Associations between epidermal growth factor receptor and topoisomerase II-alpha gene copy number variations, human papillomavirus positivity, and cytologic analysis in cervical cell lesions.

BACKGROUND: Cervical cancer is the second most common gynecologic cancer worldwide. Human papillomavirus (HPV) infection is a leading etiological factor in cervical carcinoma.The aim of this study was to compare HPV positivity, EGFR and TOP2A gene copy number variations and cervical cytologic findings. MATERIALS AND METHODS: The study group comprised 100 female volunteers between 21-64 years old. Cytologic analysis was performed using the liquid-based cytology technique. HPV DNA testing was performed in all cases. Copy number variations that belong to EGFR and TOP2A genes evaluated by using FISH analysis. RESULTS: Cytologic analysis of the cervical samples revealed abnormal findings in 13 of the 100 study subjects. ASCUS , LSIL, HSIL were determined in 8, 2 and 3 cases respectively as the result of cytologic analysis on all cases. Forty-one (41%) of the 100 women were HPV-positive. Chi-square analysis confirmed that HPV-positive women showed significantly more abnormal cytology (P = 0.035). EGFR deletion, TOP2A deletion and both EGFR and TOP2A deletion were determined in 1, 8 and 1 cases respectively. We found no statistical difference in abnormal cytologic findings between subjects with these gene deletions and subjects with normal gene copy numbers (P > 0.05 for both). No cases of amplification were determined for either gene. CONCLUSION: As a result, HPV positivity and the determination of changes that may occur in the gene copy number in patients with abnormal cytology can be an important tool on account of prognosis. Research with more patients may be suggested.

A novel splice site mutation of FGD1 gene in an Aarskog-Scott syndrome patient with a large anterior fontanel.

Aarskog-Scott syndrome (ASS) is a rare X-linked recessive genetic disorder caused by FGD1 mutations. FGD1 regulates the actin cytoskeleton and regulates cell growth and differentiation by activating the c-Jun N-terminal kinase signaling cascade. ASS is characterized by craniofacial dysmorphism, short stature, interdigital webbing and shawl scrotum. However, there is a wide phenotypic heterogeneity because of the additional clinical features. ASS and some syndromes including the autosomal dominant inherited form of Robinow syndrome, Noonan syndrome, pseudohypoparathyroidism, Silver-Russel and SHORT syndrome have some overlapping phenotypic features. Herein, we report a patient with ASS and a large anterior fontanel who was initially diagnosed as Robinow syndrome. He was found to have a novel c.1340+2 T>A splice site mutation on the FGD1 gene.

Association between gene polymorphisms in TIM1, TSLP, IL18R1 and childhood asthma in Turkish population.

UNLABELLED: Many immunologic and inflammatory mechanisms play a role in asthma etiology. The aim of this study was to investigate the susceptibility of asthma patients in the Turkish population with demonstrating genes for polymorphisms in TIM1, TSLP and IL18R1. All of the genomic DNA samples were isolated from blood samples according to a standard salting-out protocol. DNA samples were stored at -20°C until the genotype analysis was performed. rs3806933 (TSLP -847 C > T) and TIM1 -416G > C were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The rs3806933 (TSLP -847 C > T) was genotyped by PCR using our new primers and HphI restriction enzyme digestion. rs2287033 (IL18R1 c. 1270+150 A > G), rs3213733 (IL18R1 c. 626-196 G > T), and rs3771166 (IL18R1- c. 302+1694 C > T) were genotyped using SYBR green dye based real time PCR assay. RESULTS: The allele frequencies of 5 SNPs in TSLP, TIM-1, and IL18R1 genes were determined in 139 asthmatic patients and 126 healthy controls of in Turkish population. The investigated SNPs are as follows; rs3806933 (TSLP -847 C > T), TIM1 -416G > C, rs2287033 (IL18R1 c. 1270+150 A > G), rs3213733 (IL18R1 c. 626-196 G > T), and rs3771166 (IL18R1- c. 302+1694 C > T). Results suggest that IL18R1 c. 626-196 G > T (rs3213733) and TIM1 -416G > C are significantly associated with asthma in patients in Turkish population. Patients with AA genotypes of rs2287033 (IL18R1 c. 1270+150 A > G), have significantly less total serum IgE levels when compared with patients having GG or GA genotypes (p < 0.012; 381.77±239.46 vs 557.52±549.96, respectively). CONCLUSION: This study showed that IL18R1 c. 626 -196 G > T (rs3213733) and TIM1 -416G > C are significantly associated with asthma patients in Turkish population.

SYBR green dye-based probe-free SNP genotyping: introduction of T-Plex real-time PCR assay.

Single-nucleotide polymorphism (SNP) genotyping is widely used in genetic association studies to characterize genetic factors underlying inherited traits. Despite many recent advances in high-throughput SNP genotyping, inexpensive and flexible methods with reasonable throughput levels are still needed. Real-time PCR methods for discovering and genotyping SNPs are becoming increasingly important in various fields of biology. In this study, we introduce a new, single-tube strategy that combines the tetra-primer ARMS PCR assay, SYBR Green I-based real-time PCR, and melting-point analysis with primer design strategies to detect the SNP of interest. This assay, T-Plex real-time PCR, is based on the T(m) discrimination of the amplified allele-specific amplicons in a single tube. The specificity, sensitivity, and robustness of the assay were evaluated for common mutations in the FV, PII, MTHFR, and FGFR3 genes. We believe that T-Plex real-time PCR would be a useful alternative for either individual genotyping requests or large epidemiological studies.

Development and validation of a cost-effective in-house method, tetra-primer ARMS PCR assay, in genotyping of seven clinically important point mutations.

The single nucleotide polymorphism (SNP) genotyping is currently considered as a particularly valuable tool for the diagnosis of different pathologies. For this reason, over the past several years a great deal of effort has been devoted to developing accurate, rapid, and cost-effective technologies for SNP analysis. Although a large number of distinct approaches has been reported each laboratory use one of the published methods based on their technical and economical capacity. This article presents an application of an in-house assay, tetra-primer ARMS PCR assay, and its application in SNP genotyping. We have shown that this assay could be more advantageous when compared with PCR-RFLP, real time PCR, and DNA sequencing. We have shown that the assay is successful in genotyping using archived paraffin-embedded tissues, heparinated samples and amniotic fluids with meconium. These low-costed (3$/reaction) assays could be completed within 3-4 h after specimen receipt allowing for a reasonable turn-around time in the laboratory. Since tetra-primer ARMS PCR assay does not require any special equipment, the assay could be set up in most clinical diagnostic laboratories.

Rapid diagnosis of spinal muscular atrophy using tetra-primer ARMS PCR assay: simultaneous detection of SMN1 and SMN2 deletion.

Spinal muscular atrophy (SMA), the leading genetic cause of death in childhood, is an autosomal recessive neuromuscular disorder characterized by progressive muscle weakness, associated with deletions of the survival motor neuron 1 (SMN1) gene. Approximately 94% of SMA patients carry homologous deletions of SMN1 exon(s) 7 (and 8). Because of the high incidence and severity of the disease, precise detection and quantification of SMN1 and SMN2 gene copy numbers is essential for diagnosis and genetic counseling. We have developed a reliable single-tube tetra-primer PCR assay to simultaneously detect both the SMN1 and SMN2 exon 7 deletion using the advantage of C/T difference at nucleotide position of 840 in exon 7. The assay has been optimized and tested in 48 healthy controls, 20 known patients with SMA, 12 carriers (one SMN1 copy), and 8 amniotic fluids suspected of having SMA for whom we had determined the SMN1/SMN2 deletion by an additional PCR-RFLP method. We have observed complete concordance between methods. Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for simultaneous detection of both SMN1 and SMN2 deletion, which could be used even in "low-tech" laboratories.

An improved tetra-primer PCR approach for the detection of the FGFR3 G380R mutation responsible for achondroplasia.

Achondroplasia is the most common form of dwarfism and has an incidence of approximately 1/7500. In more than 98% of cases, the disease is associated with a G to A or G to C substitution at nucleotide position 1138 (p.G380R) of the fibroblast growth factor receptor 3 (FGFR3) gene. We have developed a sensitive single tube tetra-primer PCR assay to detect both the c.1138G>A and c.1138G>C mutations and can successfully distinguish DNA samples that are homozygous and heterozygous for the c.1138G>A mutation. Titration studies showed that the assay could reliably detect one copy of the mutant allele in a mix of 100 wild-type alleles. The assay has been tested in 50 healthy controls, 3 known patients with achondroplasia, and 5 amniotic fluids suspected of having achondroplasia and for whom we had previously determined the genotypes for the c.1138G>A mutation by PCR-RFLP. We have observed complete concordance between methods. Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for FGFR3 p.G380R genotyping, which could be used even in "low-tech" laboratories.

Primer-engineered multiplex PCR-RFLP for detection of MTHFR C677T, prothrombin G20210A and factor V Leiden mutations.

Single-nucleotide polymorphisms in the genes that code for coagulation factors V (factor V Leiden) and II (prothrombin, G20210A), as well as the methylenetetrahydrofolate reductase (MTHFR, C677T) gene, have been implicated in the majority of cases of hereditary thrombophilia. We have developed a multiplex PCR-RFLP assay based on MnlI endonuclease digestion for the simultaneous detection of mutations in the FV, FII, and MTHFR genes. Digested amplification products were analyzed by gel electrophoresis in a single gel lane and visualized by ethidium bromide. This approach is a rapid and convenient method, hence economic, that alternate to others described for the detection of FVL, G20210A and C677T mutations.

A tetra-primer polymerase chain reaction approach for the detection of JAK2 V617F mutation.

Recently, an acquired somatic point mutation (p.V617F) in a highly conserved residue of the pseudokinase domain of the JAK2 tyrosine kinase was shown to be associated with myeloproliferative disorders. Because of the clinical importance of this mutation in diagnosing myeloproliferative disorders and its relevance for disease progression, we have developed a tetra-primer polymerase chain reaction (PCR) assay to detect JAK2 p.V617F. Titration studies showed that the assay could reliably detect one copy of the mutant allele in a mix of 50 wild-type alleles suggesting that the lower detection limit of this assay is estimated to be 2%. This study demonstrates that genotyping and quantifying of the JAK2 V617F mutation can be performed by tetra-primer PCR using both freshly isolated and formalin-fixed tissues. Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for the detection of JAK2 p.V617F, which could be used even in low-tech laboratories.

Symptomatic hypoglycemia: an unusual side effect of oral purine analogues for treatment of ALL.

Symptomatic hypoglycemia is an unusual complication in children receiving oral purine analogues for treatment of childhood acute lymphoblastic leukemia (ALL). The exact mechanism of the hypoglycemic effect of the antimetabolic therapy remains unclear. Reduced hepatic glycogen stores or impaired hepatic glyconeogenesis may partly explain the hypoglycemia. To prevent hypoglycemia, food containing complex carbohydrates is recommended before sleep. In severe cases of hypoglycemia due to 6-mercaptopurine (6-MP), the dose can be given in the morning and if this fails 6-MP can be discontinued for a short period of time. We report a 3-year-old child who developed severe early morning hypoglycemia episodes that resolved after decreasing 6-MP while receiving non-high risk ALL therapy.

Hyperbaric oxygenation and antioxidant vitamin combination reduces ischemia-reperfusion injury in a rat epigastric island skin-flap model.

Reperfusion injury, caused by free oxygen radicals, is a chain of events that occurs in tissues exposed to a constant period of ischemia. The antioxidant vitamins E and C (VEC) and hyperbaric oxygenation (HBO) have beneficial effects in treating ischemic tissues following skin flap operations. In our study, we aimed to compare the effects of VEC and/or HBO in ischemia-reperfusion injury induced by free oxygen radicals in an experimental rat epigastric island skin-flap model. Eight hours of ischemia was provided by clamping the inferior epigastric pedicle following the flap elevation. The flap survey was determined to be 28.6% in controls, 59.2% in HBO group, 66.3% in VEC + HBO group, and 82% in VEC group (p < 0.05). We conclude that although HBO and/or VEC increased the flap viability significantly by reducing ischemia-reperfusion injury, the most promising results were obtained in the antioxidant vitamins group.

Multiplex PCR-RFLP assay for detection of factor V Leiden and prothrombin G20210A.

Factor V Leiden and prothrombin G20210A are clinically relevant genetic risk factors for venous thrombosis. Molecular diagnostic testing for factor V Leiden and prothrombin G20210A is widespread, and laboratories use a variety of technical approaches. Here we introduce a multiplex polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) based on single (Mn/l) restriction endonuclease digestion. The assay was shown to simultaneously and accurately detect factor V Leiden and prothrombin G20210A mutations.

A combined allele-specific PCR and RFLP assay to detect the 35delG mutation in the Connexin 26 gene.

Mutations in the Connexin-26 (specified GJB2) gene have been shown to be a major cause of nonsyndromic recessive deafness (NSRD), and a single mutation 35delG in the GJB2 gene accounts for the majority of cases of NSRD. For diagnostic analyses and for scientific studies of large numbers of patients, fast and economic assays that can be performed with standard polymerase chain reaction (PCR) instruments are highly desirable. We have developed an allele-specific amplification (ASA)-based restriction fragment length polymorphism (RFLP) assay. We evaluated the multiplex method for its ability to 35delG mutation. Our method is a stable, reproducible and concordend with previously reported PCR-RFLP assays.