Genetics in the Third Millennium
Volume:14 Issue: 1, 2016

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.

The sarcoglycanopathies (SGPs) are a subgroup of autosomal recessive limb girdle muscular dystrophies (LGMDs). They are caused by mutations in gamma, alpha, beta, and delta sarcoglycans (SGs) genes. Alpha-SGPs are the most frequent form of SGPs. Muscle biopsy studies in patients with sarcoglycanopathies have indicated that loss of one SG subunit leads to instability of whole SG complex.
Autozygosity mapping is a powerful gene mapping approach for rare recessive inherited disorders in consanguineous families.
two unrelated Iranian families, having 12affected patients, were investigated.Patient’screatine kinase level was high. IHC findings revealed muscular dystrophy suggestive of sarcoglycanopathy.
Autozygosity mapping, using short tandem repeat (STR) markers linked to the SG genes, showed co-segregation of the phenotype with STR markers linked to the SGCA gene.
Mutation analyses revealed novel homozygous deletions in two families; one of them was 11 base pairs in exon 4 and the other was a 2 nucleotide deletion in exon 6
deletions causeframeshift and premature stop codon. They result ineliminating the expression of the downstream part of the extracellular domain of the protein. This domain has a critical role by associating with other molecules of dystrophin–glycoprotein complexes. IHC studies combined with autozygosity mapping and mutation screening is an efficient diagnostic method in the sarcoglycanopathies.

Charcot-Marie-Tooth (CMT) diseases represent a heterogeneous genetic disorder with more than 80 genes implicated, however sharing a similar phenotype. In recent years, advances in molecular genetics and molecular biology, and also the development of various animal models of CMT, have led to a better understanding. This knowledge represents a prerequisite for the development of future therapies in CMT.
In this review, we discuss current research progress and recent promising preclinical work for CMT1A and the development of new biomarkers in CMT. We also describe CMT therapeutic development and ongoing clinical trials. While no effective therapy is known to date, ongoing new therapeutic trials such as PXT3003 (a low dose combination of the three already approved drugs baclofen, naltrexone, and D-sorbitol) give hopes for potential curative treatment.
This summary of CMT research identifies some of the gaps which may have an impact on upcoming clinical trials.

Limb girdle muscular dystrophies (LGMDs) are group of neuromuscular disorders which are characterized by progressive muscle weakness and they mostly affect the pelvic and shoulder girdle muscles. This disease can be inherited as autosomal dominant (LGMD1) and autosomal recessive (LGMD2). So far seven autosomal dominant and 20 autosomal recessive forms of this disease have been recognized reflecting high level of genetic heterogeneity. Autosomal recessive types constitute about 90% of all cases, and are more likely to happen in countries with high rates of consanguineous marriages such as Iran. The limb-girdle muscular dystrophies typically show degeneration/regeneration (dystrophic changes) on muscle biopsy, which is usually associated with elevated serum creatine kinase concentration. For an affected individual it is necessary to first rule out an X-linked dystrophinopathy such as Duchene and Becker muscular dystrophies (DMD/BMD). Biochemical testings (i.e., protein testing by immunostaining or immunblotting) performed on a muscle biopsy have shown several subtypes such as sarcoglycanopathy, calpainopathy, dysferlinopathy, and O-linked glycosylation defects (also known as dystroglycanopathy).
The genetic test is primarily performed to aid prenatal diagnosis and carrier detection. For the one has to rule out X-linked dystrophinopathy such as DMD/BMD. For this one may use MLPA technique. Indirect methods such as haplotyping by the use of short tandem repeat (STR) markers linked to dystrophin gene have shown to be valuable. MLPA can detect deletion and duplication of dystrophin gene which account for 60 to 70% of dystrophinopathies. If DMD/BMD has been rule out, haplotype analysis using STR markers linked to genes responsible for most prevalent forms of LGMDs will be performed. The next step is the Sanger sequencing of the candidate gene. Ruling out of dystrophinopathies especially in pedigrees including only one isolated patient or just male affected patients are diagnostic problems of LGMDs which should be concerned.
Nowadays all these difficulties have been solved by the advent of high-throughput next generation sequencing which soon will replace most cumbersome methods.

congenital muscular dystrophy (CMD) is an umbrella term collecting a heterogeneous groups of genetic disorders , mostly with Autosomal recessive mode of inheritance , and are characterized by muscle weakness since birth or in early infancy , with a dystrophic pattern on muscle biopsy . these children are usually hypotonic and may have joint contractures . The serum creatine kinase level can be elevated. The clinical course is usually static, but occasionally slow regression and sometimes a relative improvement can be noticed . A dozen number of genes are known to cause congenital muscular dystrophy and many individuals with CMD remain unclassified .
CMD can be subdivided based on the expression of the extracellular matrix protein , Laminin-alpha2 (Merosin) on muscle biopsy , into Merosin negative and positive . Some clinical features are crucial for making more accurate diagnosis such as distal laxity (common in collagen 6 disorders) and rigid spine (seen in Selenopathies) .

Hereditary Motor Sensory Neuropathies (HSMN/CMT) is the most common form of inherited polyneuropathy and is typically associated with an insidious onset of muscle wasting, distal predominant motor and sensory loss. HSMN/CMT is usually presenting with genetic heterogeneity, leading to diagnostic considerations that are dramatically developing for this disease. Clinical presentations, gene mutation frequencies, inheritance pattern in the pedigree plus electrodiagnosticsl are also beneficial in framing testing algorithms in practical clinical settings.
Next-generation sequencing (NGS), joined with specific testing panels, is increasing the efficiency of multigene analysis and is very quickly overtaking targeted testing strategies. Other types of hereditary neuropathies, including sensory predominant or motor predominant forms, are included in the general classification of CMT; however, for the purpose of this abstract, we will focus primarily on the forms accompanied with sensory and motor insufficiencies.
Currently, in the clinical practice multigene panel testing and NGS may be considered first-line in many cases. However, it is worth mentioning that to obtain to initial targeted testing for the PMP22 duplication in CMT patients with demyelinating conduction velocities is a reasonable decision. With the improvement of technology and the price-cut, targeted testing will be soon replaced by multigene NGS panels that can perceive the full range of CMT mutations. Furthermore, clinical insight is still necessary given the variants of uncertain significance accompanied with NGS. Despite the current limitations, the genetic diagnosis of CMT is critical for accurate prognostication, genetic counseling, specific targeted therapies hopefully in future. Although whole exome and whole genome sequencing strategies have the power to further elucidate the genetics of CMT, continued technological advances are desirable.

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.

Farber lipogranulomatosis is a rare inherited condition involving the breakdown and use of fats in the body (lipid metabolism). Characteristics are early-onset subcutaneous nodules, painful and progressively deformed joints, and hoarseness by laryngeal involvement In affected individuals, lipids accumulate abnormally in cells and tissues throughout the body, particularly around the joints. Three classic signs occur in Farber lipogranulomatosis: a hoarse voice or a weak cry, small lumps of fat under the skin and in other tissues (lipogranulomas), and swollen and painful joints. Affected individuals may also have difficulty breathing, an enlarged liver and spleen (hepatosplenomegaly), and developmental delay.
Here we report 6 patients with the diagnosis of farberlipogranulomatosis in the past 7 years, confirmed by mutation analysis, and detected 4 novel mutations in them. Clinical pictures in our patient were mostly,joint swelling and tenderness, and weak cry, 5 of the patients were female and only one affected boy who died at Newborn period. Three of them showed hepatosplenomegaly. Three of the patients are alive. We analysed ASAH1 gene and detected 4 novel mutations on them.

NP-C is a severe, progressive and irreversible neurovisceral disease, which is invariably fatal. NP-C is a rare disease, with an estimated minimal incidence of 1/120,000 live births . NP-C is caused by mutations in NPC1 (~95% of patients) or NPC2 genes .Defective NPC1 and NPC2 proteins result in a disruption of lipid metabolism . One of special features of this disorder is heterogeneous manifestations. Overall various clinical manifestation of NPC disease can be categorized in three main groups: Visceral or systemic, neurological and psychiatric. The most important clinical features of each group are as follow: Visceral (prolonged neonatal jaundice, unexplained splenomegaly with or without hepatomegaly), neurological (vertical supranuclear gaze palsy, gelastic cataplexy), Psychiatric (early cognitive decline or dementia).In addition of variable clinical features, NPC disease has a wide range of age manifestation, from neonatal period through adulthood. Neurologic features unlike visceral symptoms are not common under early infancy period. After that neurological symptoms become prominent and finally from juvenile period through adolescent/adult age psychiatric symptoms in addition of neurological signs will present.Therefore with considering the variability in clinical presentations and age manifestation of NPC disease, it seems a little hard to diagnose the disease.
The NP-C Guidelines Working Group revised the recommendations for the diagnosis and management of Niemann-Pick type C disease in 2012, to provide the most up-to-date information about NP-C. A new tool – the NP-C Suspicion Index – has also been developed for healthcare professionals to help identify patients for whom further investigation is required. This will hopefully help to achieve earlier and improved diagnosis of NP-C in patients suspected of having the disease . Suspicion index is one of important tools for early diagnosis of NPC disease that developed in 2012 by Wijburg et al. Early diagnosis is important, because it help us to start early treatment with Zavesca (the only available drug for NPC disease that acts as a substrate reduction therapy). This process finally helps to patients with reducing the progression of disease. From a physician’s point of view the Suspicion Index works both as a reminder of the complex and varied symptoms characteristic of NP-C, as well as support in making the right referral decision.Suspicion index likes a checklist and fill it tells us the NPC risk prediction score. The three main categories of disease symptoms have been ranked into five groups according it’s importance. Co-Occurrence of symptoms (within and across categories) and family history are also taken into account to define the Risk Prediction Score.

Stroke is the third cause of death in the world after the cancer and cardiovascular disease. It has been shown that stroke in Northeast of Iran occurs approximately one decade earlier than in Western countries. Reasons for the high stroke incidence among Persian are not yet clear. It is the first gene-association study in Persian population, which determines the relationship between 25 gene variations and stroke. This genes are involved in 3 cellular pathways and in Single nucleotide polymorphisms (SNPs) in miRNA genes. So we made a Genetic stroke databases with more than 1000 Stroke patients for this region. 25 gene polymorphisms were analyzed and registries in this database. Furthermore this database is part of INTERNATIONAL STROKE GENETICS CONSORTIUM . In the present study aimed to determine if there is any association between 22 genetic variations in protein-coding genes and also 11 polymorphisms in miRNA-coding regions. In this case-control study patients with ischemic stroke and subjects without any history of vascular diseases were recruited. All cases were diagnosed via computed tomography (CT) scans and magnetic resonance imaging (MRI). Genotyping was gen in cases and controls using Real-Time, PCR-RFLP and multiplex ARMS-PCR method. Statistical analyses were performed using SPSS v.21 software and a pvalue

Sporadic Alzheimer’s disease (SAD) is a multi-factorial disease caused by genetic, epigenetic, environmental and metabolic factors. Current understandings of the possible mechanisms of AD such as inflammation and oxidative stresses in the brain have led us to investigation of potential AD therapeutics. Currently herbal medicines with fewer side effects comparing to other chemical medicine are in the point of attention. SemililTM is a herbal extract with possible role as an anti-inflammatory and anti-oxidant agent that can improve the blood circulation, lymphedema and immune system functions. Among genes that have been implicated in SAD, three genes including Daxx, Nfkb and Vegf have shown significant statistical diversity in Alzheimer human brain as apoptosis mediator, pro-inflammatory transcription factor and key factor in orchestrating angiogenesis respectively. With this knowledge these genes have been chosen in our study to be investigated for neuroprotective effect of Semilil. This study was performed by comparing the expression level of the mentioned genes in the hippocampus of SAD rat model using qPCR method in treated and untreated groups. The therapeutic effect of this extract was studied at the behavioral, learning and memory level using Morris Water Maze (MWM) test as well. Five rat groups (control, sham, SAD model, herbal extract treated and ethanol treated) were used for the study. Drug interventions were started on the 21st day after modeling and each treatment group received the drug by intra-peritoneal route for 21 days. Gene expressions were measured using qPCR technique among groups. MWM was applied to determine the spatial learning and memory ability of the rats. All genes showed lower expression in SAD rat’s model comparing to control group but only Nfkb gene showed higher expression in SAD rat’s model treated with herbal extract. Two other genes did not show any expression change between the studied groups. In MWM, the significant changes in spatial learning that had been observed in rat’s model group did not show any alteration in the herbal-treated group.

Sporadic Alzheimer’s disease (SAD) is affected by genetic risk factors, aging and oxidative stresses. The herbal extract of R. canina, T. vulgare and U. dioica has a beneficial role in aging, as an anti-inflammatory and anti-oxidative agent. We investigate the neuroprotective effects of this herbal extract in the rat model of SAD.
The rats were divided into control, sham, model, herbal extract -treated and ethanol-treated groups. Drug interventions were started on the 21st day after modeling and each treatment group was given the drugs by intraperitoneal (I.P.) for 21 days. The expression levels of the five important genes for pathogenesis of SAD including Syp, Psen1, Mapk3, Map2 and Tnf-α were measured by qPCR between the hippocampus of SAD model which were treated by this herbal extract and control groups. The Morris Water Maze was adapted to test spatial learning and memory ability of the rats.
Treatment of the rat model of SAD with herbal extract induced a significant change in expression of Syp (P=0.001) and Psen1 (P=0.029). In Morris Water Maze, significant disturbed changes in spatial learning that was seen in the rat model group were improved in herbal-treated group.
This herbal extract could have anti-dementia properties and improve spatial learning and memory in SAD model rats.

Suicide is a major public health concern, with approximately one million people committing suicide world-wide each year .Risk factors for suicidal behavior include, psychiatric and medical illness, impulsivity, aggression, alcohol and drug abuse specially stimulants, and stress. Neurobiological, brain mappings and biochemical studies have revealed that suicide victims experiencing a large number of changes in metabolic pathways that end to committing suicide. Our study aimed to discover gene expression changes in these subjects.
Blood samples collected from 84 saved suicide victims with at least one attempt to suicide in last 12 months that suffering from psychosis (50 SCZ, 19MDD, 15 BPD) and 70 gender , age , socioeconomic matched subjects with psychosis (40 SCZ,12MDD,18BPD) without any suicidal thoughts . After RNA extraction and cDNA synthesis, Gene expression profiling analysis was done using the Affymetrix GeneChip Human Genome U133 plus 2.0 Array Platform containing probes representing 39,000 genes. Preparation of labeled and fragmented aRNA targets, hybridization, and scanning were carried out according to the manufacturer's protocol (Affymetrix Santa Clara, CA).Microarray results confirmed by real time PCR. Gene ontology analysis was conducted for differentially expressed genes(fold change greater than 2 and a P value less than 0.05) using the enrichment algorithm integrated in the online Database for Annotation, Visualization and Integrated Discovery (DAVID 6.7)
Results showed significantly over expression of 65 genes including dopamine receptors and mitochondrial complex I and II genes in suicide victims. Also significantly low expression of 21 genes including COMT, NRG1 and GRM3 has been detected in suicide victims. Regulation of dopamine metabolic process and Central Nervous System Development were main terms indicated in enriched gene ontology calculations.
It seems that gene expression changes in neurodevelopmental and dopaminergic pathways are correlated to suicide tendency and this is related to neuorobilogical functions and decision making processes of brain. Results of this project can help to predict the possibility of committing suicide in psychotic patients and suggesting potential markers for suicide thoughts.

Schizophrenia (SCZ) is a complex disorder with no clarified etiology or biological diagnosis.
Symptoms of schizophrenia including positive, negative and cognitive deficits.The neurodegenrative and neurodevelopmental hypothesis are main views about the pathophysiology of schizophrenia. Neuregulin 1 is one of four proteins in the neuregulin family that act on the EGFR family of receptors. NRG1 gene, locating at 8p21.1-22, is produced in numerous isoforms by alternative splicing, which allows it to perform a wide variety of functions. It is essential for the normal development of the nervous system and the heart.At least six major types of neuregulin 1 exist in humans. type I, II and III NRG1 are expressed in excitatory and inhibitory neurons, as well as astrocytes , and some types (I and IV) can be regulated by neuronal activity.
We studied expression of types I, II, III of NRG1 gene in 31 SCZ patients and 30 normal subjects using quantitative Real time PCR. Also positive and negative symptom scale (PANSS) and brief psychiatric rating scale (BPRS) obtained from patients.
The findings showed significant (p

In this presentation, we review briefly on biogenesis of peroxisomes with regard to the recent findings on biogenesis. Peroxisomes perform a range of various functions as oxidation of very long chain fatty acids, generation and removal of hydrogen peroxide, while peroxisomes have also been implicated in β-oxidation of aromatic and cyclic compounds, synthesis of plasmalogens, isoprenoids, lysine and glycine betaine, metabolism of purines and pyrimidines, and catabolism of polyamines, D-amino acids and methanol. Moreover peroxisomes are participated in signaling and developmental pathways. Disruption of those functions in human leads to severe disorders, mainly cause death several weeks after the birth. Peroxisome biogenesis disorders (PBDs) are caused by defects in import of peroxisome matrix proteins and biosynthesis of peroxisomal membrane proteins. Thus the proper function of peroxisome needs a well performance of a series of events that result in correct biogenesis and assembly of peroxisome. A number of genes have been identified which are responsible for peroxisome biogenesis termed PEX genes which encoded functional proteins (Pex) required for the event of peroxisome formation in the cells. Thirty two PEX genes have so far been identified. Among these genes, PEX11β, a peroxisomal membrane elongation factor, is involved in regulation of size, shape and number of peroxisomes. To investigate role of PEX11β in neural differentiation of mouse embryonic stem cells (mESCs), we generated a stably transduced mESCs line that derives expression of a shRNA against Pex11β gene following doxycycline (Dox) induction. Knock-down of Pex11β, during neural differentiation, significantly reduced expression of neural progenitor cells (NPCs) and mature neuronal markers. Interestingly, pretreatment of the cell with peroxisome proliferator-activated receptor γ (PPARγ) agonist (pioglitazone) ameliorated the inhibitory effects of Pex11β knock down on neural differentiation. Pioglitazone also significantly increased expression of neural progenitor and mature neuronal markers besides the expression of peroxisomal genes in transduced mESC. The observation that pioglitazone recovered peroxisomal function, improved neural differentiation of Pex11β knocked-down mESCs, proposes a potential new pharmacological implication of pioglitazone for neurogenesis in patients with peroxisomal defects.

The Autism Spectrum Disorders (ASDs) are common neurodevelopmental disorders estimated to affect 1 in 88 children. ASD is a complex condition, result of genetic, epigenetic and environmental factors. However, Genetic comopnent seems to play an important role. The loss/Gain of 1KB and more nucleotides, Copy number variation (CNV), is the significant genetic factor in the etiology of ASD. The CNV rate is reported as 10-15% in children with ASD.
In this study we investigated CNV in 50 Iranian patients with sporadic Autism using High resolution Cytogenetics banding, MLPA, and Array-CGH techniques. All patients had additional features such as Intellectual Disability, Seizure, and Craniofacial anomalies.
Two out of 50 (4%) patients showed chromosome abnormality including 16p duplication (16p13.11-p13.3) and 15q deletion (15q11.2q13.1). MLPA using both sub-telomeic (p036 and p070) and Autism (p343 and p396) kits was done for 50 patients and CNV was detected in 5 (10%) patients both in subtelomeric and interstitial regions, one overlapping the cytogenetic finding. Array CGH was performed for 15 patients most of whom had normal results with the Cytogenetic and MLPA techniques. Six out of 15 (40%) patients using array-CGH showed significant CNVs including pathogenic (such as 15q24 Microdeletion), likely pathogenic (such as Xq28 Microdeletion) and Uncertain/ Could be Significant Ones (such as Xp22.33 Microduplication). We performed genotype-phenotype analysis and compared our results with other similar studies.
To our knowledge, this is the first study on CNV in Iranian patients with ASD. We strongly recommend the investigation of CNV in patients with Autism with or without additional features.

Microdeletion syndromes are contiguous gene deletion syndromes of less than 5 Megabases. Most often, many of these syndromes are not detectable by routine chromosomal analysis and require more specific testing techniques such as FISH or more accurate general coverage like array comparative genomic hybridization.
As many of these syndromes are phenotypically recognizable and allow for easy clinical diagnosis, FISH technique is still a common method for consolidation of clinical diagnosis.
In our laboratory we perform FISH for common microdeletion syndromes including Di George I, Di George II, Prader-Willi, Angelman, Williams, Miller Dieker, Wolf Hirschhorn, Cri du chat, Smith Magenis, 22q13.3 microdeletion, 1p36 microdeletion, and SHOX.
In the past ten years we have performed 245 FISH tests for microdeletion syndromes. 205 tests were performed on peripheral blood and 40 tests were performed prenatally on amniotic fluid cells or chorionic villi samples. The frequency of requests were as follows: 62 for Di George I, 5 for Di George II, 37 for Angelman, 80 for Prader Willi, 46 for Williams, 6 for Miller Dieker, 1 for Smith Magenis, 2 for cri du chat, 5 for Wolf-Hirschhorn.
Results were positive in 7 Di George cases, 10 Angelman, 13 Prader Willi, 34 Williams, 1 cri du chat syndromes. The highest rate of clinical estimation of phenotype is for Williams syndrome, which is probably the most recognizable phenotype.
Considering that Di George is the most frequent microdeletion syndrome 1/4000 in humans, it can be argued that there is not sufficient referral and recognition of symptoms in our clinical setting. The second most frequent microdeletion/deletion syndrome is 1p36 which occurs in 1/5000. Again, a lack of clinical recognition is probably accountable for a lack of referral for this microdeletion syndrome. On the other hand, we get a significant number of referrals for PWS/AS and a good rate of confirmation 23/126.
We would recommend a familiarization with the phenotype of microdeletion syndromes in the clinical setting which could optimize diagnosis.

Hearing loss (HL) is the most common communication disorder affecting about 1/1000 births worldwide caused by environmental or genetic factors. About 30-50% is attributed to genetic factors and till now more than 85 genes have been implicated in non-syndromic HL. In Iran, HL is second to intellectual disability as the most common disability, affecting 1 of every 166 persons. About 15 years ago the studies of genes causing deafness have been started in Genetics Research Center (GRC) of University of Social Welfare and Rehabilitation Sciences, Tehran, Iran. Over 2500 families with hereditary HL have been referred to GRC from different parts of Iran. Almost all families have been investigated for the frequency of GJB2 gene mutations.The mutation in this gene is the most prevalent gene causing hereditary HL (HHL) in Iran. Total of 395 families had GJB2 gene mutations. The prevalence of GJB2-related deafness is relatively low in our country comparison with North American and European countries. We have also determined the prevalence of other known genes in our heterogeneous population.
In order to determine Iranian AR hereditary HL gene spectrum we used a custom targeted genomic enrichment panel which included all the 116 known HHL genes. A total of 302 GJB2-negative families were selected to be studied using targeted NGS panel. We established a genetic diagnosis for 67% of probands and their families, with over half of all diagnoses attributable to variants in five genes: SLC26A4, MYO15A, MYO7A, CDH23 and PCDH15. Taken together, it can be concluded that the overall diagnosis rate of HHL in Iran is about 83%. The families which failed to identify plausible disease-causing variants using targeted NGS are a valuable cohort for novel deafness-gene discovery. Among them 23 families have been subjected to whole exome sequencing till now for whom we have identified 7 novel genes so far. In conclusion it should be mentioned that we have identify over 83% of Hereditary hearing loss genes in Iranian population and we have already identify number of candidate genes for the remaining 17% of the families.

With prevalence figures close to 0.2% at birth, hearing loss (HL) is the most frequent sensory impairment in childhood. In developed countries, genetic causes account for more than 60% of congenital HL, most often resulting in non-syndromic deafness, which is usually autosomal recessive.
Hereditary nonsyndromic hearing loss (NSHL) in Iran is highly heterogeneous, rendering molecular diagnosis difficult. Whole-exome sequencing (WES) has recently opened a new page in Mendelian disease gene discovery – enabling to study autosomal recessive HL in a new way. The aim of this study is to find more causative genes and their mutations for NSARHL in ten Iranian families by WES.
After DNA extraction and ruling out for prevalent mutations related to NSARHL in Iranian population, the proband of each family has been subjected to WES. Each individual was captured with the Agilent SureSelect Human All Exon kit, sequenced on the Illumina Hiseq 2000, and the resulting data processed and annotated with Burrows-Wheeler Aligner (BWA), Genome Analysis Toolkit (GATK), and Annovar.
Normative population databases (eg, 1000 Genomes SNP database, dbSNP, and HapMap) were used for comparison. The pathogenicity of variants was predicated using bioinformatics software such as SIFT, PolyPhen, ConSeq, CADD, GRPEE, dbNSFP and so on. Candidate pathogenetic variants have been co-segregate in families using Sanger Sequencing.
Result & A homozygous missense mutation in SLC26A4 and a novel mutation in PTPRQ genes identified in two families and confirmed by Sanger sequencing. Data analysis revealed a novel stop codon mutation in MYO7A gene in a family but co- segregation analysis failed to confirm this variant as the only cause of hearing loss in this family. Further clinical examination showed that the phenotypic variations in family exist and therefore involvement of 2 different genes causing both syndromic and non-syndromic hearing loss is possible. In addition, two novel candidate genes resulting hearing loss have been identified in two families. Further studies for confirmation of the pathogenecity of these variations and data analysis of remaining families are under investigation.

Cutis laxa is an acquired or inherited condition characterized by redundant, sagging and inelastic skin. The inherited form is heterogeneous condition with autosomal dominant, autosomal recessive and X-linked inheritance. Autosomal dominant cutis laxa is divided into three types, type I, II and III and the responsible genes are ELN, FBLN5 and ALDH18A1 respectively. An X-linked form of cutis laxa also called occipital horn is allelic to Menkes syndrome and caused by mutations in ATP7A gene. It is characterized by hyperelastic and bruisable skin, hernias, bladder diverticula, hyperextensible joints, varicosities. Mild neurological findings might be present in some patients. The autosomal recessive forms are divided into types IA, IB, IC, IIA, IIB, IIIA, and IIIB. The genes responsible for these types are FBLN4, FBLN5, LTBP4, ATP6V0, PYCR1, ALDH18A1 and PYCR1 respectively.
Neurological findings are found mainly in the autosomal recessive forms of cutis laxa. The similarities and differences of each type are discussed. Intellectual disability and hypotonia are features found in types IIA, IIB, IIIA, IIIB. Microcephaly can be seen in type IIA, IIB and IIIA, IIIB. Athetoid movements and dystonia are a distinguishing factor for type IIB, IIIA, IIIB. MRI finding that is occasionally found in type IIA is cobblestone like dysgenesis and agenesis of corpus callosum in IIA, IIIA, IIIB.
We also present data on a novel type of cutis laxa caused by mutations in the E subunit of the V-ATPase complex that affects intracellular trafficking and secretion of major extracellular matrix constituents.

Spastic Paraplegia 18 is an autosomal recessive disorder characterized by motor dysfunction, joint contracture and mental retardation. We describe two families as three cases. Case 1 is a 35-year-old woman with and spasticity and mild weakness in lower limbs. Case 2 and 3 are a sister and brother aged six and two respectively. The older sister suffered from lower limb spasticity, equinovarus and weakness in lower and upper hands. The brother had spasticity in lower limbs. Parents of both families were consanguineous. Based on positive clinical findings Hereditary Spastic Paraplegia (HSP) was suspected and targeted Next Generation Sequencing was performed for genes responsible for HSP identifying a homozygote 37607361 AC>A mutation in ERLIN2. In cases 2 and 3 a homozygous mutation was identified by whole exome sequencing. To date all patients, except one, reported with ERLIN2 mutations have intellectual disability. Our patient with normal intelligence, without additional findings highlights the fact that ERLIN2 mutations can present as uncomplicated HSP.