing, we recover ∼40% of known miR-29b targets and find conservation of the focal adhesion and apoptotic target pathways in mouse and human. We also identify hundreds of novel targets, including NRAS, HOXA10, and KLF11, with a validation rate of 71% for a subset of 73 novel target transcripts interrogated using a high-throughput luciferase assay. Consistent with previous reports, we show that both endogenous miR-29b and CNVK-miR-29b are trafficked to the nucleus, but find no evidence of nuclear-specific miR-29b transcript binding. This may indicate that miR-29b nuclear sequestration is a regulatory mechanism in itself. We suggest that CNVK-containing small RNA mimics may find applicability in other experimental models.


Assuntos
Carbazóis/química , MicroRNAs/metabolismo , Nitrilos/química , RNA Antissenso/genética , Compostos de Vinila/química , Animais , Apoptose/fisiologia , Proteínas Argonauta/química , Caenorhabditis elegans/genética , Proteínas de Ciclo Celular/química , Adesões Focais/metabolismo , GTP Fosfo-Hidrolases/química , Proteínas de Homeodomínio/química , Humanos , Proteínas de Membrana/química , Camundongos , MicroRNAs/química , Proteínas Repressoras/química
9.
Brain ; 140(12): 3105-3111, 2017 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-29186371

RESUMO

Hypomyelinating leukodystrophies are a heterogeneous group of disorders with a clinical presentation that often includes early-onset nystagmus, ataxia and spasticity and a wide range of severity. Using next-generation sequencing techniques and GeneMatcher, we identified four unrelated patients with brain hypomyelination, all with the same recurrent dominant mutation, c.754G>A p.(Asp252Asn), in TMEM106B. The mutation was confirmed as de novo in three of the cases, and the mildly affected father of the fourth affected individual was confirmed as mosaic for this variant. The protein encoded by TMEM106B is poorly characterized but is reported to have a role in regulation of lysosomal trafficking. Polymorphisms in TMEM106B are thought to modify disease onset in frontotemporal dementia, but its relation to myelination is not understood. Clinical presentation in three of the four patients is remarkably benign compared to other hypomyelinating disorders, with congenital nystagmus and mild motor delay. These findings add TMEM106B to the growing list of genes causing hypomyelinating disorders and emphasize the essential role lysosomes play in myelination.

10.
Neurogenetics ; 18(4): 185-194, 2017 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-28842795

RESUMO

An X-linked condition characterized by the combination of hypomyelinating leukodystrophy and spondylometaphyseal dysplasia (H-SMD) has been observed in only four families, with linkage to Xq25-27, and recent genetic characterization in two families with a common AIFM1 mutation. In our study, 12 patients (6 families) with H-SMD were identified and underwent comprehensive assessment accompanied by whole-exome sequencing (WES). Pedigree analysis in all families was consistent with X-linked recessive inheritance. Presentation typically occurred between 12 and 36 months. In addition to the two disease-defining features of spondylometaphyseal dysplasia and hypomyelination on MRI, common clinical signs and symptoms included motor deterioration, spasticity, tremor, ataxia, dysarthria, cognitive defects, pulmonary hypertension, nystagmus, and vision loss due to retinopathy. The course of the disease was slowly progressive. All patients had maternally inherited or de novo mutations in or near exon 7 of AIFM1, within a region of 70 bp, including synonymous and intronic changes. AIFM1 mutations have previously been associated with neurologic presentations as varied as intellectual disability, hearing loss, neuropathy, and striatal necrosis, while AIFM1 mutations in this small region present with a distinct phenotype implicating bone. Analysis of cell lines derived from four patients identified significant reductions in AIFM1 mRNA and protein levels in osteoblasts. We hypothesize that AIFM1 functions in bone metabolism and myelination and is responsible for the unique phenotype in this condition.


Assuntos
Fator de Indução de Apoptose/genética , Genes Ligados ao Cromossomo X/genética , Predisposição Genética para Doença , Mutação/genética , Humanos , Deficiência Intelectual/genética , Masculino , Bainha de Mielina/genética , Bainha de Mielina/metabolismo , Osteocondrodisplasias/genética , Linhagem , Fenótipo , Análise de Sequência de DNA
11.
Am J Hum Genet ; 101(2): 255-266, 2017 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-28777932

RESUMO

Breast cancer risk is strongly associated with an intergenic region on 11q13. We have previously shown that the strongest risk-associated SNPs fall within a distal enhancer that regulates CCND1. Here, we report that, in addition to regulating CCND1, this enhancer regulates two estrogen-regulated long noncoding RNAs, CUPID1 and CUPID2. We provide evidence that the risk-associated SNPs are associated with reduced chromatin looping between the enhancer and the CUPID1 and CUPID2 bidirectional promoter. We further show that CUPID1 and CUPID2 are predominantly expressed in hormone-receptor-positive breast tumors and play a role in modulating pathway choice for the repair of double-strand breaks. These data reveal a mechanism for the involvement of this region in breast cancer.


Assuntos
Neoplasias da Mama/genética , Cromossomos Humanos Par 11/genética , Ciclina D1/genética , Reparo do DNA/genética , RNA Longo não Codificante/genética , Linhagem Celular Tumoral , Cromatina/metabolismo , Quebras de DNA de Cadeia Dupla , Dano ao DNA/genética , Elementos Facilitadores Genéticos/genética , Estrogênios/metabolismo , Feminino , Regulação Neoplásica da Expressão Gênica , Predisposição Genética para Doença/genética , Humanos , Células MCF-7 , Polimorfismo de Nucleotídeo Único/genética , Regiões Promotoras Genéticas/genética , Interferência de RNA , RNA Guia/genética , RNA Interferente Pequeno/genética
12.
JMIR Res Protoc ; 6(3): e42, 2017 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-28292741

RESUMO

BACKGROUND: Diabetes mellitus is Australia's fastest growing chronic disease, and has high comorbidity with depression. Both subthreshold depression and diabetes distress are common amongst people with type 1 or type 2 diabetes, and are associated with poorer diabetes self-care. A need exists for low-intensity self-help interventions for large numbers of people with diabetes and diabetes distress or subthreshold depression, as part of a stepped-care approach to meeting the psychological needs of people with diabetes. Benefit-finding writing is a very brief intervention that involves writing about any positive thoughts and feelings about a stressful experience, such as an illness. Benefit-finding writing has been associated with increases in positive affect and positive growth, and has demonstrated promising results in trials amongst other clinical populations. However, benefit-finding writing has not yet been examined in people with diabetes. OBJECTIVE: The aim of this randomized controlled trial (RCT) is to evaluate the efficacy of an Internet-based benefit-finding writing (iBFW) intervention for adults with type 1 or type 2 diabetes (compared to a control writing condition) for reducing diabetes distress and increasing benefit-finding in diabetes, and also improving a range of secondary outcomes. METHODS: A two-arm RCT will be conducted, using the online program Writing for Health. Adults with type 1 or type 2 diabetes living in Australia will be recruited using diabetes-related publications and websites, and through advertisements in diabetes services and general practitioners' offices. Potential participants will be referred to the study-specific website for participant information and screening. All data will be collected online. Participants will be randomized to either iBFW about diabetes, or a control writing condition of writing about use-of-time. Both conditions involve three daily sessions (once per day for three consecutive days) of 15-minute online writing exercises. Outcome measures will be administered online at baseline, one-month, and three-month follow-ups. RESULTS: This trial is currently underway. The primary outcomes will be diabetes distress and benefit-finding in diabetes. Secondary outcomes will be depression, anxiety, diabetes self-care, perceived health, and health care utilization. We aim to recruit 104 participants. All stages of the study will be conducted online using the Writing for Health program. Group differences will be analyzed on an intention-to-treat basis using mixed models repeated measures. Linguistic analyses of the writing exercise scripts, and examinations of the immediate emotional responses to the writing exercises, will also be undertaken. CONCLUSIONS: This RCT will be the first study to examine iBFW for adults with type 1 or type 2 diabetes. If iBFW is found to be efficacious in reducing diabetes distress and improving diabetes self-care and other outcomes, iBFW may offer the potential to be a low-cost, easily accessible self-help intervention to improve the wellbeing of adults with diabetes. TRIAL REGISTRATION: Australia and New Zealand Clinical Trials Registry (ACTRN12615000241538).

13.
Am J Med Genet A ; 170(10): 2694-7, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27345729

RESUMO

Hennekam lymphangiectasia-lymphedema syndrome is an autosomal recessive disorder, with 25% of patients having mutations in CCBE1. We identified a family with two brothers presenting with primary lymphedema, and performed exome sequencing to determine the cause of their disease. Analysis of four family members showed that both affected brothers had the same rare compound heterozygous mutations in CCBE1. The presumed paternally inherited NM_133459.3:c.310G>A; p.(Asp104Asn), lies adjacent to other known pathogenic CCBE1 mutations, while the maternally inherited NM_133459.3:c.80T>C; p.(Leu27Pro) lies in the CCBE1 signal peptide, which has not previously been associated with disease. Functional analysis in a zebrafish model of lymphatic disease showed that both mutations lead to CCBE1 loss of function, confirming the pathogenicity of these variants and expanding the genotypic spectrum of lymphatic disorders. © 2016 Wiley Periodicals, Inc.


Assuntos
Proteínas de Ligação ao Cálcio/genética , Anormalidades Craniofaciais/diagnóstico , Anormalidades Craniofaciais/genética , Genótipo , Linfangiectasia Intestinal/diagnóstico , Linfangiectasia Intestinal/genética , Linfedema/diagnóstico , Linfedema/genética , Mutação , Proteínas Supressoras de Tumor/genética , Alelos , Sequência de Aminoácidos , Animais , Linhagem Celular , Expressão Gênica , Frequência do Gene , Humanos , Recém-Nascido , Masculino , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA , Peixe-Zebra
14.
Sci Rep ; 6: 26657, 2016 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-27226347

RESUMO

Thousands of sense-antisense mRNA-lncRNA gene pairs occur in the mammalian genome. While there is usually little doubt about the function of the coding transcript, the function of the lncRNA partner is mostly untested. Here we examine the function of the homeotic Evx1-Evx1as gene locus. Expression is tightly co-regulated in posterior mesoderm of mouse embryos and in embryoid bodies. Expression of both genes is enhanced by BMP4 and WNT3A, and reduced by Activin. We generated a suite of deletions in the locus by CRISPR-Cas9 editing. We show EVX1 is a critical downstream effector of BMP4 and WNT3A with respect to patterning of posterior mesoderm. The lncRNA, Evx1as arises from alternative promoters and is difficult to fully abrogate by gene editing or siRNA approaches. Nevertheless, we were able to generate a large 2.6 kb deletion encompassing the shared promoter with Evx1 and multiple additional exons of Evx1as. This led to an identical dorsal-ventral patterning defect to that generated by micro-deletion in the DNA-binding domain of EVX1. Thus, Evx1as has no function independent of EVX1, and is therefore unlikely to act in trans. We predict many antisense lncRNAs have no specific trans function, possibly only regulating the linked coding genes in cis.


Assuntos
Padronização Corporal/fisiologia , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/fisiologia , Embrião de Mamíferos/embriologia , Gastrulação/fisiologia , Regulação da Expressão Gênica no Desenvolvimento/fisiologia , Proteínas de Homeodomínio/biossíntese , RNA Longo não Codificante/biossíntese , Animais , Proteína Morfogenética Óssea 4/genética , Proteína Morfogenética Óssea 4/metabolismo , Sistemas CRISPR-Cas , Edição de Genes , Proteínas de Homeodomínio/genética , Camundongos , RNA Longo não Codificante/genética , Proteína Wnt3A/genética , Proteína Wnt3A/metabolismo
15.
Genome Res ; 26(5): 705-16, 2016 05.
Artigo em Inglês | MEDLINE | ID: mdl-27197243

RESUMO

Targeted RNA sequencing (CaptureSeq) uses oligonucleotide probes to capture RNAs for sequencing, providing enriched read coverage, accurate measurement of gene expression, and quantitative expression data. We applied CaptureSeq to refine transcript annotations in the current murine GRCm38 assembly. More than 23,000 regions corresponding to putative or annotated long noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted sequencing across five mouse tissues and three brain subregions. The results illustrate that the mouse transcriptome is considerably more complex than previously thought. We assemble more complete transcript isoforms than GENCODE, expand transcript boundaries, and connect interspersed islands of mapped reads. We describe a novel filtering pipeline that identifies previously unannotated but high-quality transcript isoforms. In this set, 911 GENCODE neighboring genes are condensed into 400 expanded gene models. Additionally, 594 GENCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq. Finally, we validate our observations using current FANTOM and Mouse ENCODE resources.


Assuntos
Perfilação da Expressão Gênica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , RNA Longo não Codificante/biossíntese , RNA Longo não Codificante/genética , Transcriptoma , Animais , Camundongos
16.
Ann Neurol ; 79(6): 1031-1037, 2016 06.
Artigo em Inglês | MEDLINE | ID: mdl-27159321

RESUMO

Here we report whole exome sequencing (WES) on a cohort of 71 patients with persistently unresolved white matter abnormalities with a suspected diagnosis of leukodystrophy or genetic leukoencephalopathy. WES analyses were performed on trio, or greater, family groups. Diagnostic pathogenic variants were identified in 35% (25 of 71) of patients. Potentially pathogenic variants were identified in clinically relevant genes in a further 7% (5 of 71) of cases, giving a total yield of clinical diagnoses in 42% of individuals. These findings provide evidence that WES can substantially decrease the number of unresolved white matter cases. Ann Neurol 2016;79:1031-1037.


Assuntos
Análise Mutacional de DNA , Exoma/genética , Leucoencefalopatias/diagnóstico , Leucoencefalopatias/genética , Substância Branca/patologia , Adolescente , Adulto , Criança , Pré-Escolar , Feminino , Humanos , Leucoencefalopatias/patologia , Masculino , Mutação , Adulto Jovem
17.
Am J Hum Genet ; 96(4): 675-81, 2015 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-25817015

RESUMO

Mutations in genes encoding aminoacyl-tRNA synthetases are known to cause leukodystrophies and genetic leukoencephalopathies-heritable disorders that result in white matter abnormalities in the central nervous system. Here we report three individuals (two siblings and an unrelated individual) with severe infantile epileptic encephalopathy, clubfoot, absent deep tendon reflexes, extrapyramidal symptoms, and persistently deficient myelination on MRI. Analysis by whole exome sequencing identified mutations in the nuclear-encoded alanyl-tRNA synthetase (AARS) in these two unrelated families: the two affected siblings are compound heterozygous for p.Lys81Thr and p.Arg751Gly AARS, and the single affected child is homozygous for p.Arg751Gly AARS. The two identified mutations were found to result in a significant reduction in function. Mutations in AARS were previously associated with an autosomal-dominant inherited form of axonal neuropathy, Charcot-Marie-Tooth disease type 2N (CMT2N). The autosomal-recessive AARS mutations identified in the individuals described here, however, cause a severe infantile epileptic encephalopathy with a central myelin defect and peripheral neuropathy, demonstrating that defects of alanyl-tRNA charging can result in a wide spectrum of disease manifestations.


Assuntos
Anormalidades Múltiplas/genética , Alanina-tRNA Ligase/genética , Epilepsia/genética , Modelos Moleculares , Bainha de Mielina/patologia , Doenças do Sistema Nervoso Periférico/genética , Fenótipo , Anormalidades Múltiplas/patologia , Alanina-tRNA Ligase/química , Sequência de Aminoácidos , Sequência de Bases , Epilepsia/patologia , Genes Recessivos/genética , Humanos , Lactente , Recém-Nascido , Dados de Sequência Molecular , Mutação/genética , Doenças do Sistema Nervoso Periférico/patologia , Estudos Prospectivos , Análise de Sequência de DNA , Síndrome , Estados Unidos
18.
Nat Methods ; 12(4): 339-42, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25751143

RESUMO

We compared quantitative RT-PCR (qRT-PCR), RNA-seq and capture sequencing (CaptureSeq) in terms of their ability to assemble and quantify long noncoding RNAs and novel coding exons across 20 human tissues. CaptureSeq was superior for the detection and quantification of genes with low expression, showed little technical variation and accurately measured differential expression. This approach expands and refines previous annotations and simultaneously generates an expression atlas.


Assuntos
Perfilação da Expressão Gênica , RNA Longo não Codificante/genética , RNA/genética , Análise de Sequência/métodos , Humanos , Células K562 , Reação em Cadeia da Polimerase , RNA/sangue , RNA/química
20.
Genome Res ; 25(2): 290-303, 2015 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-25561518

RESUMO

During the splicing reaction, the 5' intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate into the mature RNA and forming an intron lariat, which is excised. Despite a critical role in gene splicing, the locations and features of human splicing branchpoints are largely unknown. We use exoribonuclease digestion and targeted RNA-sequencing to enrich for sequences that traverse the lariat junction and, by split and inverted alignment, reveal the branchpoint. We identify 59,359 high-confidence human branchpoints in >10,000 genes, providing a first map of splicing branchpoints in the human genome. Branchpoints are predominantly adenosine, highly conserved, and closely distributed to the 3' splice site. Analysis of human branchpoints reveals numerous novel features, including distinct features of branchpoints for alternatively spliced exons and a family of conserved sequence motifs overlapping branchpoints we term B-boxes, which exhibit maximal nucleotide diversity while maintaining interactions with the keto-rich U2 snRNA. Different B-box motifs exhibit divergent usage in vertebrate lineages and associate with other splicing elements and distinct intron-exon architectures, suggesting integration within a broader regulatory splicing code. Lastly, although branchpoints are refractory to common mutational processes and genetic variation, mutations occurring at branchpoint nucleotides are enriched for disease associations.


Assuntos
Sequência Consenso , Genômica , Íntrons , Processamento de RNA , Processamento Alternativo , Animais , Biologia Computacional/métodos , Evolução Molecular , Éxons , Variação Genética , Genômica/métodos , Humanos , Motivos de Nucleotídeos , Matrizes de Pontuação de Posição Específica , Sítios de Splice de RNA
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