Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 42
Filtrar
Filtros adicionais











País/Região como assunto
Intervalo de ano
1.
J Clin Res Pediatr Endocrinol ; 11(3): 319-326, 2019 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-30563316

RESUMO

Primary polyneuropathy in the context of Seip-Berardinelli type 1 seipinopathy, or congenital generalized lipodystrophy type 1 (CGL1) has not been previously reported. We report the case history of a 27 year old female CGL1 patient presenting with an unusual additional development of non-diabetic peripheral neuropathy and learning disabilities in early adolescence. Whole exome sequencing (WES) of the patient genome identified a novel variant, homozygous for a 52 bp intronic deletion in the AGPAT2 locus, coding for 1-acylglycerol-3-phosphate O-acyltransferase 2, which is uniquely associated with CGL1 seipinopathies, with no molecular evidence for dual diagnosis. Functional studies using RNA isolated from patient peripheral blood leucocytes showed abnormal RNA splicing resulting in the loss of 25 amino acids from the patient AGPAT2 protein coding sequence. Stability and transcription levels for the misspliced AGPAT2 mRNA in our patient nonetheless remained normal. Any AGPAT2 protein produced in our patient is therefore likely to be dysfunctional. However, formal linkage of this deletion to the neuropathy observed remains to be shown. The classical clinical presentation of a patient with AGPAT2-associated lipodystrophy shows normal cognition and no development of polyneuropathy. Cognitive disabilities and polyneuropathy are features associated exclusively with clinical CGL type 2 arising from seipin (BSCL2) gene mutations. This case study suggests that in some genetic contexts, AGPAT2 mutations can also produce phenotypes with primary polyneuropathy.

2.
Eur J Hum Genet ; 26(8): 1121-1131, 2018 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-29706646

RESUMO

Malformations of cortical development (MCDs) manifest with structural brain anomalies that lead to neurologic sequelae, including epilepsy, cerebral palsy, developmental delay, and intellectual disability. To investigate the underlying genetic architecture of patients with disorders of cerebral cortical development, a cohort of 54 patients demonstrating neuroradiologic signs of MCDs was investigated. Individual genomes were interrogated for single-nucleotide variants (SNV) and copy number variants (CNV) with whole-exome sequencing and chromosomal microarray studies. Variation affecting known MCDs-associated genes was found in 16/54 cases, including 11 patients with SNV, 2 patients with CNV, and 3 patients with both CNV and SNV, at distinct loci. Diagnostic pathogenic SNV and potentially damaging variants of unknown significance (VUS) were identified in two groups of seven individuals each. We demonstrated that de novo variants are important among patients with MCDs as they were identified in 10/16 individuals with a molecular diagnosis. Three patients showed changes in known MCDs genes  and a clinical phenotype beyond the usual characteristics observed, i.e., phenotypic expansion, for a particular known disease gene clinical entity. We also discovered 2 likely candidate genes, CDH4, and ASTN1, with human and animal studies supporting their roles in brain development, and 5 potential candidate genes. Our findings emphasize genetic heterogeneity of MCDs disorders and postulate potential novel candidate genes involved in cerebral cortical development.

3.
Genome Med ; 9(1): 26, 2017 03 21.
Artigo em Inglês | MEDLINE | ID: mdl-28327206

RESUMO

BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease. Pilot project data included 74 families, consisting mostly of parent-offspring trios. Analyses performed on a research basis employed both WES from additional family members and complementary bioinformatics approaches and protocols. RESULTS: Analysis of all possible modes of Mendelian inheritance, focusing on both single nucleotide variants (SNV) and copy number variant (CNV) alleles, yielded a likely contributory variant in 36% (27/74) of cases. If one includes candidate genes with variants identified within a single family, a potential contributory variant was identified in a total of ~51% (38/74) of cases enrolled in this pilot study. The molecular diagnosis was achieved in 30/63 trios (47.6%). Besides this, the analysis workflow yielded evidence for pathogenic variants in disease-associated genes in 4/6 singleton cases (66.6%), 1/1 multiplex family involving three affected siblings, and 3/4 (75%) quartet families. Both the analytical pipeline and the collaborative efforts between the diagnostic and research laboratories provided insights that allowed recent disease gene discoveries (PURA, TANGO2, EMC1, GNB5, ATAD3A, and MIPEP) and increased the number of novel genes, defined in this study as genes identified in more than one family (DHX30 and EBF3). CONCLUSION: An efficient genomics pipeline in which clinical sequencing in a diagnostic laboratory is followed by the detailed reanalysis of unsolved cases in a research environment, supplemented with WES data from additional family members, and subject to adjuvant bioinformatics analyses including relaxed variant filtering parameters in informatics pipelines, can enhance the molecular diagnostic yield and provide mechanistic insights into Mendelian disorders. Implementing these approaches requires collaborative clinical molecular diagnostic and research efforts.


Assuntos
Biologia Computacional/métodos , Variações do Número de Cópias de DNA , Doenças Genéticas Inatas/diagnóstico , Genômica/métodos , Polimorfismo de Nucleotídeo Único , Análise de Sequência de DNA/métodos , ATPases Associadas a Diversas Atividades Celulares , Adenosina Trifosfatases/genética , Proteínas de Ligação a DNA/genética , Exoma , Feminino , Subunidades beta da Proteína de Ligação ao GTP/genética , Doenças Genéticas Inatas/genética , Doenças Genéticas Inatas/metabolismo , Humanos , Masculino , Proteínas de Membrana/genética , Metaloendopeptidases/genética , Proteínas Mitocondriais/genética , Projetos Piloto , Fatores de Transcrição/genética
4.
J Allergy Clin Immunol ; 139(1): 232-245, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-27577878

RESUMO

BACKGROUND: Primary immunodeficiency diseases (PIDDs) are clinically and genetically heterogeneous disorders thus far associated with mutations in more than 300 genes. The clinical phenotypes derived from distinct genotypes can overlap. Genetic etiology can be a prognostic indicator of disease severity and can influence treatment decisions. OBJECTIVE: We sought to investigate the ability of whole-exome screening methods to detect disease-causing variants in patients with PIDDs. METHODS: Patients with PIDDs from 278 families from 22 countries were investigated by using whole-exome sequencing. Computational copy number variant (CNV) prediction pipelines and an exome-tiling chromosomal microarray were also applied to identify intragenic CNVs. Analytic approaches initially focused on 475 known or candidate PIDD genes but were nonexclusive and further tailored based on clinical data, family history, and immunophenotyping. RESULTS: A likely molecular diagnosis was achieved in 110 (40%) unrelated probands. Clinical diagnosis was revised in about half (60/110) and management was directly altered in nearly a quarter (26/110) of families based on molecular findings. Twelve PIDD-causing CNVs were detected, including 7 smaller than 30 Kb that would not have been detected with conventional diagnostic CNV arrays. CONCLUSION: This high-throughput genomic approach enabled detection of disease-related variants in unexpected genes; permitted detection of low-grade constitutional, somatic, and revertant mosaicism; and provided evidence of a mutational burden in mixed PIDD immunophenotypes.


Assuntos
Síndromes de Imunodeficiência/genética , Adolescente , Adulto , Idoso , Criança , Pré-Escolar , Variações do Número de Cópias de DNA , Feminino , Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Adulto Jovem
6.
J Allergy Clin Immunol ; 138(4): 1142-1151.e2, 2016 10.
Artigo em Inglês | MEDLINE | ID: mdl-27484032

RESUMO

BACKGROUND: Primary immunodeficiency diseases (PIDDs) are inherited disorders of the immune system. The most severe form, severe combined immunodeficiency (SCID), presents with profound deficiencies of T cells, B cells, or both at birth. If not treated promptly, affected patients usually do not live beyond infancy because of infections. Genetic heterogeneity of SCID frequently delays the diagnosis; a specific diagnosis is crucial for life-saving treatment and optimal management. OBJECTIVE: We developed a next-generation sequencing (NGS)-based multigene-targeted panel for SCID and other severe PIDDs requiring rapid therapeutic actions in a clinical laboratory setting. METHODS: The target gene capture/NGS assay provides an average read depth of approximately 1000×. The deep coverage facilitates simultaneous detection of single nucleotide variants and exonic copy number variants in one comprehensive assessment. Exons with insufficient coverage (<20× read depth) or high sequence homology (pseudogenes) are complemented by amplicon-based sequencing with specific primers to ensure 100% coverage of all targeted regions. RESULTS: Analysis of 20 patient samples with low T-cell receptor excision circle numbers on newborn screening or a positive family history or clinical suspicion of SCID or other severe PIDD identified deleterious mutations in 14 of them. Identified pathogenic variants included both single nucleotide variants and exonic copy number variants, such as hemizygous nonsense, frameshift, and missense changes in IL2RG; compound heterozygous changes in ATM, RAG1, and CIITA; homozygous changes in DCLRE1C and IL7R; and a heterozygous nonsense mutation in CHD7. CONCLUSION: High-throughput deep sequencing analysis with complete clinical validation greatly increases the diagnostic yield of severe primary immunodeficiency. Establishing a molecular diagnosis enables early immune reconstitution through prompt therapeutic intervention and guides management for improved long-term quality of life.


Assuntos
Análise de Sequência de DNA , Imunodeficiência Combinada Severa/diagnóstico , Imunodeficiência Combinada Severa/genética , Adolescente , Criança , Feminino , Variação Genética , Humanos , Masculino , Patologia Molecular/normas , Patologia Molecular/tendências
7.
Am J Hum Genet ; 99(3): 704-710, 2016 09 01.
Artigo em Inglês | MEDLINE | ID: mdl-27523599

RESUMO

GNB5 encodes the G protein ß subunit 5 and is involved in inhibitory G protein signaling. Here, we report mutations in GNB5 that are associated with heart-rate disturbance, eye disease, intellectual disability, gastric problems, hypotonia, and seizures in nine individuals from six families. We observed an association between the nature of the variants and clinical severity; individuals with loss-of-function alleles had more severe symptoms, including substantial developmental delay, speech defects, severe hypotonia, pathological gastro-esophageal reflux, retinal disease, and sinus-node dysfunction, whereas related heterozygotes harboring missense variants presented with a clinically milder phenotype. Zebrafish gnb5 knockouts recapitulated the phenotypic spectrum of affected individuals, including cardiac, neurological, and ophthalmological abnormalities, supporting a direct role of GNB5 in the control of heart rate, hypotonia, and vision.


Assuntos
Bradicardia/genética , Bradicardia/fisiopatologia , Deficiências do Desenvolvimento/genética , Subunidades beta da Proteína de Ligação ao GTP/genética , Genes Recessivos/genética , Mutação/genética , Nó Sinoatrial/fisiopatologia , Adolescente , Animais , Criança , Deficiências do Desenvolvimento/fisiopatologia , Feminino , Subunidades beta da Proteína de Ligação ao GTP/deficiência , Refluxo Gastroesofágico/genética , Refluxo Gastroesofágico/fisiopatologia , Deleção de Genes , Frequência Cardíaca/genética , Heterozigoto , Humanos , Masculino , Hipotonia Muscular/genética , Mutação de Sentido Incorreto/genética , Linhagem , Fenótipo , Doenças Retinianas/genética , Doenças Retinianas/fisiopatologia , Convulsões/genética , Síndrome , Adulto Jovem , Peixe-Zebra/genética , Peixe-Zebra/fisiologia
8.
Pediatr Neurol ; 60: 83-7, 2016 07.
Artigo em Inglês | MEDLINE | ID: mdl-27343026

RESUMO

BACKGROUND: Progressive encephalopathy with edema, hypsarrhythmia and optic atrophy (PEHO) syndrome is a distinct neurodevelopmental disorder. Patients without optic nerve atrophy and brain imaging abnormalities but fulfilling other PEHO criteria are often described as a PEHO-like syndrome. The molecular bases of both clinically defined conditions remain unknown in spite of the widespread application of genome analyses in both clinic and research. METHODS: We enrolled two patients with a prior diagnosis of PEHO and two individuals with PEHO-like syndrome. All four individuals subsequently underwent whole-exome sequencing and comprehensive genomic analysis. RESULTS: We identified disease-causing mutations in known genes associated with neurodevelopmental disorders including GNAO1 and CDKL5 in two of four individuals. One patient with PEHO syndrome and a de novoGNAO1 mutation was found to have an additional de novo mutation in HESX1 that is associated with optic atrophy. CONCLUSIONS: We hypothesize that PEHO and PEHO-like syndrome may represent a severe end of the spectrum of the early-onset encephalopathies and, in some instances, its complex phenotype may result from an aggregated effect of mutations at two loci.


Assuntos
Edema Encefálico/genética , Doenças Neurodegenerativas/genética , Atrofia Óptica/genética , Espasmos Infantis/genética , Edema Encefálico/diagnóstico por imagem , Edema Encefálico/patologia , Criança , Pré-Escolar , Feminino , Subunidades alfa Gi-Go de Proteínas de Ligação ao GTP/genética , Humanos , Lactente , Masculino , Mutação , Doenças Neurodegenerativas/diagnóstico por imagem , Doenças Neurodegenerativas/patologia , Atrofia Óptica/diagnóstico por imagem , Atrofia Óptica/patologia , Fenótipo , Proteínas Serina-Treonina Quinases/genética , Espasmos Infantis/diagnóstico por imagem , Espasmos Infantis/patologia
9.
Genet Med ; 18(7): 678-85, 2016 07.
Artigo em Inglês | MEDLINE | ID: mdl-26633545

RESUMO

PURPOSE: Whole-exome sequencing (WES) is increasingly used as a diagnostic tool in medicine, but prior reports focus on predominantly pediatric cohorts with neurologic or developmental disorders. We describe the diagnostic yield and characteristics of WES in adults. METHODS: We performed a retrospective analysis of consecutive WES reports for adults from a diagnostic laboratory. Phenotype composition was determined using Human Phenotype Ontology terms. RESULTS: Molecular diagnoses were reported for 17.5% (85/486) of adults, which is lower than that for a primarily pediatric population (25.2%; P = 0.0003); the diagnostic rate was higher (23.9%) for those 18-30 years of age compared to patients older than 30 years (10.4%; P = 0.0001). Dual Mendelian diagnoses contributed to 7% of diagnoses, revealing blended phenotypes. Diagnoses were more frequent among individuals with abnormalities of the nervous system, skeletal system, head/neck, and growth. Diagnostic rate was independent of family history information, and de novo mutations contributed to 61.4% of autosomal dominant diagnoses. CONCLUSION: Early WES experience in adults demonstrates molecular diagnoses in a substantial proportion of patients, informing clinical management, recurrence risk, and recommendations for relatives. A positive family history was not predictive, consistent with molecular diagnoses often revealed by de novo events, informing the Mendelian basis of genetic disease in adults.Genet Med 18 7, 678-685.


Assuntos
Doenças Genéticas Inatas/diagnóstico , Testes Genéticos , Genoma Humano , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Adulto , Exoma/genética , Feminino , Doenças Genéticas Inatas/epidemiologia , Predisposição Genética para Doença , Humanos , Masculino , Patologia Molecular/métodos
10.
Genet Med ; 18(5): 443-51, 2016 05.
Artigo em Inglês | MEDLINE | ID: mdl-26378787

RESUMO

PURPOSE: Charcot-Marie-Tooth (CMT) disease is a heterogeneous group of genetic disorders of the peripheral nervous system. Copy-number variants (CNVs) contribute significantly to CMT, as duplication of PMP22 underlies the majority of CMT1 cases. We hypothesized that CNVs and/or single-nucleotide variants (SNVs) might exist in patients with CMT with an unknown molecular genetic etiology. METHODS: Two hundred patients with CMT, negative for both SNV mutations in several CMT genes and for CNVs involving PMP22, were screened for CNVs by high-resolution oligonucleotide array comparative genomic hybridization. Whole-exome sequencing was conducted on individuals with rare, potentially pathogenic CNVs. RESULTS: Putatively causative CNVs were identified in five subjects (~2.5%); four of the five map to known neuropathy genes. Breakpoint sequencing revealed Alu-Alu-mediated junctions as a predominant contributor. Exome sequencing identified MFN2 SNVs in two of the individuals. CONCLUSION: Neuropathy-associated CNV outside of the PMP22 locus is rare in CMT. Nevertheless, there is potential clinical utility in testing for CNVs and exome sequencing in CMT cases negative for the CMT1A duplication. These findings suggest that complex phenotypes including neuropathy can potentially be caused by a combination of SNVs and CNVs affecting more than one disease-associated locus and contributing to a mutational burden.Genet Med 18 5, 443-451.


Assuntos
Doença de Charcot-Marie-Tooth/genética , GTP Fosfo-Hidrolases/genética , Proteínas Mitocondriais/genética , Proteínas da Mielina/genética , Polineuropatias/genética , Adulto , Idade de Início , Doença de Charcot-Marie-Tooth/fisiopatologia , Pré-Escolar , Hibridização Genômica Comparativa , Variações do Número de Cópias de DNA/genética , Exoma/genética , Feminino , Predisposição Genética para Doença , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Masculino , Neurônios Motores/metabolismo , Neurônios Motores/patologia , Proteína P0 da Mielina/genética , Condução Nervosa/genética , Polimorfismo de Nucleotídeo Único/genética , Polineuropatias/fisiopatologia
11.
Neuron ; 88(3): 499-513, 2015 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-26539891

RESUMO

Development of the human nervous system involves complex interactions among fundamental cellular processes and requires a multitude of genes, many of which remain to be associated with human disease. We applied whole exome sequencing to 128 mostly consanguineous families with neurogenetic disorders that often included brain malformations. Rare variant analyses for both single nucleotide variant (SNV) and copy number variant (CNV) alleles allowed for identification of 45 novel variants in 43 known disease genes, 41 candidate genes, and CNVs in 10 families, with an overall potential molecular cause identified in >85% of families studied. Among the candidate genes identified, we found PRUNE, VARS, and DHX37 in multiple families and homozygous loss-of-function variants in AGBL2, SLC18A2, SMARCA1, UBQLN1, and CPLX1. Neuroimaging and in silico analysis of functional and expression proximity between candidate and known disease genes allowed for further understanding of genetic networks underlying specific types of brain malformations.


Assuntos
Encéfalo/patologia , Redes Reguladoras de Genes/genética , Variação Genética/genética , Análise da Randomização Mendeliana/métodos , Doenças do Sistema Nervoso/diagnóstico , Doenças do Sistema Nervoso/genética , Encéfalo/anormalidades , Estudos de Coortes , Bases de Dados Genéticas , Feminino , Estudos de Associação Genética/métodos , Humanos , Masculino , Linhagem
12.
J Clin Neuromuscul Dis ; 17(2): 69-71, 2015 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-26583493

RESUMO

OBJECTIVE: In the past decade, hereditary forms of motor neuron disease (spinal muscular atrophy and/or amyotrophic lateral sclerosis) are increasingly identified. As advanced genetic testing is performed, molecular diagnosis can be obtained. Identifying new gene mutations can lead to further understanding of disease. METHODS AND RESULTS: We report a single case of a patient with early-onset amyotrophic lateral sclerosis, evaluated at University of Texas Health Houston Science Center from 2011-2014. Initial genetic testing did not reveal an etiology in this patient. Through whole-exome sequencing, a VRK1 mutation was identified. CONCLUSIONS AND RELEVANCE: We identify a possible new cause of hereditary amyotrophic lateral sclerosis, VRK1 mutation. This case report also expands the phenotypic spectrum of this mutation in neurologic diseases.


Assuntos
Peptídeos e Proteínas de Sinalização Intracelular/genética , Doença dos Neurônios Motores/genética , Mutação/genética , Proteínas Serina-Treonina Quinases/genética , Adulto , Biologia Computacional , Testes Genéticos , Humanos , Masculino , Doença dos Neurônios Motores/patologia , Músculo Esquelético/patologia , Fenótipo
13.
Cell Rep ; 12(7): 1169-83, 2015 Aug 18.
Artigo em Inglês | MEDLINE | ID: mdl-26257172

RESUMO

Charcot-Marie-Tooth (CMT) disease is a clinically and genetically heterogeneous distal symmetric polyneuropathy. Whole-exome sequencing (WES) of 40 individuals from 37 unrelated families with CMT-like peripheral neuropathy refractory to molecular diagnosis identified apparent causal mutations in ∼ 45% (17/37) of families. Three candidate disease genes are proposed, supported by a combination of genetic and in vivo studies. Aggregate analysis of mutation data revealed a significantly increased number of rare variants across 58 neuropathy-associated genes in subjects versus controls, confirmed in a second ethnically discrete neuropathy cohort, suggesting that mutation burden potentially contributes to phenotypic variability. Neuropathy genes shown to have highly penetrant Mendelizing variants (HPMVs) and implicated by burden in families were shown to interact genetically in a zebrafish assay exacerbating the phenotype established by the suppression of single genes. Our findings suggest that the combinatorial effect of rare variants contributes to disease burden and variable expressivity.


Assuntos
Doença de Charcot-Marie-Tooth/genética , Exoma , Carga Genética , Doenças do Sistema Nervoso Periférico/genética , Fenótipo , Animais , Feminino , Variação Genética , Proteínas de Choque Térmico HSP40/genética , Humanos , Masculino , Mutação , Proteína P2 de Mielina/genética , Linhagem , Penetrância , Serina C-Palmitoiltransferase/genética , Supressão Genética , Peixe-Zebra
14.
Am J Hum Genet ; 97(2): 199-215, 2015 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-26166479

RESUMO

Discovering the genetic basis of a Mendelian phenotype establishes a causal link between genotype and phenotype, making possible carrier and population screening and direct diagnosis. Such discoveries also contribute to our knowledge of gene function, gene regulation, development, and biological mechanisms that can be used for developing new therapeutics. As of February 2015, 2,937 genes underlying 4,163 Mendelian phenotypes have been discovered, but the genes underlying ∼50% (i.e., 3,152) of all known Mendelian phenotypes are still unknown, and many more Mendelian conditions have yet to be recognized. This is a formidable gap in biomedical knowledge. Accordingly, in December 2011, the NIH established the Centers for Mendelian Genomics (CMGs) to provide the collaborative framework and infrastructure necessary for undertaking large-scale whole-exome sequencing and discovery of the genetic variants responsible for Mendelian phenotypes. In partnership with 529 investigators from 261 institutions in 36 countries, the CMGs assessed 18,863 samples from 8,838 families representing 579 known and 470 novel Mendelian phenotypes as of January 2015. This collaborative effort has identified 956 genes, including 375 not previously associated with human health, that underlie a Mendelian phenotype. These results provide insight into study design and analytical strategies, identify novel mechanisms of disease, and reveal the extensive clinical variability of Mendelian phenotypes. Discovering the gene underlying every Mendelian phenotype will require tackling challenges such as worldwide ascertainment and phenotypic characterization of families affected by Mendelian conditions, improvement in sequencing and analytical techniques, and pervasive sharing of phenotypic and genomic data among researchers, clinicians, and families.


Assuntos
Doenças Genéticas Inatas/genética , Genética Médica/métodos , Genética Médica/tendências , Fenótipo , Proteínas/genética , Humanos
15.
Genome Med ; 7(1): 54, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26195989

RESUMO

BACKGROUND: Besides its growing importance in clinical diagnostics and understanding the genetic basis of Mendelian and complex diseases, whole exome sequencing (WES) is a rich source of additional information of potential clinical utility for physicians, patients and their families. We analyzed the frequency and nature of single nucleotide variants (SNVs) considered secondary findings and recessive disease allele carrier status in the exomes of 8554 individuals from a large, randomly sampled cohort study and 2514 patients from a study of presumed Mendelian disease having undergone WES. METHODS: We used the same sequencing platform and data processing pipeline to analyze all samples and characterized the distributions of reported pathogenic (ClinVar, Human Gene Mutation Database (HGMD)) and predicted deleterious variants in the pre-specified American College of Medical Genetics and Genomics (ACMG) secondary findings and recessive disease genes in different ethnic groups. RESULTS: In the 56 ACMG secondary findings genes, the average number of predicted deleterious variants per individual was 0.74, and the mean number of ClinVar reported pathogenic variants was 0.06. We observed an average of 10 deleterious and 0.78 ClinVar reported pathogenic variants per individual in 1423 autosomal recessive disease genes. By repeatedly sampling pairs of exomes, 0.5 % of the randomly generated couples were at 25 % risk of having an affected offspring for an autosomal recessive disorder based on the ClinVar variants. CONCLUSIONS: By investigating reported pathogenic and novel, predicted deleterious variants we estimated the lower and upper limits of the population fraction for which exome sequencing may reveal additional medically relevant information. We suggest that the observed wide range for the lower and upper limits of these frequency numbers will be gradually reduced due to improvement in classification databases and prediction algorithms.

16.
Nat Genet ; 47(6): 654-60, 2015 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-25894502

RESUMO

Unbiased genetic studies have uncovered surprising molecular mechanisms in human cellular immunity and autoimmunity. We performed whole-exome sequencing and targeted sequencing in five families with an apparent mendelian syndrome of autoimmunity characterized by high-titer autoantibodies, inflammatory arthritis and interstitial lung disease. We identified four unique deleterious variants in the COPA gene (encoding coatomer subunit α) affecting the same functional domain. Hypothesizing that mutant COPA leads to defective intracellular transport via coat protein complex I (COPI), we show that COPA variants impair binding to proteins targeted for retrograde Golgi-to-ER transport. Additionally, expression of mutant COPA results in ER stress and the upregulation of cytokines priming for a T helper type 17 (TH17) response. Patient-derived CD4(+) T cells also demonstrate significant skewing toward a TH17 phenotype that is implicated in autoimmunity. Our findings uncover an unexpected molecular link between a vesicular transport protein and a syndrome of autoimmunity manifested by lung and joint disease.


Assuntos
Artrite/genética , Doenças Autoimunes/genética , Proteína Coatomer/genética , Complexo de Golgi/metabolismo , Doenças Pulmonares Intersticiais/genética , Sequência de Aminoácidos , Pré-Escolar , Retículo Endoplasmático/metabolismo , Estresse do Retículo Endoplasmático , Feminino , Estudos de Associação Genética , Predisposição Genética para Doença , Células HEK293 , Humanos , Lactente , Escore Lod , Masculino , Dados de Sequência Molecular , Linhagem , Transporte Proteico
17.
Am J Med Genet A ; 167A(4): 831-6, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-25736269

RESUMO

Congenital diaphragmatic hernia (CDH) is a relatively common, life--threatening birth defect. We present a family with recurrent CDH--paraesophageal and central--for whom exome sequencing (ES) revealed a frameshift mutation (c.4969_4970insA, p.Ile1657Asnfs*30) in the fibrillin 1 gene (FBN1) that causes Marfan syndrome. A diagnosis of Marfan syndrome had not been considered previously in this family. However, a review of the literature demonstrated that FBN1 mutations have an unusual pattern of CDH in which paraesophageal hernias are particularly common. Subsequent clinical evaluations revealed evidence for ectopia lentis in affected family members supporting a clinical diagnosis of Marfan syndrome. Since only two other cases of familial CDH have been described in association with FBN1 mutations, we investigated an oligogenic hypothesis by examining ES data for deleterious sequence changes in other CDH-related genes. This search revealed putatively deleterious sequence changes in four other genes that have been shown to cause diaphragm defects in humans and/or mice--FREM1, DES, PAX3 and MET. It is unclear whether these changes, alone or in aggregate, are contributing to the development of CDH in this family. However, their individual contribution is likely to be small compared to that of the frameshift mutation in FBN1. We conclude that ES can be used to identify both major and minor genetic factors that may contribute to CDH. These results also suggest that ES should be considered in the diagnostic evaluation of individuals and families with CDH, particularly when other diagnostic modalities have failed to reveal a molecular etiology.


Assuntos
Hérnias Diafragmáticas Congênitas/diagnóstico , Síndrome de Marfan/diagnóstico , Proteínas dos Microfilamentos/genética , Adulto , Pré-Escolar , Análise Mutacional de DNA , Exoma , Feminino , Fibrilina-1 , Fibrilinas , Mutação da Fase de Leitura , Estudos de Associação Genética , Hérnias Diafragmáticas Congênitas/genética , Humanos , Masculino , Síndrome de Marfan/genética , Linhagem
18.
Cell ; 159(1): 200-214, 2014 Sep 25.
Artigo em Inglês | MEDLINE | ID: mdl-25259927

RESUMO

Invertebrate model systems are powerful tools for studying human disease owing to their genetic tractability and ease of screening. We conducted a mosaic genetic screen of lethal mutations on the Drosophila X chromosome to identify genes required for the development, function, and maintenance of the nervous system. We identified 165 genes, most of whose function has not been studied in vivo. In parallel, we investigated rare variant alleles in 1,929 human exomes from families with unsolved Mendelian disease. Genes that are essential in flies and have multiple human homologs were found to be likely to be associated with human diseases. Merging the human data sets with the fly genes allowed us to identify disease-associated mutations in six families and to provide insights into microcephaly associated with brain dysgenesis. This bidirectional synergism between fly genetics and human genomics facilitates the functional annotation of evolutionarily conserved genes involved in human health.


Assuntos
Doença/genética , Drosophila melanogaster/genética , Testes Genéticos , Padrões de Herança , Interferência de RNA , Animais , Modelos Animais de Doenças , Humanos , Cromossomo X
19.
Am J Med Genet A ; 164A(9): 2328-34, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25045128

RESUMO

GAPO syndrome (OMIM#230740) is the acronym for growth retardation, alopecia, pseudoanodontia, and optic atrophy. About 35 cases have been reported, making it among one of the rarest recessive conditions. Distinctive craniofacial features including alopecia, rarefaction of eyebrows and eyelashes, frontal bossing, high forehead, mid-facial hypoplasia, hypertelorism, and thickened eyelids and lips make GAPO syndrome a clinically recognizable phenotype. While this genomic study was in progress mutations in ANTXR1 were reported to cause GAPO syndrome. In our study we performed whole exome sequencing (WES) for five affected individuals from three Turkish kindreds segregating the GAPO trait. Exome sequencing analysis identified three novel homozygous mutations including; one frame-shift (c.1220_1221insT; p.Ala408Cysfs*2), one splice site (c.411A>G; p.Gln137Gln), and one non-synonymous (c.1150G>A; p.Gly384Ser) mutation in the ANTXR1 gene. Our studies expand the allelic spectrum in this rare condition and potentially provide insight into the role of ANTXR1 in the regulation of the extracellular matrix.


Assuntos
Alopecia/genética , Anodontia/genética , Exoma/genética , Transtornos do Crescimento/genética , Mutação/genética , Proteínas de Neoplasias/genética , Atrofias Ópticas Hereditárias/genética , Receptores de Superfície Celular/genética , Adolescente , Adulto , Sequência de Bases , Criança , Segregação de Cromossomos/genética , Análise Mutacional de DNA , Facies , Família , Feminino , Humanos , Masculino , Dados de Sequência Molecular , Proteínas de Neoplasias/química , Linhagem , Estrutura Terciária de Proteína , Receptores de Superfície Celular/química
20.
Cell ; 157(3): 636-50, 2014 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-24766809

RESUMO

CLP1 is a RNA kinase involved in tRNA splicing. Recently, CLP1 kinase-dead mice were shown to display a neuromuscular disorder with loss of motor neurons and muscle paralysis. Human genome analyses now identified a CLP1 homozygous missense mutation (p.R140H) in five unrelated families, leading to a loss of CLP1 interaction with the tRNA splicing endonuclease (TSEN) complex, largely reduced pre-tRNA cleavage activity, and accumulation of linear tRNA introns. The affected individuals develop severe motor-sensory defects, cortical dysgenesis, and microcephaly. Mice carrying kinase-dead CLP1 also displayed microcephaly and reduced cortical brain volume due to the enhanced cell death of neuronal progenitors that is associated with reduced numbers of cortical neurons. Our data elucidate a neurological syndrome defined by CLP1 mutations that impair tRNA splicing. Reduction of a founder mutation to homozygosity illustrates the importance of rare variations in disease and supports the clan genomics hypothesis.


Assuntos
Doenças do Sistema Nervoso Central/genética , Mutação de Sentido Incorreto , Proteínas Nucleares/metabolismo , Doenças do Sistema Nervoso Periférico/genética , Fosfotransferases/metabolismo , RNA de Transferência/metabolismo , Fatores de Transcrição/metabolismo , Anormalidades Múltiplas/genética , Anormalidades Múltiplas/patologia , Animais , Doenças do Sistema Nervoso Central/patologia , Cérebro/patologia , Pré-Escolar , Endorribonucleases/metabolismo , Feminino , Fibroblastos/metabolismo , Humanos , Lactente , Masculino , Camundongos , Camundongos Endogâmicos CBA , Microcefalia/genética , Doenças do Sistema Nervoso Periférico/patologia , RNA de Transferência/genética
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA