[Show abstract][Hide abstract] ABSTRACT: Most cases of CHARGE syndrome are sporadic and autosomal dominant. CHD7 is a major causative gene of CHARGE syndrome. In this study, we screened CHD7 in two Turkish patients who had CHARGE syndrome symptoms as coloboma, heart defect, choanal atresia, retarded growth and ear anomalies and found a novel splice-site mutation (c.2443-2A>G) and a previously known frameshift mutation (c.2504_2508delATCTT). We performed exon trapping analysis to determine the effect of the c.2443-2A>G mutation at the transcriptional level, and found that it caused a complete skip of exon 7 and splicing at a cryptic splice acceptor site. Our current study is the second study demonstrating an exon 7 deficit in CHD7. Results of previous studies suggest that the c.2443-2A>G mutation affects the formation of nasal tissues and the neural retina during early development, resulting in choanal atresia and coloboma, respectively. The findings of the present study will improve our understanding of the genetic causes of CHARGE syndrome.
[Show abstract][Hide abstract] ABSTRACT: 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. VIDEO ABSTRACT.
[Show abstract][Hide abstract] ABSTRACT: Cornelia de Lange syndrome (CdLS) is a genetically heterogeneous disorder that presents with extensive phenotypic variability, including facial dysmorphism, developmental delay/intellectual disability (DD/ID), abnormal extremities, and hirsutism. About 65% of patients harbor mutations in genes that encode subunits or regulators of the cohesin complex, including NIPBL, SMC1A, SMC3, RAD21, and HDAC8. Wiedemann-Steiner syndrome (WDSTS), which shares CdLS phenotypic features, is caused by mutations in lysine-specific methyltransferase 2A (KMT2A). Here, we performed whole-exome sequencing (WES) of 2 male siblings clinically diagnosed with WDSTS; this revealed a hemizygous, missense mutation in SMC1A that was predicted to be deleterious. Extensive clinical evaluation and WES of 32 Turkish patients clinically diagnosed with CdLS revealed the presence of a de novo heterozygous nonsense KMT2A mutation in 1 patient without characteristic WDSTS features. We also identified de novo heterozygous mutations in SMC3 or SMC1A that affected RNA splicing in 2 independent patients with combined CdLS and WDSTS features. Furthermore, in families from 2 separate world populations segregating an autosomal-recessive disorder with CdLS-like features, we identified homozygous mutations in TAF6, which encodes a core transcriptional regulatory pathway component. Together, our data, along with recent transcriptome studies, suggest that CdLS and related phenotypes may be "transcriptomopathies" rather than cohesinopathies.
The Journal of clinical investigation 01/2015; DOI:10.1172/JCI77435 · 13.22 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Cancer is still one of the dominating causes of deaths worldwide, although there have been important enhancements for detection and diagnosis of cancer recently. miRNAs are shown to participate in carcinogenesis of several types of tumors and their aberrant expression of miRNAs has been detected in cell lines, xenografts and clinical samples. miRNAs are thought to target and modulate the expression of more than 60% of human genes, which makes the expressional regulation by miRNAs the most abundant post-transcriptional regulation mode. Here, we have reviewed the most current literature to shed a light on the functions of miRNAs on human carcinogenesis. Possible roles of miRNAs in oncogenesis through both genetic and epigenetic changes occurring during cancer initiation, progression, invasion or metastasis are summarized.
[Show abstract][Hide abstract] ABSTRACT: 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.
[Show abstract][Hide abstract] ABSTRACT: Dyggve-Melchior-Clausen syndrome (DMC) (MIM #223800) is a rare autosomal-recessive type of skeletal dysplasia accompanied by variable degrees of intellectual disability (ID). It is characterized by progressive spondyloepimetaphyseal dysplasia leading to disproportionate short stature, microcephaly, and coarse facies. The radiographic appearance of generalized platyspondyly with double-humped end plates and the lace-like appearance of iliac crests are pathognomonic in this syndrome. The disorder results from mutations in the dymeclin (DYM) mapped to the 18q12-12.1 chromosomal region. Here, we report two cases with DMC: one with disproportionate short stature, developmental delay, and severe ID with a novel frameshift mutation (c.1028_1056del29) leading to a premature stop codon, and the second patient with classical clinical and radiological features of DMC with mild ID and rectal prolapse, which is very rare. The clinical diagnosis was confirmed with molecular analysis of DYM with a known mutation at c.580C>T (p.R194X). The parents and sibling of the second patient were heterozygous carriers with mild skeletal changes and short stature.
[Show abstract][Hide abstract] ABSTRACT: Despite the availability of several antiepileptic drugs, drug resistance remains one of the major challenges in epilepsy therapy. Genetic factors are known to play a significant role in the prognosis and treatment of epilepsy. The aim of this study was to determine the frequencies of alleles for CYP2C9, CYP2C19, and CYP2D6 genes in Turkish children with epilepsy, and to investigate the relationship between the genetic polymorphism of these genes with multiple drug resistance in epilepsy patients.
We genotyped 132 epileptic patients (60 drug resistant and 72 drug responsive) and 55 healthy controls for six single nucleotide polymorphisms (SNPs) in CYP2C9, CYP2C19, and CYP2D6. Genotype, allele, and haplotype frequencies were compared between groups.
The frequencies of CYP2C9*3/*3 genotype and CYP2C9*3 allele, and the haplotype CCGG (CYP2C9*2 C>T, CYP2C9*3 A>C, and CYP2C19*2 G>A, CYP2C19* G>A) were significantly higher in drug-resistant versus -responsive patients.
Our results demonstrated the important role of the CYP2C9*3 allelic variant in preventing epilepsy patients from developing drug resistance. These data suggest that CYP2C9, CYP2C19, and CYP2D6 SNPs and haplotypes may affect the response to antiepileptic drugs.
[Show abstract][Hide abstract] ABSTRACT: One-third of all individuals with epilepsy are resistant to antiepileptic drug (AED) treatment. Antiepileptic treatment response has been suggested to be modulated by genetic polymorphisms of drug efflux transporters. Several polymorphic variants within the multidrug resistance 1 (MDR1) gene, which encodes the major transmembrane efflux transporter P-glycoprotein, have been proposed to be associated with AED resistance in epilepsy patients. The aim of this study was to evaluate the effect of C3435T and G2677T/A polymorphisms of MDR1 on AED resistance in Turkish children with epilepsy. MDR1 C3435T and G2677T/A were genotyped in 152 patients with epilepsy, classified as drug-resistant in 69 and drug-responsive in 83. Genotypes of the C3435T and G2677T/A polymorphisms were determined by polymerase chain reaction followed by restriction fragment length polymorphism. Genotype and allele frequencies of C3435T and G2677T/A polymorphisms of the MDR1 gene did not differ between drug-resistant and drug-responsive epilepsy patients. Our results suggest that MDR1 C3435T and G2677T/A polymorphisms are not associated with AED resistance in Turkish epileptic patients. To clarify the exact clinical implication of the MDR1 polymorphisms on the multidrug resistance in epilepsy, further investigations in various ethnic populations would be necessary.
[Show abstract][Hide abstract] ABSTRACT: Craniofrontonasal syndrome (CFNS, MIM #304110) is a rare X-linked dominant developmental disorder that shows paradoxically greater severity in affected females than in affected males. Our female patient with frontonasal dysplasia, craniosynostosis and additional malformations was consistent with CFNS. EFNB1, which encodes a member of the ephrin family of transmembrane ligands for Eph receptor tyrosine kinases, is the only gene in which mutation is known to cause CFNS. Here, we describe 402T>C, a novel de novo mutation on EFNB1. This mutation results in substitution of highly conserved isoleucine at 134th residue to threonine.
[Show abstract][Hide abstract] ABSTRACT: Background:
Infantile neuroaxonal dystrophy (INAD) is a recessive disease that results in total neurological degeneration and death in childhood. PLA2G6 mutation is the underlying genetic defect, but rare genetic heterogeneity has been demonstrated. One of the five families we studied did not link to PLA2G6 locus, and in the family one of the two affected siblings additionally had atypical features including facial dysmorphism, pectus carinatum, scoliosis, pes varus, zygodactyly and bilateral cryptorchidism as well as cerebellar atrophy, as previously reported.
Sural biopsy was investigated by electron microscopy. PLA2G6 was screened for mutations by Sanger sequencing. In the mutation-free family, candidate disease loci were found via linkage analysis using data from single nucleotide polymorphism genome scans. Exome sequencing was applied to find the variants at the loci.
PLA2G6 mutations were identified in four families including the one with an unusually severe phenotype that led to death within the first 2 years of life. In the remaining family, seven candidate loci totalling 15.2 Mb were found and a homozygous truncating mutation p.Q642X was identified in NALCN at 13q32.3. The patients are around 20-years-old.
NALCN is the gene responsible for INAD with facial dysmorphism. The patients have lived to adulthood despite severe growth and neuromotor retardation. NALCN forms a voltage-independent ion channel with a role in the regulation of neuronal excitability. Our findings broaden the spectrum of genes associated with neuroaxonal dystrophy. Testing infants with idiopathic severe growth retardation and neurodegeneration for NALCN mutations could benefit families.
Journal of Medical Genetics 06/2013; 50(8). DOI:10.1136/jmedgenet-2013-101634 · 6.34 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Purpose:
The accumulation of free radicals may lead to seizures and increase the risk of their recurrence. Glutathione peroxidase and superoxide dismutase are 2 major enzymes that are involved in antioxidative defense mechanisms. Selenium (Se), zinc (Zn), and copper (Cu) are important trace elements that participate in the structure of these enzymes. The purpose of this study was to evaluate the possible associations between trace elements and idiopathic intractable epilepsy (IIE) by comparing the levels of Se, Zn, and Cu between patients with IIE and healthy children.
Our study was designed as a case-control study with 70 IIE patients and 60 healthy children who were matched for age, ethnicity, and socioeconomic status. The levels of serum Se, Zn, and Cu were measured with an atomic absorption spectrophotometer. The results were statistically analyzed with SPSS version 16.0.
We found that the patients with IIE had significantly decreased levels of serum Se and Zn compared to those of the control group (p<0.05).
We believe that this study presents the first reports of decreased levels of Se and Zn in patients with IIE. These results may provide new insights for delineating the etiological basis of IIE and its potential therapeutic options.
Epilepsy research 10/2012; 104(1-2). DOI:10.1016/j.eplepsyres.2012.09.013 · 2.02 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A 25-year-old female was referred for short stature and joint deformities. Except for previous corneal transplantation, her medical history was unremarkable. Initial physical examination revealed the presence of a coarse facies, short neck, kyphosis, restricted joint movements and deformities, and cardiac murmur besides a normal intellect. Urine glycosaminoglycan levels were high, and blood enzyme assay indicated significantly low alpha-L-iduronidase levels. Mucopolysaccharidosis I (MPS I) was diagnosed and prompted the onset of enzyme replacement therapy (ERT), which significantly improved articular complaints, while cardiac pathology remained stable. At the eighteenth month of ERT, sudden vision loss developed. She spontaneously recovered her vision in a month. MPS I is a progressive disease, in which tissue accummulation of heparan and dermatan sulphate result from defective activity or lack of alpha-L-iduronidase. ERT in MPS I usually presents favourable outcomes or at least stabilization of symptoms. This present case qualifies as the first report ofa MPS I patient developing sudden vision loss under ERT. We suggest that further research studies are warranted for defining the efficiency and possible limitations of ERT.
[Show abstract][Hide abstract] ABSTRACT: We report a case with a new syndrome that presents with glaucoma, cryptorchidism, oculocutaneous albinism, ataxia, hypotonia, autistic behaviour besides various major and minor craniofacial dysmorphic, skeletal, and neuroimaging findings, and suggest that this case represents a new syndrome not reported previously.
[Show abstract][Hide abstract] ABSTRACT: Three brothers, born to parents who were first cousins, were referred for progressive diffuse dystonia. Initial physical examinations revealed minor dysmorphic features, e.g., bifrontal narrowing, downslanting palpebral fissures, low-set ears, upturned nostrils, and microretrognathia, as well as neurodevelopmental delay. Absence of eye contact and head control, diffuse dystonia, hypokinesia, choreoathetosis, tremor, increased deep tendon reflexes, diffuse muscle atrophy, and spasticity were evident during neurologic evaluations. After laboratory investigations, imaging studies, and the exclusion of other causes of childhood dystonia, the children were diagnosed with Segawa syndrome. A molecular analysis of the tyrosine hydroxylase gene revealed a novel P492R (1475 C>G) mutation, further confirming the clinical diagnosis. After 1-month therapy with 2 mg/kg/day l-dopa, no changes in signs were evident. Selegiline was added, which greatly improved the clinical picture. Segawa syndrome in three brothers resulted from a novel mutation in the tyrosine hydroxylase gene. Treatment with a combination of l-dopa and selegiline led to favorable outcomes.
[Show abstract][Hide abstract] ABSTRACT: Oxidative stress seems to be an important factor in the development of age-related macular degeneration (AMD). The role of DNA repair mechanisms has also received attention recently in AMD pathogenesis. This case-control study was conducted to determine the frequency of polymorphisms in two DNA repair enzyme genes, xeroderma pigmentosum complementation group D (XPD), codons 312 and 751, and x-ray cross-complementing group 1 (XRCC1), codons 194 and 399, in patients with AMD and in disease-free control subjects.
Polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) were used to analyze XPD Asp312Asn and Lys751Gln and XRCC1 Arg194Trp and Arg399Gln in 120 patients with AMD (65 with dry type and 55 with wet type) and in age-matched 205 disease-free control subjects.
Genotypic and allelic distributions of the polymorphisms were detected. For the XPD polymorphism, although the allele frequencies were not different between the patients and healthy control subjects, there was a significant difference between frequencies for the XPD751 Gln/Gln genotype in AMD patients (9%) and healthy control subjects (19%; P=0.02). The XPD751 Gln/Gln genotype seemed to have a protective effect against development of AMD (odds ratio, 0.41; 95% confidence interval, 0.19-0.88). Stratification by subtype of AMD revealed that the XPD751 Gln/Gln genotype was significantly lower only in the patients with dry type (P=0.02). These interactions remained nearly significant after Bonferroni correction (P<0.0125). Haplotype analysis for the two XPD polymorphisms revealed that the haplotype GC (312Asp-(751)Gln) was a protective haplotype against AMD. No statistically significant difference was found for the genotypic and allelic distributions of the polymorphisms in the XRCC1 gene between the patients and the control subjects.
Polymorphism in XPD codon 751 may be associated with the development of AMD.
[Show abstract][Hide abstract] ABSTRACT: We report a 4-year-old Turkish boy with Warburg Micro syndrome born to consanguineous parents. He had ptosis, deep-set eyes, microphthalmia, microcornea, microcephaly, prominent ears and nasal root, micrognathia, hypertrichosis, spastic diplegia, skin hyperextensibility and joint hypermobility, hypogenitalism, cerebral atrophy and hypoplasia of corpus callosum and cerebellum. Sequence analysis of exon 8 of the RAB3GAP gene has confirmed the presence of a splice donor mutation (748+1G>A) in the homozygous state. Skin hyperextensibility and joint hypermobility in the affected child have not been reported in Warburg Micro syndrome cases to date. This report compares the symptoms and features of the case with previously reported cases of Warburg Micro syndrome.