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1.
Hum Genomics ; 18(1): 30, 2024 Mar 25.
Artículo en Inglés | MEDLINE | ID: mdl-38523294

RESUMEN

BACKGROUND: SLCO1B1 plays an important role in mediating hepatic clearance of many different drugs including statins, angiotensin-converting enzyme inhibitors, chemotherapeutic agents and antibiotics. Several variants in SLCO1B1 have been shown to have a clinically significant impact, in relation to efficacy of these medications. This study provides a comprehensive overview of SLCO1B1 variation in Saudi individuals, one of the largest Arab populations in the Middle East. METHODS: The dataset of 11,889 (9,961 exomes and 1,928 pharmacogenetic gene panel) Saudi nationals, was used to determine the presence and frequencies of SLCO1B1 variants, as described by the Clinical Pharmacogenetic Implementation Consortium (CPIC). RESULTS: We identified 141 previously described SNPs, of which rs2306283 (50%) and rs4149056 (28%), were the most common. In addition, we observed six alleles [*15 (24.7%) followed by *20 (8.04%), *14 (5.86%), *5 (3.84%), *31 (0.21%) and *9 (0.03%)] predicted to be clinically actionable. Allele diplotype to phenotype conversion revealed 41 OATP1B1 diplotypes. We estimated the burden of rare, and novel predicted deleterious variants, resulting from 17 such alterations. CONCLUSIONS: The data we present, from one of the largest Arab cohorts studied to date, provides the most comprehensive overview of SLCO1B1 variants, and the subsequent OATP1B1 activity of this ethnic group, which thus far remains relatively underrepresented in available international genomic databases. We believe that the presented data provides a basis for further clinical investigations and the application of personalized statin drug therapy guidance in Arabs.


Asunto(s)
Secuenciación de Nucleótidos de Alto Rendimiento , Farmacogenética , Humanos , Arabia Saudita , Transportador 1 de Anión Orgánico Específico del Hígado/genética , Polimorfismo de Nucleótido Simple/genética
2.
Hum Genet ; 141(1): 101-126, 2022 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-34853893

RESUMEN

Fetal abnormalities are detected in 3% of all pregnancies and are responsible for approximately 20% of all perinatal deaths. Chromosomal microarray analysis (CMA) and exome sequencing (ES) are widely used in prenatal settings for molecular genetic diagnostics with variable diagnostic yields. In this study, we aimed to determine the diagnostic yield of trio-ES in detecting the cause of fetal abnormalities within a highly consanguineous population. In families with a history of congenital anomalies, a total of 119 fetuses with structural anomalies were recruited and DNA from invasive samples were used together with parental DNA samples for trio-ES and CMA. Data were analysed to determine possible underlying genetic disorders associated with observed fetal phenotypes. The cohort had a known consanguinity of 81%. Trio-ES led to diagnostic molecular genetic findings in 59 fetuses (with pathogenic/likely pathogenic variants) most with multisystem or renal abnormalities. CMA detected chromosomal abnormalities compatible with the fetal phenotype in another 7 cases. Monogenic ciliopathy disorders with an autosomal recessive inheritance were the predominant cause of multisystem fetal anomalies (24/59 cases, 40.7%) with loss of function variants representing the vast majority of molecular genetic abnormalities. Heterozygous de novo pathogenic variants were found in four fetuses. A total of 23 novel variants predicted to be associated with the phenotype were detected. Prenatal trio-ES and CMA detected likely causative molecular genetic defects in a total of 55% of families with fetal anomalies confirming the diagnostic utility of trio-ES and CMA as first-line genetic test in the prenatal diagnosis of multisystem fetal anomalies including ciliopathy syndromes.


Asunto(s)
Aberraciones Cromosómicas , Ciliopatías/genética , Feto/anomalías , Feto/fisiopatología , Variación Genética , Estudios de Cohortes , Consanguinidad , Femenino , Predisposición Genética a la Enfermedad , Pruebas Genéticas/métodos , Humanos , Análisis por Micromatrices , Fenotipo , Embarazo , Diagnóstico Prenatal/métodos , Secuenciación del Exoma
3.
Am J Hum Genet ; 104(6): 1202-1209, 2019 06 06.
Artículo en Inglés | MEDLINE | ID: mdl-31079898

RESUMEN

The wobble hypothesis was proposed to explain the presence of fewer tRNAs than possible codons. The wobble nucleoside position in the anticodon stem-loop undergoes a number of modifications that help maintain the efficiency and fidelity of translation. AlkB homolog 8 (ALKBH8) is an atypical member of the highly conserved AlkB family of dioxygenases and is involved in the formation of mcm5s2U, (S)-mchm5U, (R)-mchm5U, mcm5U, and mcm5Um at the anticodon wobble uridines of specific tRNAs. In two multiplex consanguineous families, we identified two homozygous truncating ALKBH8 mutations causing intellectual disability. Analysis of tRNA derived from affected individuals showed the complete absence of these modifications, consistent with the presumptive loss of function of the variants. Our results highlight the sensitivity of the brain to impaired wobble modification and expand the list of intellectual-disability syndromes caused by mutations in genes related to tRNA modification.


Asunto(s)
Homólogo 8 de AlkB ARNt Metiltransferasa/genética , Codón/metabolismo , Genes Recesivos/genética , Discapacidad Intelectual/etiología , Mutación , ARN de Transferencia/metabolismo , Uridina/metabolismo , Adolescente , Adulto , Niño , Preescolar , Codón/genética , Femenino , Humanos , Discapacidad Intelectual/patología , Masculino , ARN de Transferencia/genética , Uridina/química , Uridina/genética , Adulto Joven , ARNt Metiltransferasas/metabolismo
4.
Am J Hum Genet ; 104(6): 1182-1201, 2019 06 06.
Artículo en Inglés | MEDLINE | ID: mdl-31130284

RESUMEN

We report the results of clinical exome sequencing (CES) on >2,200 previously unpublished Saudi families as a first-tier test. The predominance of autosomal-recessive causes allowed us to make several key observations. We highlight 155 genes that we propose to be recessive, disease-related candidates. We report additional mutational events in 64 previously reported candidates (40 recessive), and these events support their candidacy. We report recessive forms of genes that were previously associated only with dominant disorders and that have phenotypes ranging from consistent with to conspicuously distinct from the known dominant phenotypes. We also report homozygous loss-of-function events that can inform the genetics of complex diseases. We were also able to deduce the likely causal variant in most couples who presented after the loss of one or more children, but we lack samples from those children. Although a similar pattern of mostly recessive causes was observed in the prenatal setting, the higher proportion of loss-of-function events in these cases was notable. The allelic series presented by the wealth of recessive variants greatly expanded the phenotypic expression of the respective genes. We also make important observations about dominant disorders; these observations include the pattern of de novo variants, the identification of 74 candidate dominant, disease-related genes, and the potential confirmation of 21 previously reported candidates. Finally, we describe the influence of a predominantly autosomal-recessive landscape on the clinical utility of rapid sequencing (Flash Exome). Our cohort's genotypic and phenotypic data represent a unique resource that can contribute to improved variant interpretation through data sharing.


Asunto(s)
Consanguinidad , Secuenciación del Exoma/métodos , Genes Recesivos , Enfermedades Genéticas Ligadas al Cromosoma X/epidemiología , Enfermedades Genéticas Ligadas al Cromosoma X/genética , Predisposición Genética a la Enfermedad , Mutación , Niño , Estudios de Cohortes , Femenino , Homocigoto , Humanos , Masculino , Fenotipo , Embarazo , Arabia Saudita/epidemiología
5.
Hum Genomics ; 15(1): 52, 2021 08 11.
Artículo en Inglés | MEDLINE | ID: mdl-34380564

RESUMEN

BACKGROUND: Familial transthyretin (TTR) amyloidosis (ATTR) is an autosomal dominant disease with significant phenotypic heterogeneity. Its prevalence in Saudi Arabia has not previously been investigated. An existing exome variant database of Saudi individuals, sequenced to globally investigate rare diseases in the population, was mined for TTR variants and filtered for missense mutations resulting in single amino acid changes. A total of 13,906 Saudi exomes from unrelated individuals were analyzed blindly. RESULTS: Three TTR variants known to be associated with ATTR amyloidosis were identified. Additionally, three novel TTR mutations were identified. Structural analysis of the three novel variants suggests that at least two could be amyloidogenic. The most common variant associated with amyloidosis was p.Val142Ile (allele frequency 0.001). Further investigation of these variants and their translation to clinical practice may help to diagnose, monitor, and manage patients with ATTR amyloidosis. CONCLUSION: Multiple TTR variants potentially associated with systemic ATTR amyloidosis were identified in the Saudi population. Early diagnosis and intervention, facilitated by familial genetic testing of patients with ATTR amyloidosis, may benefit in the management of this disease. Early diagnosis could be enhanced through inclusion of ATTR variants in existing population-based screening programs.


Asunto(s)
Neuropatías Amiloides Familiares/genética , Predisposición Genética a la Enfermedad , Pruebas Genéticas , Prealbúmina/genética , Adolescente , Adulto , Anciano , Neuropatías Amiloides Familiares/epidemiología , Neuropatías Amiloides Familiares/patología , Niño , Minería de Datos , Femenino , Frecuencia de los Genes , Variación Genética/genética , Humanos , Masculino , Persona de Mediana Edad , Mutación Missense/genética , Arabia Saudita/epidemiología , Adulto Joven
6.
Brain ; 144(3): 769-780, 2021 04 12.
Artículo en Inglés | MEDLINE | ID: mdl-33764426

RESUMEN

Membrane trafficking is a complex, essential process in eukaryotic cells responsible for protein transport and processing. Deficiencies in vacuolar protein sorting (VPS) proteins, key regulators of trafficking, cause abnormal intracellular segregation of macromolecules and organelles and are linked to human disease. VPS proteins function as part of complexes such as the homotypic fusion and vacuole protein sorting (HOPS) tethering complex, composed of VPS11, VPS16, VPS18, VPS33A, VPS39 and VPS41. The HOPS-specific subunit VPS41 has been reported to promote viability of dopaminergic neurons in Parkinson's disease but to date has not been linked to human disease. Here, we describe five unrelated families with nine affected individuals, all carrying homozygous variants in VPS41 that we show impact protein function. All affected individuals presented with a progressive neurodevelopmental disorder consisting of cognitive impairment, cerebellar atrophy/hypoplasia, motor dysfunction with ataxia and dystonia, and nystagmus. Zebrafish disease modelling supports the involvement of VPS41 dysfunction in the disorder, indicating lysosomal dysregulation throughout the brain and providing support for cerebellar and microglial abnormalities when vps41 was mutated. This provides the first example of human disease linked to the HOPS-specific subunit VPS41 and suggests the importance of HOPS complex activity for cerebellar function.


Asunto(s)
Ataxia Cerebelosa/genética , Predisposición Genética a la Enfermedad/genética , Trastornos del Neurodesarrollo/genética , Transporte de Proteínas/genética , Proteínas de Transporte Vesicular/genética , Adolescente , Adulto , Animales , Niño , Preescolar , Femenino , Variación Genética , Humanos , Masculino , Linaje , Adulto Joven , Pez Cebra
7.
Am J Hum Genet ; 102(5): 858-873, 2018 05 03.
Artículo en Inglés | MEDLINE | ID: mdl-29727687

RESUMEN

The exosome is a conserved multi-protein complex that is essential for correct RNA processing. Recessive variants in exosome components EXOSC3, EXOSC8, and RBM7 cause various constellations of pontocerebellar hypoplasia (PCH), spinal muscular atrophy (SMA), and central nervous system demyelination. Here, we report on four unrelated affected individuals with recessive variants in EXOSC9 and the effect of the variants on the function of the RNA exosome in vitro in affected individuals' fibroblasts and skeletal muscle and in vivo in zebrafish. The clinical presentation was severe, early-onset, progressive SMA-like motor neuronopathy, cerebellar atrophy, and in one affected individual, congenital fractures of the long bones. Three affected individuals of different ethnicity carried the homozygous c.41T>C (p.Leu14Pro) variant, whereas one affected individual was compound heterozygous for c.41T>C (p.Leu14Pro) and c.481C>T (p.Arg161∗). We detected reduced EXOSC9 in fibroblasts and skeletal muscle and observed a reduction of the whole multi-subunit exosome complex on blue-native polyacrylamide gel electrophoresis. RNA sequencing of fibroblasts and skeletal muscle detected significant >2-fold changes in genes involved in neuronal development and cerebellar and motor neuron degeneration, demonstrating the widespread effect of the variants. Morpholino oligonucleotide knockdown and CRISPR/Cas9-mediated mutagenesis of exosc9 in zebrafish recapitulated aspects of the human phenotype, as they have in other zebrafish models of exosomal disease. Specifically, portions of the cerebellum and hindbrain were absent, and motor neurons failed to develop and migrate properly. In summary, we show that variants in EXOSC9 result in a neurological syndrome combining cerebellar atrophy and spinal motoneuronopathy, thus expanding the list of human exosomopathies.


Asunto(s)
Cerebelo/patología , Complejo Multienzimático de Ribonucleasas del Exosoma/genética , Exosomas/metabolismo , Variación Genética , Neuronas Motoras/patología , Proteínas de Unión al ARN/genética , Médula Espinal/patología , Secuencia de Aminoácidos , Animales , Atrofia , Secuencia de Bases , Cerebelo/diagnóstico por imagen , Preescolar , Complejo Multienzimático de Ribonucleasas del Exosoma/química , Femenino , Fibroblastos/metabolismo , Fibroblastos/patología , Técnicas de Silenciamiento del Gen , Haplotipos/genética , Humanos , Lactante , Masculino , Músculo Esquelético/metabolismo , Linaje , Proteínas de Unión al ARN/química , Pez Cebra
8.
Hepatology ; 71(6): 2067-2079, 2020 06.
Artículo en Inglés | MEDLINE | ID: mdl-31595528

RESUMEN

BACKGROUND AND AIMS: The clinical consequences of defective primary cilium (ciliopathies) are characterized by marked phenotypic and genetic heterogeneity. Although fibrocystic liver disease is an established ciliopathy phenotype, severe neonatal cholestasis is rarely recognized as such. APPROACH AND RESULTS: We describe seven individuals from seven families with syndromic ciliopathy clinical features, including severe neonatal cholestasis (lethal in one and necessitating liver transplant in two). Positional mapping revealed a single critical locus on chromosome 7. Whole-exome sequencing revealed three different homozygous variants in Tetratricopeptide Repeat Domain 26 (TTC26) that fully segregated with the phenotype. TTC26 (intraflagellar transport [IFT] 56/DYF13) is an atypical component of IFT-B complex, and deficiency of its highly conserved orthologs has been consistently shown to cause defective ciliary function in several model organisms. We show that cilia in TTC26-mutated patient cells display variable length and impaired function, as indicated by dysregulated sonic hedgehog signaling, abnormal staining for IFT-B components, and transcriptomic clustering with cells derived from individuals with closely related ciliopathies. We also demonstrate a strong expression of Ttc26 in the embryonic mouse liver in a pattern consistent with its proposed role in the normal development of the intrahepatic biliary system. CONCLUSIONS: In addition to establishing a TTC26-related ciliopathy phenotype in humans, our results highlight the importance of considering ciliopathies in the differential diagnosis of severe neonatal cholestasis even in the absence of more typical features.


Asunto(s)
Colestasis Intrahepática/genética , Enfermedades del Recién Nacido/genética , Péptidos y Proteínas de Señalización Intracelular/genética , Repeticiones de Tetratricopéptidos/genética , Animales , Ciliopatías , Diagnóstico Diferencial , Proteínas Hedgehog , Humanos , Recién Nacido , Ratones , Proteínas Asociadas a Microtúbulos/genética , Mutación , Transporte de Proteínas/genética , Índice de Severidad de la Enfermedad , Secuenciación del Exoma/métodos
9.
Clin Genet ; 99(4): 572-576, 2021 04.
Artículo en Inglés | MEDLINE | ID: mdl-33410500

RESUMEN

We describe an 11-year-old girl with PLACK Syndrome (peeling skin, leukonychia, acral punctate keratosis, cheilitis, and knuckle pads), who was found to have a novel homozygous variant in CAST, the pathogenicity of which was confirmed using blood-derived RNA. There is no established treatment for PLACK syndrome. However, we demonstrate for the first time that this condition is associated with low levels of vitamin A and essential fatty acids, which prompted us to consider a potential treatment strategy. Indeed, we initiated this patient on intravenous lipid infusion (Vitalipid®; an emulsion of fat-soluble vitamins and lipofundin-MCT/LCT 20%) and the response was dramatic. Following the fourth monthly course of treatment, pruritis disappeared and the skin lesions showed remarkable objective improvement. PLACK syndrome is a very rare genodermatosis and only six families have been described to date with pathogenic CAST variants. This is the first report of an objective response to a therapeutic agent, which suggests that PLACK is a potentially treatable condition. The remarkable response we report and the relative safety of the intervention should prompt healthcare providers who care for PLACK syndrome patients to explore this as a potential treatment strategy in future studies.


Asunto(s)
Dermatitis Exfoliativa/tratamiento farmacológico , Hipopigmentación/tratamiento farmacológico , Enfermedades de la Uña/congénito , Fosfolípidos/uso terapéutico , Enfermedades Cutáneas Genéticas/tratamiento farmacológico , Aceite de Soja/uso terapéutico , Vesícula/etiología , Proteínas de Unión al Calcio/genética , Queilitis/tratamiento farmacológico , Queilitis/genética , Niño , Consanguinidad , Dermatitis Exfoliativa/genética , Emulsiones/administración & dosificación , Emulsiones/uso terapéutico , Femenino , Humanos , Hipopigmentación/genética , Infusiones Intravenosas , Queratosis/tratamiento farmacológico , Queratosis/genética , Enfermedades de la Uña/tratamiento farmacológico , Enfermedades de la Uña/genética , Linaje , Fosfolípidos/administración & dosificación , Prurito/tratamiento farmacológico , Prurito/genética , Inducción de Remisión , Enfermedades Cutáneas Genéticas/genética , Aceite de Soja/administración & dosificación , Síndrome , Resultado del Tratamiento
10.
Clin Genet ; 99(5): 724-731, 2021 05.
Artículo en Inglés | MEDLINE | ID: mdl-33506509

RESUMEN

The dysfunction of microtubules (α/ß-tubulin polymers) underlies a wide range of nervous system genetic abnormalities. Defects in TBCD, a tubulin-folding cofactor, cause diseases highlighted with early-onset encephalopathy with or without neurodegeneration, intellectual disability, seizures, microcephaly and tetraparaperesis. Utilizing various molecular methods, we describe nine patients from four unrelated families with two novel exon 18 variants in TBCD exhibiting the typical neurological phenotype of the disease. Interestingly, all the investigated patients had previously unreported hematological findings in the form of neutropenia and mild degree of anemia and thrombocytopenia. In addition to delineating the neurological phenotype in several patients with TBCD variants, our study stresses on the new association of neutropenia, in particular, with the disease.


Asunto(s)
Encefalopatías/sangre , Encefalopatías/genética , Proteínas Asociadas a Microtúbulos/genética , Mutación Missense , Adulto , Anemia/etiología , Encefalopatías/complicaciones , Encefalopatías/diagnóstico por imagen , Niño , Femenino , Humanos , Lactante , Imagen por Resonancia Magnética , Masculino , Neutropenia/etiología , Linaje , Trombocitopenia/etiología , Adulto Joven
11.
Curr Rheumatol Rep ; 23(8): 64, 2021 07 03.
Artículo en Inglés | MEDLINE | ID: mdl-34216291

RESUMEN

PURPOSE OF REVIEW: We describe the clinical and genetic findings in four patients from a single family who presented with refractory psoriatic arthritis and were hemizygous in the forkhead box protein 3 (FOXP3) gene (c.1222G>A). RECENT FINDINGS: We report four siblings with hemizygous mutation in the FOXP3 gene (c.1222G>A) who presented with type 1 diabetes mellitus and psoriatic arthritis poorly responsive to treatment. Our findings expand the phenotype spectrum of FOXP3 mutations. Immune dysregulation, polyendocrinopathy, and enteropathy, X-linked (IPEX) syndrome is a rare disorder caused by mutations in FOXP3 gene, which lead to early onset of constellation of autoimmune manifestations. This report highlights the influence of immune dysregulation in juvenile arthritis.


Asunto(s)
Artritis Juvenil , Enfermedades Genéticas Ligadas al Cromosoma X , Artritis Juvenil/genética , Análisis por Conglomerados , Factores de Transcripción Forkhead/genética , Enfermedades Genéticas Ligadas al Cromosoma X/genética , Humanos , Mutación , Linfocitos T Reguladores
12.
Int J Cancer ; 145(3): 830-841, 2019 08 01.
Artículo en Inglés | MEDLINE | ID: mdl-30719702

RESUMEN

Breast cancer remains the second cause of tumor-related mortality in women worldwide mainly due to chemoresistance and metastasis. The chemoresistance and metastasis are attributed to a rare subpopulation with enriched stem-like characteristics, thus called Cancer Stem Cells (CSCs). We have previously reported aberrant expression of the actin-bundling protein (fascin) in breast cancer cells, which enhances their chemoresistance, metastasis and enriches CSC population. The intracellular mechanisms that link fascin with its downstream effectors are not fully elucidated. Here, loss and gain of function approaches in two different breast cancer models were used to understand how fascin promotes disease progression. Importantly, findings were aligned with expression data from actual breast cancer patients. Expression profiling of a large breast cancer dataset (TCGA, 530 patients) showed statistically significant correlation between fascin expression and a key adherence molecule, ß1 integrin (ITGB1). In vitro manipulation of fascin expression in breast cancer cells exhibited its direct effect on ITGB1 expression. Fascin-mediated regulation of ITGB1 was critical for several breast cancer cell functions including adhesion to different extracellular matrix, self-renewability and chemoresistance. Importantly, there was a significant relationship between fascin and ITGB1 co-expression and short disease-free as well as overall survival in chemo-treated breast cancer patients. This novel role of fascin effect on ITGB1 expression and its outcome on cell self-renewability and chemoresistance strongly encourages for dual targeting of fascin-ITGB1 axis as a therapeutic approach to halt breast cancer progression and eradicate it from the root.


Asunto(s)
Neoplasias de la Mama/patología , Proteínas Portadoras/biosíntesis , Integrina beta1/biosíntesis , Proteínas de Microfilamentos/biosíntesis , Células Madre Neoplásicas/patología , Neoplasias de la Mama/genética , Neoplasias de la Mama/metabolismo , Proteínas Portadoras/genética , Proteínas Portadoras/metabolismo , Adhesión Celular/fisiología , Línea Celular Tumoral , Progresión de la Enfermedad , Femenino , Expresión Génica , Humanos , Inmunohistoquímica , Integrina beta1/genética , Integrina beta1/metabolismo , Proteínas de Microfilamentos/genética , Proteínas de Microfilamentos/metabolismo , Células Madre Neoplásicas/metabolismo , Análisis de Supervivencia , Regulación hacia Arriba
13.
Genet Med ; 21(1): 185-188, 2019 01.
Artículo en Inglés | MEDLINE | ID: mdl-29892088

RESUMEN

PURPOSE: Wolf-Hirschhorn syndrome (WHS) is a genomic disorder with a recognizable dysmorphology profile caused by hemizygosity at 4p16.3. Previous attempts have failed to map the minimal critical locus to a single gene, leaving open the possibility that the core phenotypic components of the syndrome are caused by the combined haploinsufficiency of multiple genes. METHODS: Clinical exome sequencing and "reverse" phenotyping. RESULTS: We identified two patients with de novo truncating variants in WHSC1, which maps to the WHS critical locus. The phenotype of these two individuals is consistent with WHS, which suggests that haploinsufficiency of WHSC1 is sufficient to recapitulate the core phenotype (characteristic facies, and growth and developmental delay) of this classic microdeletion syndrome. CONCLUSION: Our study expands the list of microdeletion syndromes that are solved at the single-gene level, and establishes WHSC1 as a disease gene in humans. Given the severe nature of the reported variants, the full phenotypic expression of WHSC1 may be further expanded by future reports of milder variants.


Asunto(s)
Discapacidades del Desarrollo/genética , Predisposición Genética a la Enfermedad , N-Metiltransferasa de Histona-Lisina/genética , Proteínas Represoras/genética , Síndrome de Wolf-Hirschhorn/genética , Preescolar , Deleción Cromosómica , Hibridación Genómica Comparativa , Discapacidades del Desarrollo/diagnóstico , Discapacidades del Desarrollo/patología , Femenino , Haploinsuficiencia/genética , Humanos , Masculino , Fenotipo , Síndrome de Wolf-Hirschhorn/diagnóstico , Síndrome de Wolf-Hirschhorn/patología
14.
Genet Med ; 21(3): 736-742, 2019 03.
Artículo en Inglés | MEDLINE | ID: mdl-30237576

RESUMEN

PURPOSE: Establishing links between Mendelian phenotypes and genes enables the proper interpretation of variants therein. Autozygome, a rich source of homozygous variants, has been successfully utilized for the high throughput identification of novel autosomal recessive disease genes. Here, we highlight the utility of the autozygome for the high throughput confirmation of previously published tentative links to diseases. METHODS: Autozygome and exome analysis of patients with suspected Mendelian phenotypes. All variants were classified according to the American College of Medical Genetics and Genomics guidelines. RESULTS: We highlight 30 published candidate genes (ACTL6B, ADAM22, AGTPBP1, APC, C12orf4, C3orf17 (NEPRO), CENPF, CNPY3, COL27A1, DMBX1, FUT8, GOLGA2, KIAA0556, LENG8, MCIDAS, MTMR9, MYH11, QRSL1, RUBCN, SLC25A42, SLC9A1, TBXT, TFG, THUMPD1, TRAF3IP2, UFC1, UFM1, WDR81, XRCC2, ZAK) in which we identified homozygous likely deleterious variants in patients with compatible phenotypes. We also identified homozygous likely deleterious variants in 18 published candidate genes (ABCA2, ARL6IP1, ATP8A2, CDK9, CNKSR1, DGAT1, DMXL2, GEMIN4, HCN2, HCRT, MYO9A, PARS2, PLOD3, PREPL, SCLT1, STX3, TXNRD2, WIPI2) although the associated phenotypes are sufficiently different from the original reports that they represent phenotypic expansion or potentially distinct allelic disorders. CONCLUSIONS: Our results should facilitate the timely relabeling of these candidate disease genes in relevant databases to improve the yield of clinical genomic sequencing.


Asunto(s)
Enfermedad/genética , Genómica/métodos , Análisis de Secuencia de ADN/métodos , Variación Biológica Poblacional/genética , Niño , Preescolar , Diagnóstico , Técnicas y Procedimientos Diagnósticos , Femenino , Pruebas Genéticas/normas , Variación Genética , Genotipo , Herencia/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Homocigoto , Humanos , Lactante , Recién Nacido , Masculino , Mutación , Fenotipo
15.
Clin Genet ; 95(2): 310-319, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-30561787

RESUMEN

Defects in the peroxisomes biogenesis and/or function result in peroxisomal disorders. In this study, we describe the largest Arab cohort to date (72 families) of clinically, biochemically and molecularly characterized patients with peroxisomal disorders. At the molecular level, we identified 43 disease-causing variants, half of which are novel. The founder nature of many of the variants allowed us to calculate the minimum disease burden for these disorders in our population ~1:30 000, which is much higher than previous estimates in other populations. Clinically, we found an interesting trend toward genotype/phenotype correlation in terms of long-term survival. Nearly half (40/75) of our peroxisomal disorders patients had documented survival beyond 1 year of age. Most unusual among the long-term survivors was a multiplex family in which the affected members presented as adults with non-specific intellectual disability and epilepsy. Other unusual presentations included the very recently described peroxisomal fatty acyl-CoA reductase 1 disorder as well as CRD, spastic paraparesis, white matter (CRSPW) syndrome. We conclude that peroxisomal disorders are highly heterogeneous in their clinical presentation. Our data also confirm the demonstration that milder forms of Zellweger spectrum disorders cannot be ruled out by the "gold standard" very long chain fatty acids assay, which highlights the value of a genomics-first approach in these cases.


Asunto(s)
Árabes , Trastorno Peroxisomal/epidemiología , Trastorno Peroxisomal/etiología , Árabes/genética , Biomarcadores , Encéfalo/anomalías , Encéfalo/diagnóstico por imagen , Estudios de Cohortes , Consanguinidad , Costo de Enfermedad , Manejo de la Enfermedad , Susceptibilidad a Enfermedades , Facies , Femenino , Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Humanos , Imagen por Resonancia Magnética , Masculino , Mutación , Linaje , Trastorno Peroxisomal/diagnóstico , Trastorno Peroxisomal/terapia , Fenotipo , Vigilancia de la Población , Pronóstico
16.
Brain ; 141(7): 1934-1945, 2018 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-29868776

RESUMEN

The post-translational modification of proteins through the addition of UFM1, also known as ufmylation, plays a critical developmental role as revealed by studies in animal models. The recent finding that biallelic mutations in UBA5 (the E1-like enzyme for ufmylation) cause severe early-onset encephalopathy with progressive microcephaly implicates ufmylation in human brain development. More recently, a homozygous UFM1 variant was proposed as a candidate aetiology of severe early-onset encephalopathy with progressive microcephaly. Here, we establish a locus for severe early-onset encephalopathy with progressive microcephaly based on two families, and map the phenotype to a novel homozygous UFM1 mutation. This mutation has a significantly diminished capacity to form thioester intermediates with UBA5 and with UFC1 (the E2-like enzyme for ufmylation), with resulting impaired ufmylation of cellular proteins. Remarkably, in four additional families where eight children have severe early-onset encephalopathy with progressive microcephaly, we identified two biallelic UFC1 mutations, which impair UFM1-UFC1 intermediate formation with resulting widespread reduction of cellular ufmylation, a pattern similar to that observed with UFM1 mutation. The striking resemblance between UFM1- and UFC1-related clinical phenotype and biochemical derangements strongly argues for an essential role for ufmylation in human brain development. The hypomorphic nature of UFM1 and UFC1 mutations and the conspicuous depletion of biallelic null mutations in the components of this pathway in human genome databases suggest that it is necessary for embryonic survival, which is consistent with the embryonic lethal nature of knockout models for the orthologous genes.


Asunto(s)
Encefalopatías/genética , Proteínas/genética , Enzimas Ubiquitina-Conjugadoras/genética , Adolescente , Adulto , Encéfalo/crecimiento & desarrollo , Encéfalo/metabolismo , Encefalopatías/fisiopatología , Niño , Preescolar , Femenino , Células HEK293 , Humanos , Masculino , Microcefalia/genética , Mutación , Linaje , Procesamiento Proteico-Postraduccional , Proteínas/fisiología , Enzimas Activadoras de Ubiquitina/genética , Enzimas Ubiquitina-Conjugadoras/fisiología
19.
Genet Med ; 20(12): 1609-1616, 2018 12.
Artículo en Inglés | MEDLINE | ID: mdl-29620724

RESUMEN

PURPOSE: To describe our experience with a large cohort (411 patients from 288 families) of various forms of skeletal dysplasia who were molecularly characterized. METHODS: Detailed phenotyping and next-generation sequencing (panel and exome). RESULTS: Our analysis revealed 224 pathogenic/likely pathogenic variants (54 (24%) of which are novel) in 123 genes with established or tentative links to skeletal dysplasia. In addition, we propose 5 genes as candidate disease genes with suggestive biological links (WNT3A, SUCO, RIN1, DIP2C, and PAN2). Phenotypically, we note that our cohort spans 36 established phenotypic categories by the International Skeletal Dysplasia Nosology, as well as 18 novel skeletal dysplasia phenotypes that could not be classified under these categories, e.g., the novel C3orf17-related skeletal dysplasia. We also describe novel phenotypic aspects of well-known disease genes, e.g., PGAP3-related Toriello-Carey syndrome-like phenotype. We note a strong founder effect for many genes in our cohort, which allowed us to calculate a minimum disease burden for the autosomal recessive forms of skeletal dysplasia in our population (7.16E-04), which is much higher than the global average. CONCLUSION: By expanding the phenotypic, allelic, and locus heterogeneity of skeletal dysplasia in humans, we hope our study will improve the diagnostic rate of patients with these conditions.


Asunto(s)
Exoma/genética , Heterogeneidad Genética , Predisposición Genética a la Enfermedad , Anomalías Musculoesqueléticas/genética , Alelos , Proteínas Sanguíneas/genética , Hidrolasas de Éster Carboxílico , Estudios de Cohortes , Exorribonucleasas/genética , Femenino , Proteínas Fetales/genética , Efecto Fundador , Genética de Población , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Péptidos y Proteínas de Señalización Intracelular/genética , Masculino , Proteínas de la Membrana/genética , Anomalías Musculoesqueléticas/clasificación , Anomalías Musculoesqueléticas/patología , Proteínas de Neoplasias/genética , Proteínas Oncogénicas/genética , Fenotipo , Receptores de Superficie Celular/genética , Proteína Wnt3A/genética
20.
BMC Med Genet ; 19(1): 115, 2018 07 11.
Artículo en Inglés | MEDLINE | ID: mdl-29996815

RESUMEN

BACKGROUND: Congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency (21OHD) is an autosomal recessive disorder caused by mutations in the CYP21A2. Congenital nephrogenic diabetes insipidus (NDI) is a rare X-linked recessive or autosomal recessive disorder caused by mutations in either AVPR2 or AQP2. Genotype-phenotype discordance caused by genetic mosaicism in CAH patients has not been reported, nor the concomitant CAH and NDI. CASE PRESENTATION: We investigated a patient with concomitant CAH and NDI from a consanguineous family. She (S-1) presented with clitoromegaly at 3 month of age, and polydipsia and polyuria at 13 month of age. Her parents and two elder sisters (S-2 and S-3) were clinically normal, but elevated levels of serum 17-hydroxyprogesterone (17-OHP) were observed in the mother and S-2. The coding region of CYP21A2 and AQP2 were analyzed by PCR-sequencing analysis to identify genetic defects. Two homozygous CYP21A2 mutations (p.R357W and p.P454S) were identified in the proband and her mother and S-2. The apparent genotype-phenotype discordance was due to presence of small amount of wild-type CYP21A2 alleles in S-1, S-2, and their mother's genome, thus protecting them from development of classic form of 21OHD (C21OHD). A homozygous AQP2 mutation (p.A147T) was also found in the patient. The patient was treated with hydrocortisone and hydrochlorothiazide. Her symptoms were improved with normal laboratory findings. The clitoromegaly is persisted. CONCLUSIONS: Genetic mosaicism is a novel mechanism contributing to the genotype-phenotype discordance in 21OHD and small percentage of wild-type CYP21A2 alleles may be sufficient to prevent phenotype development. This is a first report of concurrent 21OHD and NDI caused by simultaneous homozygous CYP21A2 and AQP2 mutations.


Asunto(s)
Hiperplasia Suprarrenal Congénita/genética , Diabetes Insípida Nefrogénica/genética , Adolescente , Adulto , Alelos , Acuaporina 2/genética , Niño , Femenino , Estudios de Asociación Genética/métodos , Genotipo , Humanos , Masculino , Mosaicismo , Mutación/genética , Linaje , Fenotipo , Hermanos , Esteroide 21-Hidroxilasa/genética
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