Genetic Analysis of MECP2 Gene in Iranian Patients with Rett Syndrome.

OBJECTIVES: Rett syndrome is an X linked dominant neurodevelopmental disorder which almost exclusively affects females. The syndrome is usually caused by mutations in MECP2 gene, which is a nuclear protein that selectively binds CpG dinucleotides in the genome. MATERIALS & METHODS: To provide further insights into the distribution of mutations in MECP2 gene, we investigated 24 females with clinical characters of Rett syndrome referred to Alzahra University Hospital in Isfahan, Iran during 2015-2017. We sequenced the entire MECP2 coding region and splice sites for detection of point mutations in this gene. Freely available programs including JALVIEW, SIFT, and PolyPhen were used to find out the damaging effects of unknown mutations. RESULTS: Direct sequencing revealed MECP2 mutations in 13 of the 24 patients. We identified in 13 patients, 10 different mutations in MECP2 gene. Three of these mutations have not been reported elsewhere and are most likely pathogenic. CONCLUSION: Defects in MECP2 gene play an important role in pathogenesis of Rett syndrome. Mutations in MECP2 gene can be found in the majority of Iranian RTT patients. We failed to identify mutations in MECP2 gene in 46% of our patients. For these patients, further molecular analysis might be necessary.

Genomic rearrangement screening of the BRCA1 from seventy Iranian high-risk breast cancer families.

BACKGROUND: The second leading cause of cancer deaths in women is breast cancer. Germline mutations in susceptibility breast cancer gene BRCA1 increase the lifetime risk of breast cancer. Eighty-one large genomic rearrangements (LGRs) have been reported up to date in BRCA1 gene, and evaluation of these rearrangements helps with precise risk assessment in high-risk individuals. In this study, we have investigated LGRs in BRCA1 among Iranian high-risk breast cancer families. MATERIALS AND METHODS: Seventy patients with breast cancer who were identified negative for point mutations or small deletions/insertions of BRCA1 gene were selected. Deletions and duplications of BRCA1 gene were evaluated using multiplex ligation-dependent probe amplification (MLPA). RESULTS: Two deletions, deletion of exons 1A/1B-2 and exon 24, were detected in two patients with breast cancer. The former alteration was found in a woman with a strong family history of breast cancer while the latter one was detected in a woman with early onset of breast cancer. CONCLUSION: Although our data confirm that LGRs in BRCA1 comprise a relatively small proportion of mutations in hereditary breast cancer in the Iranian population, MLPA analysis might be considered for screening of LGRs in high-risk individuals. It is worth to note that our results are consistent with previous studies in various Asian and European countries.

Mutation spectrum of autosomal recessive non-syndromic hearing loss in central Iran.

OBJECTIVE: To identify the spectrum of mutations in connexin 26 gene and frequency of two deletions in connexin 30 gene in central Iran. METHODS: After extraction of DNA from 300 blood samples, connexin 26 gene coding region was amplified using specific primers. PCR products were used for bidirectional sequencing. Multiplex PCR was used for detection of del(GJB6-D13S1830) and del(GJB6-D13S1854) in the GJB6 gene. RESULTS: Eighteen different mutations including two novel variants in GJB2 gene were detected. The GJB2 mutations were observed in 23.3% of all the subjects. In addition, none of the deaf patients carried the del(GJB6-D13S1830) and del(GJB6-D13S1854) in the GJB6 gene. The 35delG mutation was the most common mutation, accounting for 32.65% of the mutant alleles. CONCLUSION: The present study indicates that mutations in the GJB2 gene particularly 35delG are important causes for ARNSHL. 60% of the patients were heterozygous carriers. Thus, further investigation is needed to detect the genetic cause of hearing loss in patients with mono allelic mutations in the coding region of GJB2.

Structural and functional impact of missense mutations in TPMT: An integrated computational approach.

BACKGROUND: Thiopurine S-methyltransferase (TPMT) detoxifies thiopurine drugs which are used for treatment of various diseases including inflammatory bowel disease (IBD), and hematological malignancies. Individual variation in TPMT activity results from mutations in TPMT gene. In this study, the effects of all the known missense mutations in TPMT enzyme were studied at the sequence and structural level METHODS: A broad set of bioinformatic tools was used to assess all the known missense mutations affecting enzyme activity. The effects of these mutations on protein stability, aggregation propensity, and residue interaction network were analyzed. RESULTS: Our results indicate that the missense mutations have diverse effects on TPMT structure and function. Stability and aggregation propensities are affected by various mutations. Several mutations also affect residues in ligand binding site. CONCLUSIONS: In vitro study of missense mutation is laborious and time-consuming. However, computational methods can be used to obtain information about effects of missense mutations on protein structure. In this study, the effects of most of the mutations on enzyme activity could be explained by computational methods. Thus, the present approach can be used for understanding the protein structure-function relationships.

A new compound heterozygous mutation in GJB2 causes nonsyndromic hearing loss in a consanguineous Iranian family.

OBJECTIVE: To investigate mutations in GJB2 in a consanguineous Iranian family with multiple members affected by non-syndromic hearing loss. METHODS: DNA was extracted from blood samples and the coding region of the conexin 26 gene was amplified using PCR. Bidirectional sequencing was carried out on PCR products. RESULTS: Direct sequencing of the PCR products led to the identification of a novel compound heterozygous mutation of c.551G>C/c.397T>G (p.R184P/p.W133G) and a previously reported homozygous mutation c.551G>C (R184P/R184P). Compound heterozygous mutation was identified in the father and his daughter and homozygous mutation was identified in his affected son. In silico analysis of p.W133G predicted mutation has deleterious effect on protein structure. CONCLUSION: These results show the usefulness of GJB2 mutation screening and bioinformatic analysis for genetic diagnosis and counseling of non-syndromic hearing loss.

Detection of intragenic SMN1 mutations in spinal muscular atrophy patients with a single copy of SMN1.

Proximal spinal muscular atrophy is an autosomal recessive disorder characterized by symmetrical muscle weakness due to degeneration of alpha motor neurons in the spinal cord. Homozygous deletions in the SMN1 have been reported in more than 90% of spinal muscular atrophy cases. Compound heterozygous patients account for approximately 4% of spinal muscular atrophy cases. In this study, we performed a quantitative test in 20 of 87 spinal muscular atrophy patients who did not have homozygous deletion of SMN1. Mutation screening of SMN1 gene was performed in 4 patients who have only 1 copy of SMN1 to identify intragenic mutations. In addition to a previously described missense mutation in exon 4 (p.A188S/ c.562G>T), we identified 2 novel mutations including a single nucleotide insertion in exon 7 (c.861_862insT/p.R288X) and a deletion of nucleotide G in exon 3 (c.286delG/p.D96Tfs*53). Our results suggested that about 4% of spinal muscular atrophy patients have subtle mutations and might be considered in laboratory examination.

Evaluation of multiplex ligation-dependent probe amplification analysis versus multiplex polymerase chain reaction assays in the detection of dystrophin gene rearrangements in an Iranian population subset.

BACKGROUND: The Duchenne muscular dystrophy (DMD) gene is located in the short arm of the X chromosome (Xp21). It spans 2.4 Mb of the human genomic DNA and is composed of 79 exons. Mutations in the Dystrophin gene result in DMD and Becker muscular dystrophy. In this study, the efficiency of multiplex ligation-dependent probe amplification (MLPA) over multiplex polymerase chain reaction (PCR) assays in an Iranian population was investigated. MATERIALS AND METHODS: Multiplex PCR assays and MLPA analysis were carried out in 74 patients affected with DMD. RESULTS: Multiplex PCR detected deletions in 51% of the patients with DMD. MLPA analysis could determine all the deletions detected by the multiplex PCR. Additionally, MLPA was able to identify one more deletion and duplication in patients without detectable mutations by multiplex PCR. Moreover, MLPA precisely determined the exact size of the deletions. CONCLUSION: Although MLPA analysis is more sensitive for detection of deletions and duplications in the dystrophin gene, multiplex PCR might be used for the initial analysis of the boys affected with DMD in the Iranian population as it was able to detect 95% of the rearrangements in patients with DMD.

Use of in silico tools for classification of novel missense mutations identified in dystrophin gene in developing countries.

DMD gene which is composed of 79 exons is the largest known gene located on X chromosome (Xp21). Point mutations in the dystrophin gene are responsible for 30-35% of cases with DMD/BMD. Mutation analysis of all the exons of the DMD gene is costly in developing countries, therefore, a few of the exons are selected to be analyzed routinely in clinical laboratories. In this study, direct sequencing was used for detection of point mutations in 10 exons of dystrophin gene in patients affected with DMD without detectable large rearrangements. Freely available programs were used to predict the damaging effects of the mutations. Point mutations were successfully detected in three patients. Three novel mutations, two missense mutations located on nonconservative domains and a single nucleotide deletion, were detected. Missense mutations were predicted to change splicing efficiency. Detection of point mutations by DNA analysis followed by prediction of the pathogenecity by using bioinformatic tool might be an asset to provide proper diagnosis or genetic counseling to patients and their family.