فهرست مطالب raheleh vazehan

Ion channel dysfunction in the brain can lead to impairment of neuronal membranes and generate several neurological diseases, especially neurodevelopmental disorders.

In this study, we set out to delineate the genotype and phenotype spectrums of 14 Iranian patients from 7 families with intellectual disability (ID) and/or developmental delay (DD) in whom genetic mutations were identified by next-generation sequencing (NGS) in 7 channel-encoding genes: KCNJ10, KCNQ3, KCNK6, CACNA1C, CACNA1G, SCN8A, and GRIN2B. Moreover, the data of 340 previously fully reported ID and/or DD cases with a mutation in any of these seven genes were combined with our patients to clarify the genotype and phenotype spectrum in this group.

In total, the most common phenotypes in 354 cases with ID/DD in whom mutation in any of these 7 channel-encoding genes was identified were as follows: ID (77.4%), seizure (69.8%), DD (59.8%), behavioral abnormality (29.9%), hypotonia (21.7%), speech disorder (21.5%), gait disturbance (20.9%), and ataxia (20.3%). Electroencephalography abnormality (33.9%) was the major brain imaging abnormality.

The results of this study broaden the molecular spectrum of channel pathogenic variants associated with different clinical presentations in individuals with ID and/or DD.

Neurodevelopmental and intellectual impairments are extremely heterogeneous disorders caused by a diverse variety of genes involved in different molecular pathways and networks. Genetic alterations in cilia, highly-conserved organelles with sensorineural and signal transduction roles can compromise their proper functions and lead to so-called “ciliopathies” featuring intellectual disability (ID) or neurodevelopmental disorders as frequent clinical manifestations. Here, we report several Iranian families affected by ID and other ciliopathy-associated features carrying known and novel variants in two ciliary genes; CEP104 and CEP290.

Whole exome and targeted exome sequencing were carried out on affected individuals. Lymphoblastoid cell lines (LCLs) derived from the members of affected families were established for two families carrying CEP104 mutations. RNA and protein expression studies were carried out on these cells using qPCR and Western blot, respectively.

A novel homozygous variant; NM_025114.3:c.7341_7344dupACTT p.(Ser2449Thrfs*8) and four previously reported homozygous variants; NM_025114.3:c.322C>T p.(Arg108*), NM_025114.3:c.4393C>T p.(Arg1465*), NM_025114.3:c.5668G>T p.(Gly1890*) and NM_025114.3:c.1666dupA p.(Ile556Asnfs*20) were identified in CEP290. In two other families, two novel homozygous variants; NM_014704:c.2356_2357insTT p.(Cys786Phefs*11) and NM_014704:c.1901_1902insT p.(Leu634Phefs*33) were identified in CEP104, another ciliary gene. qPCR and Western blot analyses showed significantly lower levels of CEP104 transcripts and protein in patients compared to heterozygous or normal family members.

We emphasize the clinical variability and pleiotropic phenotypes due to the variants of these genes. In conclusion, our findings support the pivotal role of these genes in cognitive and neurodevelopmental features.

Inherited peripheral neuropathies (IPNs) are a group of neuropathies affecting peripheral motor and sensory neurons. Charcot-Marie-Tooth (CMT) disease is the most common disease in this group. With recent advances in next-generation sequencing (NGS) technologies, more than 100 genes have been implicated for different types of CMT and other clinically and genetically inherited neuropathies. There are also a number of genes where neuropathy is a major feature of the disease such as spinocerebellar ataxia (SCA) and hereditary spastic paraplegia (HSP). We aimed to determine the genetic causes underlying IPNs in Iranian families.

We performed whole exome sequencing (WES) for 58 PMP22 deletion-/duplication-negative unrelated Iranian patients with a spectrum of phenotypes and with a preliminary diagnosis of hereditary neuropathies.

Twenty-seven (46.6%) of the cases were genetically diagnosed with pathogenic or likely pathogenic variants. In this study, we identified genetically strong variants within genes not previously linked to any established disease phenotype in five (8.6%) patients.

Our results highlight the advantage of using WES for genetic diagnosis in highly heterogeneous diseases such as IPNs. Moreover, functional analysis is required for novel and uncertain variants.

Diagnosis of hereditary hearing loss (HHL) as a heterogeneous disorder is very important especially in countries with high rates of consanguinity where the autosomal recessive pattern of inheritance is prevalent. Techniques such as next-generation sequencing, a comprehensive genetic test using targeted genomic enrichment and massively parallel sequencing (TGE + MPS), have made the diagnosis more cost-effective. The aim of this study was to determine HHL variants with comprehensive genetic testing in our country.

  Fifty GJB2 negative individuals with HHL were referred to the Kariminejad-Najmabadi Pathology and Genetics Center, Tehran, one of the reference diagnostic genetic laboratories in Iran, during a 3-year period between 2014 and 2017. They were screened with the OtoSCOPE test, the targeted genomic enrichment and massively parallel sequencing (TGE + MPS) platform after a detailed history had been taken along with clinical evaluation.

Among 32 out of 50 GJB2 negative patients (64%), 34 known pathogenic and novel variants were detected of which 16 (47%) were novel, identified in 10 genes of which the most prevalent were CDH23, MYO7A and MYO15A.

These results provide a foundation from which to make appropriate recommendations for the use of comprehensive genetic testing in the evaluation of Iranian patients with hereditary hearing loss.

The calcium channel, voltage-dependent, L-type, alpha 1S subunit (CACNA1S) gene encodes a skeletal Ca2 channel which is involved in calcium-dependent processes such as muscle contraction and neurotransmitter release. Mutations in this gene have been accompanied by hypo- and normokalemic periodic paralysis, thyrotoxic periodic paralysis, and susceptibility to malignant hyperthermia. We report the clinical and genetic findings in a patient diagnosed with metabolic myopathy who had episodic attacks of muscle pain and weakness but with no family background of the disease. Next-generation sequencing (NGS) using a panel targeting metabolic myopathy and myotonia genes identified a de novo heterozygous pathogenic variant c.3724A>G, p.Arg1242Gly, in exon 30 of CACNA1S. As the second report of this variant, this case may broaden the CACNA1S-related disease spectrum to include normokalemic periodic paralysis.

Charcot-Marie-Tooth disease (CMT) is the most common inherited neurological disorder, affecting both motor and sensory peripheral nerves. Neurophysiological patterns divide CMT into three main groups: demyelinating CMT1 (upper limb motor nerve conduction velocity (MNCV) 38 m/s) and intermediate CMT (MNCV 25-45 m/s). CMT has been also categorized based on the mode of inheritance and subtypes are defined according to the mutant genes. Duplication of 1.5 Mb of chromosome 17, encompassing PMP22 gene, accounts for up to 80% of cases with demyelinating neuropathies in its most prevalent type, CMT1A. Deletion of the same region is responsible for Hereditary Neuropathy with liability to Pressure Palsies (HNPP).
The Clinical and genetic heterogeneity of CMT disease has been always considered as one of the major challenges in diagnostic procedure. Although, most current genetic testing strategies for CMT are mainly based on the family history and data on clinical and neurophysiological assessments, variable degree of phenotypic expression and large number of genes involved in CMT bring challenges to the diagnosis. Hence, in everyday practice in genetic laboratories, the detection rate for this group of patients may significantly influenced by this genetic and clinical heterogeneity. Our aim was to present our experience on the applicability of the recommended strategies for CMT diagnosis.
Dosage analysis using multiplex ligation probe amplification (MLPA), a specific and sensitive quantitative method, is considered as the first step in the detection of demyelinating CMT. MLPA analysis of 30 unrelated individuals who were referred to Kariminejad-Najmabadi Pathology and Genetics Center with general diagnosis of polyneuropathy, revealed 7 cases of CMT1A (due to 1.5 Mb duplication) and a case with HNPP (1.5 Mb deletion).
This detection rate of about 25% for MLPA testing elucidates the need for a better understanding of the circumstances under which the genetic test is requested. Considering the clinical data, when MLPA fails to detect the causative gene, patients are supposed to be subjected to extended analysis. Implementation of NGS in diagnosis of CMT has made a powerful platform to detect the full spectrum of CMT mutations, which provides an efficient and cost effective genetic testing and therefore an increased detection rate.

Neuromuscular disorders (NMDs) include a broad range of diseases affecting muscles, nerves and neuromuscular junctions. Approximately 761 different disorders occur in this group which is subdivided into 16 different subgroups with 406 known genes. NMDs are genetically and clinically heterogeneous conditions. The advent of next generation sequencing (NGS) approaches has accelerated the pace of discovery of NMDs genes. In this study, we describe the validation of an NGS panel, for comprehensive mutation detection in NMDs patients. During a year, a total of 46 patients were examined, mostly offspring of consanguineous marriages. Data analysis was performed to identify the most probable pathogenic rare variants in known NMD genes. Co-segregation analysis and genotype–phenotype correlation led to identification of causal variants. In 33 out of 46 patients (71.7%), the pathogenic variant was identified in the following known genes: CAPN3, Col6A1, Col6A3, DMD, DYSF, FHL1, GJB1, ISPD, LAMA2, LMNA, PLEC1, RYR1, SGCA, SGCB, SYNE1, TNNT1 and 22 novel pathogenic variants were detected which is quite high compared to the overall diagnostic yield of no more than 50% in most other reports.

Hereditary ataxias are heterogeneous group of neurodegenerative disorders classified mainly into more than 40 autosomal dominant cerebellar ataxias and 50 recessive ataxias. Large amount of nearly uncommon subtypes with extensive phenotypic overlap and relatively high rate of abnormal repetitive sequence expansions, such as trinucleotide repeat expansions make diagnostic genetic testing complicated.
Here we used targeted next generation sequencing on unrelated ataxias probands for whom commonly known spinocerebellar ataxias (SCAs) caused by trinucleotide repeat expansions including 1, 2, 3, 6, 7 and 17 and Friedreich ataxia have been excluded based on in-house testing strategy. All the cases were recruited from individuals referred to Kariminezhad-Najmabadi center in Tehran, Iran between 2015-2016. We performed targeted capture on a total of 50 genes considered to be appropriate candidates for ataxia. Variants detected through next generation sequencing (NGS) were confirmed and co-segregated through Sanger sequencing. From 8 unrelated Ataxia patients that referred to our center, genetic testing revealed a total of 5 mutations in the 4 investigated patients, from which 4 were novel variants and 1 has been previously published as a pathogenic variant. Our pathogenicity interpretation pathway detected five different mutations in three different genes comprising SACS, ATM, and TTPA. Of which, we identified two frameshift variants in SACS and TTPA genes, one nonsense variant in ATM gene and a splice site variant and a missense variant in ATM gene in a compound heterozygote state and a known missense variant in ATM gene.
Considering the exact preliminary clinical diagnosis and excluding the possibility of repeat expansions, it seems that targeted next generation sequencing would be a promising method for molecular detection in hereditary ataxia.