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The advent of high-throughput sequencing technologies has led to an exponential increase in the identification of novel disease-causing genes in highly heterogeneous diseases. A novel frameshift mutation in CNKSR1 gene was detected by Next-Generation Sequencing (NGS) in an Iranian family with syndromic autosomal recessive intellectual disability (ARID). CNKSR1 encodes a connector enhancer of kinase suppressor of Ras 1, which acts as a scaffold component for receptor tyrosine kinase in mitogen-activated protein kinase (MAPK) cascades. CNKSR1 interacts with proteins which have already been shown to be associated with intellectual disability (ID) in the MAPK signaling pathway and promotes cell migration through RhoA-mediated c-Jun N-terminal kinase (JNK) activation. Lack of CNKSR1 transcripts and protein was observed in lymphoblastoid cells derived from affected patients using qRT-PCR and western blot analysis, respectively. Furthermore, RNAi-mediated knockdown of cnk, the CNKSR1 orthologue in Drosophila melanogaster brain, led to defects in eye and mushroom body (MB) structures. In conclusion, our findings support the possible role of CNKSR1 in brain development which can lead to cognitive impairment.

During pregnancy, cell-free DNA (cfDNA) in maternal blood encompasses a small percentage of cell-free fetal DNA (cffDNA), an easily accessible source for determination of fetal disease status in risk families through non-invasive procedures. In case of monogenic heritable disease, background maternal cfDNA prohibits direct observation of the maternally inherited allele. Non-invasive prenatal diagnostics (NIPD) of monogenic diseases therefore relies on parental haplotyping and statistical assessment of inherited alleles from cffDNA, techniques currently unavailable for routine clinical practice. Here, we present monogenic NIPD (MG-NIPD), which requires a blood sample from both parents, for targeted locus amplification (TLA)-based phasing of heterozygous variants selectively at a gene of interest. Capture probes-based targeted sequencing of cfDNA from the pregnant mother and a tailored statistical analysis enables predicting fetal gene inheritance. MG-NIPD was validated for 18 pregnancies, focusing on CFTR, CYP21A2, and HBB. In all cases we could predict the inherited alleles with >98% confidence, even at relatively early stages (8 weeks) of pregnancy. This prediction and the accuracy of parental haplotyping was confirmed by sequencing of fetal material obtained by parallel invasive procedures. MG-NIPD is a robust method that requires standard instrumentation and can be implemented in any clinic to provide families carrying a severe monogenic disease with a prenatal diagnostic test based on a simple blood draw. © 2017 The Authors

Background: Fanconi anemia (FA) is a rare autosomal recessive disorder characterized by short stature, skeletal anomalies, increased incidence of solid tumors and leukemia, and bone marrow failure (aplastic anemia). FA has been reported in all races and ethnic groups and affects men and women in an equal proportion. The frequency of FA has been estimated at approximately 1 per 360,000 live births. In some populations, including Ashkenazi Jews, Turks, Saudi Arabians and Iranians, this frequency appears to be higher, probably as a result of the founder effect and consanguineous marriage. Because of extensive genetic and clinical heterogeneity (the age of onset, clinical manifestations and survival), diagnosis of FA on the basis of clinical data alone is unreliable and its molecular diagnosis is difficult. The diagnosis of FA exploits the hypersensitivity of FA lymphocytes and fibroblasts to bifunctional alkylating agents such as mitomycin C (MMC), diepoxybutane (DEB) and nitrogen mustard and differentiates it from idiopathic aplastic anemia. In this study, in addition to the patients' clinical profiles, a cytogenetic test using MMC was implemented for an accurate diagnosis of Fanconi anemia.Methods: In this study, the lymphocytes of 20 patients referred for FA, and those of their normal sex-matched controls, were treated with three different concentrations of mitomycin C (20, 30, 40 ng/ml). Slides were prepared and solid stained. In order to determine the number and kind of chromosome abnormalities, 50 metaphase spreads from each culture were analyzed. Clinical information was obtained from patient files.Results: Five patients manifested increased chromosome breakage with MMC, confirming the FA diagnosis. Two different concentrations of MMC (30, 40 ng/ml) were most effective.Conclusion: The chromosomal breakage test is important for the accurate diagnosis of Fanconi anemia. DNA crosslinking agents used to treat idiopathic aplastic anemia may be lethal for patients with FA. Thus, aplastic anemia patients with unknown etiology, infants with congenital abnormalities involved in FA and siblings of FA patients should also be cytogenetically tested."n&nbsp

Background and purpose: Spinal muscular atrophy (SMA) is a common autosomal recessive neuromuscular disorder. Carrier frequency studies of SMA have been reported for various populations. Although no large-scale population-based studies of SMA have been performed in Iran, previous estimates have indicated that the incidence of autosomal recessive disorder partly because of the high prevalence of consanguineous marriage is much higher in the Iranian population than in other populations. Methods: In this study, we used a reliable and highly sensitive quantitative real-time PCR assay with SYBR green I dye to detect the copy number of the SMN1 gene to determine the carrier frequency of SMA in 200 healthy unrelated, non-consanguineous couples from different part of Iran. Results: To validate the method in our samples, we determined the relative quantification (RQ) of patients with homozygous deletion (0.00) and hemyzygous carriers (0.29-0.55). The RQ in 10 of 200 normal individuals were within the carrier range of 0.31-0.57, estimating a carrier frequency of 5% in the Iranian population. Conclusions: Our data show that the SMA carrier frequency in Iran is higher than in the European population and that further programs of population carrier detection and prenatal testing should be implemented.

The National Mutation Frequency Databases are continuously updated mutation depositories, which contain extensive information over the described genetic heterogeneity of an ethnic group or population. Here, we report the construction of the Cypriot (http://www.goldenhelix.org/cypriot) and Iranian National Mutation Frequency Databases (http://www.goldenhelix.org/iranian), both derived from an academic effort to provide high quality and up-to-date information on the underlying genetic heterogeneity of inherited disorders in the Cypriot and Iranian populations, respectively. Both databases have been built and maintained online using ETHNOS platform, a specialized software, which provides the means for national mutation database construction and curation. Each database contains brief summaries of the various genetic disorders studied for each population, and an easy-to-use query interface provides, both to specialist as well as to non-specialist users (i.e. patients and their families), instant access to the list and frequencies of the different mutations responsible for the inherited disorders in these populations. Furthermore, numerous links to the respective Online Mendelian Inheritance in Man (OMIM) entries and, when available, to the locus-specific databases fruitfully integrate the databases content into a single Web site. Both databases can serve as valuable online tools for molecular genetic testing of inherited disorders in these populations and could potentially motivate further investigations of yet unknown genetic diseases in the Cypriot and Iranian populations. 27 598 599 Cited By :15

Background: Tooth agenesis is one of the most common developmental anomalies in human and the main reasons for its occurrence are still unknown. Mutations of several genes such as PAX9, MSX1, AXIN2, KDF1 and WNT10A have been reported which are associated with non-syndromic tooth agenesis. However, PAX9, MSX1 and WNT10A are commonly reported in the literature. Hence, the aim of this study was to investigate the mutations of these genes in 4 Iranian families with non-syndromic tooth agenesis. Methods: DNA extractions from peripheral blood cells of patients with non-syndromic tooth agenesis from 4 unrelated Iranian families were performed by salting out method, and the candidate genes were amplified then followed by Sanger sequencing method. Results: One missense variant (rs4904210) and 4 Single Nucleotide Polymorphisms (SNPs) (rs2236007, rs12883298, rs12882923 and rs12883049) were found in PAX9 gene. Five variants (rs149370601, rs8670, rs186861426 and rs774949973) including a missense variant (rs36059701) were detected in MSX1 gene and no variants were found in WNT10A gene. Conclusion: All variants were analyzed based on bioinformatics websites and Iranian gene databases, and as a result, it was revealed that variants of PAX9, MSX1 and WNT10A may not play a role in non-syndromic tooth agenesis among Iranian cases.

Coronary artery disease (CAD) is the leading cause of mortality in many parts of the world. Genome-wide association studies (GWAS) have identified several genetic variants associated with CAD in Low-density lipoprotein receptor (LDLR) locus. This study was evaluated the possible association of genetic markers at LDLR locus with CAD irrespective to lipid profile and as well as the association of these SNPs with severity of CAD in Iranian population. Sequencing of 2 exons in LDLR gene (Exon 2, 12) and part of intron 30 of SMARCA4 gene include rs1122608, was performed in 170 Iranian patients angiographically confirmed CAD and 104 healthy controls by direct sequencing. Sullivan's scoring system was used for determining the severity of CAD in cases. Our results showed that homozygote genotypes of rs1122608 (P

BACKGROUND: Knowledge of the genes responsible for intellectual disability, particularly autosomal recessive forms, is rapidly expanding. Increasing numbers of the gene show great heterogeneity and supports the hypothesis that human genome may contain over 2000 causative genes with a critical role in brain development. METHODS: Since 2004, we have applied genome-wide SNP genotyping and next-generation sequencing in large consanguineous Iranian families with intellectual disability, to identify the genes harboring disease-causing mutations. The current study paved the way for identification of responsible genes in two unrelated Iranian families. RESULTS: We found two novel nonsense mutations, p.C77* and p.Q115*, in the calpain catalytic domain of CAPN10, which is a cysteine protease known to be involved in pathogenesis of noninsulin-dependent diabetes mellitus. Another different mutation in this gene (p.S138_R139ins5) has previously been reported in an Iranian family. All of these patients have common clinical features in spite of specific brain structural abnormalities on MRI. CONCLUSIONS: Different mutations in CAPN10 have already been found in three independent Iranian families. These results have strongly supported the possible role of CAPN10 in human brain development. Altogether, we proposed CAPN10 as a promising candidate gene for intellectual disability, which should be considered in diagnostic gene panels.

Background Intellectual disability (ID) has a worldwide prevalence of 1-3% and results from extraordinary heterogeneous. To shed more light on the causes of ID in Kerman Province, in Southeast Iran, we set out in 2008 to perform systematic clinical studies and homozygosity mapping in large Iranian families with ID. Methods Fifty seven families with a minimum of two mentally retarded children from Kerman Province were initially tested for metabolic disorders, by Tandem mass spectrometry. Fragile X testing and standard karyotyping were performed for all probands of families. Cases with autosomal recessive (AR) pattern of inheritance and microcephaly were subjected to homozygosity mapping by using several microsatellite markers for known MCPH loci. Results Three out of seven families with X-linked pattern of inheritance were positive for fragile X syndrome. Chromosome abnormality was not observed in any of dysmorphic patients and all families were negative for metabolic tests. Among the remaining 50 families of AR ID, six were found to be microcephalic, of which 2 linked to two MCPH loci (33.3%). The rest 4 families were not linked to any of the known loci. Conclusion The results of this study showed that ID with microcephaly comprised 12% of ID cases in Kerman Province. In two families with apparent linkage to the MCPH5 and MCPH6 locus, mutation screening was not successful, which might indicate that either the mutation is located in the regulatory sequences of the gene or that there might be another genes present in these regions, which is mutated in such cases.

Objective Autosomal recessive primary microcephaly (MCPH) is a neurodevelopmental and genetically heterogeneous disorder with decreased head circumference due to the abnormality in fetal brain growth. To date, nine loci and nine genes responsible for the situation have been identified. Mutations in the ASPM gene (MCPH5) is the most common cause of MCPH. The ASPM gene with 28 exons is essential for normal mitotic spindle function in embryonic neuroblasts. Materials & Methods We have ascertained twenty-two consanguineous families with intellectual disability and different ethnic backgrounds from Iran. Ten out of twenty-two families showed primary microcephaly in clinical examination. We investigated MCPH5 locus using homozygosity mapping by microsatellite marker. Result Sequence analysis of exon 8 revealed a deletion of nucleotide (T) in donor site of splicing site of ASPM in one family. The remaining nine families were not linked to any of the known loci .More investigation will be needed to detect the causative defect in these families Conlusion We detected a novel mutation in the donor splicing site of exon 8 of the ASPM gene. This deletion mutation can alter the ASPM transcript leading to functional impairment of the gene product.

The ATP8A2 protein is mainly located in the brain and takes part in the lipid flipping process. Mutations in the ATP8A2 gene and chromosomal translocations that interfere with the ATP8A2 gene product have been reported in association with global developmental delay and hypotonia. Here, we will report a three-year-old male presented with major phenotypic features of dysequilibrium syndrome (DES), including severe hypotonia, global developmental delay, speech problem, and strabismus. Whole exome sequencing revealed a homozygous in-frame deletion in the ATP8A2 gene (c.1286_1288delAGA, p.Lys429del). This ATP8A2 variant has not been reported yet and seems to be linked to the phenotypic features of dysequilibrium syndrome.

Objectives: Hearing loss (HL) is the most common sensory disorder, and affects 1 in 1000 newborns. About 50% of HL is due to genetics and 70% of them are non-syndromic with a recessive pattern of inheritance. Up to now, more than 50 genes have been detected which are responsible for autosomal recessive non-syndromic hearing loss, (ARNSHL). In Iran, HL is one of the most common disabilities due to consanguineous marriages. The aim was to investigate the prevalence of three new ARHL genes (GJB4, GJC3, and SLITRK6) reported in neighboring countries among Iranian families with ARNSHL. Methods: One hundred unrelated families with at least two affected siblings in consanguineous marriage, who were negative for GJB2 gene mutations, were selected. By using three STR markers for each gene, homozygosity mapping was performed. Results: Two families showed linkage to GJB4, six families were linked to GJC3 and only one family linked to SLITRK6. The samples of these families who showed linkage were sent for Sanger sequencing to detect the causative mutations. However, after analyzing the sequencing results, no mutation could be detected in either of the families. Molecular analysis for these nine families is underway in order to determine the pathogenic mutations using whole exome sequencing. Discussion: These data demonstrate a very low prevalence of mutation in these three genes (GJB4, GJC3, and SLITRK6) in the Iranian population, since no mutation was detected in our study group of 100 families.