Impact of a Missense Variation (p.S150R:AGC>AGG) in the XRCC2 Gene on Susceptibility to Colorectal Cancer.

BACKGROUND: The X-ray repair complementing defective repair in Chinese hamster cells 2 (XRCC2) is an important protein in response to DNA double-strand breaks (DSBs) in human cells. XRCC2, as a functional protein in the homologous recombination repair (HRR) process, has been identified to have several polymorphisms which might be associated with the risk of cancer. Therefore, we aimed to investigate a novel missense variation (AGC>AGG, p.Ser150Arg) in the XRCC2 gene for colorectal cancer susceptibility. METHODS: We studied 291 colorectal cancer (CRC) patients and 140 healthy individuals. ARMS PCR method was used to detect the AGC>AGG (p.Ser150Arg) variation in the XRCC2 gene. RESULTS: The results showed that there was a significant differential among CRC and controls in the genotypic and allelic frequencies (p < 0.001) of XRCC2; AGC>AGG, p.Ser150Arg. Our results demonstrated that the G allele of XRCC2; AGC>AGG, p.Ser150Arg was associated with increased CRC risk (odds ratio = 59.04, 95% confidence interval = 18.6 - 186). This variation also influenced CRC cancer susceptibility in smokers (p < 0.001). CONCLUSIONS: The G allele of XRCC2; AGC>AGG, p.Ser150Arg, may be a potential marker for CRC in Iranians and investigations in other populations are warranted for further universal application in CRC detection and prediction.

Examination of methylation changes of VIM, CXCR4, DOK7, and SPDEF genes in peripheral blood DNA in breast cancer patients.

BACKGROUND: Studying whole blood DNA methylation as a risk marker has valuable applications in either diagnosis or staging of breast cancer. We investigated whole blood DNA methylation status of VIM, CXCR4, DOK7, and SPDEF genes in breast cancer patients in comparison to healthy control subjects. MATERIALS AND METHODS: 60 patients with breast cancer and 40 healthy controls were examined. Genomic DNA isolated from peripheral blood and restriction enzyme polymerase chain reaction (REP) method was applied for analysis. Real-time PCR was used to confirm methylation status of the aforementioned genes and therefore to find out the methylation differences between normal and breast cancer subjects. RESULTS: Level of DOK7 promoter hypomethylation in normal and breast cancer samples was significant (P-value = 0.001). The study, also, showed that hypomethylation of VIM and CXCR4 genes are significant in patients compared with normal cases (P-value < 0.05). Furthermore, SPDEF promoter hypomethylation was not significantly differed between normal and breast cancer samples (P-value = 0.2). CONCLUSIONS: Hypermethylation of DOK7 gene in DNA from patients affected with breast cancer offers a biomarker for diagnosis of the breast cancer. This study indicates that methylation status of VIM and CXCR4 genes changes in breast cancer; so, they can be used as molecular biomarkers in breast cancer prognosis.

Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort.

PURPOSE: Autosomal recessive nonsyndromic deafness (ARNSD) is characterized by a high degree of genetic heterogeneity, with reported mutations in 58 different genes. This study was designed to detect deafness-causing variants in a multiethnic cohort with ARNSD by using whole-exome sequencing (WES). METHODS: After excluding mutations in the most common gene, GJB2, we performed WES in 160 multiplex families with ARNSD from Turkey, Iran, Mexico, Ecuador, and Puerto Rico to screen for mutations in all known ARNSD genes. RESULTS: We detected ARNSD-causing variants in 90 (56%) families, 54% of which had not been previously reported. Identified mutations were located in 31 known ARNSD genes. The most common genes with mutations were MYO15A (13%), MYO7A (11%), SLC26A4 (10%), TMPRSS3 (9%), TMC1 (8%), ILDR1 (6%), and CDH23 (4%). Nine mutations were detected in multiple families with shared haplotypes, suggesting founder effects. CONCLUSION: We report on a large multiethnic cohort with ARNSD in which comprehensive analysis of all known ARNSD genes identifies causative DNA variants in 56% of the families. In the remaining families, WES allows us to search for causative variants in novel genes, thus improving our ability to explain the underlying etiology in more families.Genet Med 18 4, 364-371.

A transversion mutation in non-coding exon 3 of the TMC1 gene in two ethnically related Iranian deaf families from different geographical regions; evidence for founder effect.

OBJECTIVES: Transmembrane channel-like 1 (TMC1) gene is a member of the transmembrane channel-like (TMC) gene family that encodes an integral membrane protein of the inner ear. It is suggested that mutation in this gene is one of the main causes of autosomal recessive non-syndromic hearing loss (ARNSHL) in different populations. The aim of this study was to determine the contribution of the TMC1 gene mutations in causing hearing loss in Iran. METHODS: In total 54 unrelated Iranian families containing 159 affected individuals with ARNSHL detected by audiometric and otologic examinations were analyzed. Haplotype analysis of all members of 45 GJB2- & GJB6-negative families, using four microsatellite markers linked to DFNB7/11 was performed. RESULTS: Co-segregation of hearing loss with all investigated markers for the DFNB7/11 locus was found in one family. DNA sequencing of all coding and non-coding exons and intron boundaries of the TMC1 gene identified c.-258A>C mutation in non-coding exon 3 only in individuals with hearing loss. This mutation has been previously reported in another Iranian family (G9) that share similar ethnicity. This variant was not detected in 300 ethnically matched healthy controls. CONCLUSIONS: These results increase the probability that this nucleotide variation may be a pathogenic mutation. This study showed that the ethnicity may be more useful than geographical location to design research strategy for determining which genes should be considered when a heterogeneous disorder is under investigation.

Design of a biological method for rapid detection of presence of PCR inhibitors in aged bone DNA.

BACKGROUND: Molecular human identification is one of the most important tests performed in forensic laboratories. Some of these tests are applied for identification of human remains from natural disasters, wars, etc., but problems may occur as a result of DNA degradation and external DNA contamination. We investigated effects of bacterial DNA on identifying the presence or absence of PCR inhibitors in aged bone DNA. METHODS: DNA samples were extracted from blood, bone remains and Escherichia coli. These DNA were amplified using human and bacterial specific primers. RESULTS: Using different blood, aged bone, and bacterial DNA dilutions along with PCR based methods; we checked their positive, negative effects, or detecting presence of inhibitors in aged bone DNA by PCR method. CONCLUSIONS: Our observation indicated that the addition of bacterial DNA could be a valid biological method for testing the quality of bone DNA to enable us to obtain a usable profile for the identification of human remains. This method will help to test the presence of inhibitors, quantity or even quality of DNA which are of importance in profiling archeological remains. Our method will help to determine if PCR failure is due to presence of inhibitors or lack of amplifiable DNA either because of degradation, minute amount or absence of human DNA.

Screening of OTOF mutations in Iran: a novel mutation and review.

OBJECTIVE: Mutations in OTOF have been reported to cause nonsyndromic hearing loss in different populations. The purpose of this study is screening of OTOF mutations in Iranian population. METHODS: Thirty-eight consanguineous families affected with autosomal recessive nonsyndromic hearing loss (ARNSHL) and negative for GJB2 or GJB6 mutations were screened by autozygosity mapping and Sanger sequencing to find OTOF mutations. RESULTS: A novel homozygous frameshift mutation (c.1981dupG) was found to cause hearing loss in one family and no other OTOF variants were detected in the remaining families. The affected individuals were homozygous forp. D661GfsX2 causing defect in long isoform of otoferlin. CONCLUSIONS: We conclude that OTOF mutations are not the major cause of ARNSHL in the Iranian population but still may play an important role in HL; therefore evaluation the OTOF gene is of concern.

Impact of consanguineous marriages in GJB2-related hearing loss in the Iranian population: a report of a novel variant.

Mutations in GJB2 and GJB6 genes are the main causes of autosomal recessive nonsyndromic hearing loss (ARNSHL) in many populations. Here, we investigated GJB2 and GJB6 mutations in 114 patients from 77 affected ARNSHL families including 54 consanguineous marriages and 23 nonrelative marriages in the Iranian population. Clinical studies and genetic counseling were performed for all families. GJB2 and GJB6 genes were directly sequenced. Three known GJB6 large deletions [del(GJB6-D13S1830), del(GJB6-D13S1854), and a 920 kb deletion] were also checked by quantification of a common deleted region within the GJB6 gene. The frequency of consanguinity was 70.13% among the studied families. Biallelic GJB2 mutations were 16.67% in consanguineous marriages and 4.35% in nonrelative marriages. Mutations found were 35delG, delE120, R127H, M163V, W24X, V37I, G12D, V84A, 313-326del14, and E110K. The latter was a novel variant. Neither point mutation nor a large deletion in the GJB6 gene was found in the population. Mean frequency of GJB2 mutations was 17.92%. GJB2 mutations (and not GJB6 mutations) are the major causes of hearing loss in Iran. The role of consanguineous marriages is also highlighted in occurrence of GJB2-related hearing loss. We suggest that other genes may be involved in the population.

Investigation of GJB6 large deletions in Iranian patients using quantitative real-time PCR.

BACKGROUND: Hearing loss is a serious sensory defect in the world. Mutations in the GJB2 and GJB6 genes are the major causes of autosomal recessive nonsyndromic hearing loss (NSHL). Recently, three major large deletions in the GJB6 gene including del(GJB6-D13S1830), del(GJB6-D13S1854), and a > 920 kb deletion have been reported to form double heterozygosity with GJB2. This may suggest that deletions involving GJB6 may be responsible for some NSHL. METHODS: We designed a real time SYBR green-based PCR to quantify a common deleted region in GJB6 gene. The amplified region covers the area which has been seen to be deleted in all of the above reports. We selected nine families heterozygous for different mutations in GJB2 gene to investigate the presence of deletions in the GJB6 gene. The samples were run along with controls for normal hearing and heterozygous and homozygous for GJB2 mutations to optimize our method. As a reference gene or external standard, a segment of the CLCN7 gene was also quantified as well. RESULTS: We did not detect any deletion in the GJB6 gene. CONCLUSIONS: Using this method, any deletion involving GJB6 gene can be detected in a rapid and sensitive way.

Unexpected heterogeneity due to recessive and de novo dominant mutations of GJB2 in an Iranian family with nonsyndromic hearing loss: implication for genetic counseling.

Mutations in the GJB2 gene are the most common cause of nonsyndromic autosomal recessive sensorineural hearing loss (HL). A few mutations in GJB2 have also been reported to cause dominant nonsyndromic HL. Here we report a large inbred family including two individuals with nonsyndromic sensorineural hearing loss. A dominant GJB2 mutation, c.551G>A (p.R184Q), was detected in the proband, yet his parents were negative for the mutation. The second affected person had heterozygous c.35delG mutation, which was inherited from his father. Large deletions of the GJB6 gene were not detected in this family. This study highlights the importance of mutation analysis in all affected cases within a pedigree.

High level of intrafamilial phenotypic variability of non-syndromic hearing loss in a Lur family due to delE120 mutation in GJB2 gene.

Hearing loss is the most common sensory defect in the world. The genetic basis of this condition is very complex. Molecular variations in GJB2 gene are the common cause of hearing impairment in Caucasians. One expects that affected members of a family with same mutation have similar phenotype. Here, we report phenotypic variability in hearing loss among the members of a Lur family. Two brothers from a Lur family from Lurestan province in western Iran with variable degrees of nonsyndromic sensorineural hearing loss were evaluated for genetic counseling. Clinical examinations, audiological tests and molecular studies including GJB2 gene sequencing and detection of Delta(GJB6-D13S1830) deletion were performed. Sequencing analysis of GJB2 gene revealed delE120 mutation in both brothers in homozygous form. Since one of them was profoundly deaf and the other was mild hearing loss and had normal conversation, we were expecting different genotypes or other causative effects. Delta(GJB6-D13S1830) was not found. Phenotypic variability between members of different families with the same type of mutation can be expected which may be due to the role of different modifying factors, unrecognized gap junction isoforms, or polymorphism effects.