Amplification Refractory Mutation System PCR Research Articles

Association study of IL10 gene polymorphisms (rs1800872 and rs1800896) with cervical cancer in the Bangladeshi women

ObjectiveCervical cancer is one of the most destructive diseases among females worldwide, especially in developing countries. Interleukin-10 (IL10) is a multifunctional cytokine, and polymorphisms in the IL10 gene have been identified in multiple malignancies. However, no prior studies were conducted to determine the association of IL10 polymorphisms (rs1800872 and rs1800896) with cervical cancer patients in Bangladesh. MethodsThis case-control study was carried out on 240 cervical cancer patients and 204 healthy volunteers. Genotyping was performed using the tetra-primer amplification refractory mutation system polymerase chain reaction (ARMS-PCR). ResultsIn the case of rs1800872, CA and AA genotypes significantly increased the risk of cervical cancer (OR = 1.59, 95% CI = 1.01–2.49, p = 0.043; OR = 2.75, 95% CI = 1.53–4.93, p = 0.0007, respectively) but the significance did not exist for CA genotype after Bonferroni correction (p < 0.025). An increased risk was also observed for the dominant model, recessive model, and allele model (A vs. C) of rs1800872 (dominant model: OR = 1.83, 95% CI = 1.18–2.80, p = 0.006; recessive model: OR = 2.00, 95% CI = 1.22–3.29, p = 0.006; allele model: OR = 1.55, 95% CI = 1.19–2.03, p = 0.001) which remained significant after the correction of Bonferroni. For rs1800896, only GG genotype and recessive model showed increased risk for cervical cancer (GG vs. AA: OR = 3.48, 95% CI = 1.46–8.31, p = 0.005; recessive model: OR = 3.57, 95% CI = 1.52–8.38, p = 0.003). These associations were statistically significant, and the significance existed after Bonferroni correction. Haplotype analysis revealed that AA haplotype significantly increased the risk (OR = 1.56, p = 0.001) whereas, CA haplotype significantly lowered the risk (OR = 0.42, p = 2.42x10-8), and both rs1800872 and rs1800896 are strongly in linkage disequilibrium (D’=1, r2 = 0.333). Moreover, the IL10 mRNA level was found up-regulated in silico in cervical squamous cell carcinoma tissues compared to healthy tissues (p = 1.11x10-16). ConclusionOur study suggests that rs1800872 and rs1800896 polymorphisms of IL10 gene are associated with cervical cancer in Bangladeshi females.

Value of serum tumor markers for predicting EGFR mutations in non-small cell lung cancer patients

ObjectivesWe investigated whether serum tumor markers (STMs) represent a valuable noninvasive tool to predict epidermal growth factor receptor (EGFR) mutations in non-small cell lung cancer (NSCLC) patients. MethodsA retrospective analysis was performed for 143 NSCLC patients at the Peking University International Hospital from December 2014 to December 2019. EGFR mutations in the tumor tissues were identified by amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) and next generation sequencing (NGS). The relationships between EGFR mutation and several clinicopathological features were analyzed. ResultEGFR mutation were found more frequently in female (56.67%, P = 0.01), never-smokers (55.26%, P = 0.004), and those with lung adenocarcinoma (ADC) (52.17%, P < 0.001). The positive mutation rate for the EGFR gene were higher in the squamous cell carcinoma antigen (SCCA)group (≤1.5 ng/ml) and in the gastrin-releasing peptide precursor (preGRP) increased group (≥69.2 pg/ml), and this difference was statistically significant (P < 0.05). Univariate logistic regression analysis demonstrated that females (Odd ratio [OR]: 2.435, 95% confidence interval [CI]: 1.232, 4.813, P = 0.01) and never-smokers (OR = 0.370; CI = 0.186, 0.734; P = 0.004), lung adenocarcinoma patients (OR = 9.091; CI = 2.599, 21.800; P = 0.001), the SCC group (≤1.5 ng/ml) (OR = 0.331, CI = 0.120, 0.914; P = 0.033), and the preGRP group (≥69.2 pg/ml) (OR = 5.478, CI = 1.462, 20.528; P = 0.012) patients were risk factors for EGFR gene mutation. Multivariate logistic regression analysis demonstrated that lung ADC and proGRP elevation were independent risk factors for predicting EGFR gene positivity (P < 0.05). ConclusionSTMs are associated with mutant EGFR status and could be integrated with other clinical factors to facilitate the classification of EGFR mutation status among NSCLC patients.

Investigation of the impact of an ADCY2 polymorphism as a predictive biomarker in bipolar disorder, suicide tendency and response to lithium carbonate therapy: the first report from Iran.

High rates of mortality due to both suicide and medical comorbidities in bipolar patients can be decreased through the administration of lithium, which affects the cerebral endothelium as well as neurons. To investigate the role of ADCY2 in risk of bipolar disorder, we genotyped the ADCY2 rs2290910 in bipolar patients and healthy controls using amplification refractory mutation systemPCR. This polymorphism was associated with risk of bipolar disorder (odds ratio [OR]: 0.430; 95% CI: 0.296-0.624;p=0.001). The C allele was more frequent in suicide ideation group compared other groups (OR: 2.7; 95% CI: 1.386-5.302;p=0.004). The T allele was more frequent in suicide attempt group compared with suicide ideation group (OR: 0.238; 95% CI: 0.111-0.509;p = 0.001).

The effect of NR4A3-rs12686676 and XBP1-rs2269577 polymorphisms on type 2 diabetes mellitus susceptibility in an Iranian population: Case-control study

Many genes with different impacts on β-cell function, have been known as Type 2 diabetes mellitus (T2DM) risk genes. The purpose of this investigation was the evaluation of the potential correlation between rs12686676 and rs2269577 common polymorphisms of NR4A3 and XBP1 genes which are linked to β-cell function, and risk of T2DM in an Iranian population. In the present case-control investigation, 350 people affected by T2DM and 350 subjects in control group genotyped for NR4A3-rs12686676 by Tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) method and XBP1-rs2269577 polymorphisms by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method. According to results, no correlation between T2DM risk and NR4A3-rs12686676 polymorphism was found. However, we observed that CG genotype of XBP1-rs2269577 polymorphism could significantly decrease T2DM risk (OR = 0.6, 95%CI: 0.40–0.89, P = 0.01). Moreover, we detected that XBP1-rs2269577 SNP was related to the decreased risk of T2DM in dominant genetic model (OR = 0.5, 95%CI: 0.40–0.88, P = 0.01). In conclusion, there was no connection among pathogenesis of T2DM risk and NR4A3-rs12686676 polymorphism, however we found that heterozygote genotype (CG) of XBP1-rs2269577 SNP could decrease risk of T2DM in an Iranian population. Our result is the first report to show the protective role of rs2269577 SNP on diabetes risk.

A new method to detect methylation profiles for forensic body fluid identification combining ARMS-PCR technique and random forest model

A set of DNA methylation markers was detected and evaluated to identify body fluids using the amplification refractory mutation system-PCR (ARMS-PCR) and random forest algorithm. In this study, four multiplex DNA methylation reactions composed of 22 promising methylation markers were used to identify regular forensic body fluids, including venous blood, saliva, semen, menstrual blood, and vaginal fluid. The ARMS-specific primers were used to amplify the candidate markers, and then the methylation values of each CpG site were detected through capillary electrophoresis (CE). The DNA methylation patterns of 22 highly informative methylation markers were consistent with previously reported results to a certain extent. To our knowledge, our study is a new method to apply the ARMS-PCR technique and random forest model to detect DNA methylation patterns and identify the type of body fluids in forensic science, thus providing a new method for forensic body fluid identification. Moreover, we proved that this method is robust, applicable and effective for identifying body fluids using the random forest model. The accuracy to predict all body fluids reached up to 0.9966. We firmly believe that this method will have a great potential in the detection of methylation profiles at the molecular level.

Association of rs3735025 and rs9656169 variants with autism, and schizophrenia: A GWAS-replication study in an Iranian population

The study was aimed at replicating the association of two GWAS-SNP rs3735025 and rs9656169 with Autism spectrum disorders (ASD) as well as schizophrenia (SCZ) susceptibility in an Iranian cohort. The study population consisted of 336 ASD cases, 303 SCZ cases, and 309 healthy controls. We genotyped subjects for rs3735025 and rs9656169 variants using the Tetra-primer amplification refractory mutation system PCR (ARMS-PCR) method. Our results revealed that rs9656169-TT was less frequent in ASD as compared to controls. Likewise, rs3735025-TC and –CC genotypes were less frequent in ASD patients as compared to controls. Binary logistic regression results suggested subjects with TT genotype for rs9656169 were 0.56 (95% CI 0.34–0.93) times less likely to develop autism. Also, individuals with TC + CC genotypes for rs3735025 were 0.59 (95% CI 0.42–0.83) times less likely to be diagnosed with autism. We failed to find a significant association for rs3735025 and rs9656169 variants in SCZ patients. Our findings suggest that the TT genotype for rs9656169 variant and TC + CC genotypes for rs3735025 variant are significantly associated with ASD and confer a reduced risk of the disease in an Iranian population.

Genetic Structure Analysis of Y Chromosome STR and SNP in Population of Changshu.

Objective To provide a theoretical basis for building a Y chromosome database in specific regions by analyzing the pedigree specific core haplogroup and region specific genetic structure in Changshu. Methods One thousand seven hundred and two samples from unrelated Han male individuals in Changshu were collected. Then 27 Y-STR were genotyped through YfilerTM Plus PCR Amplification Kit, Y-SNP haplogroup of each sample was speculated using Y-Predictor software and some samples were verified by amplification refractory mutation system-polymerase chain reaction （ARMS-PCR）. Results A total of 1 556 haplotypes were found on the 27 Y-STR genetic markers of the 1 702 samples. The haplotype diversity （HD） value was 0.999 827. DYS385 （0.933） had the highest gene diversity （GD） value while DYS438 （0.409） had the lowest. By the Y-Predictor software, all samples were confirmed to be from 162 sub-haplogroups of C, D, N, O, Q and R. Samples were randomly selected to verify the prediction results by the software and the prediction accuracy of Y-Predictor software was as high as 95.74%. Conclusion This study found that 27 Y-STR genetic markers have relatively high polymorphisms in the Changshu population, and have good forensic individual identification and paternity testing ability.

Association of cytokine gene polymorphisms with susceptibility to cutaneous leishmaniasis in a Turkish population.

The objective of this study was to determine the association of TNF-α -308 G/A, IFN-γ +874T/A, IL-12B+1188 A/C, IL-10 -1082 G/A and IL-4 -590 C/T polymorphisms with susceptibility to CL. A total of 55 CL patients and 110 controls from Sanlıurfa province of Turkey were included to this study. Polymorphisms were genotyped by 'polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP)' and 'amplification refractory mutation system-PCR (ARMS-PCR)' methods. A statistically significant difference was noted in the allele (P<.001, P=.002) and genotype (P<.001, P=.001,) frequencies of TNF-α -308 G/A and IL-4 -590 C/T, respectively. TNF-α 308 GG versus GA genotype (OR=19.556 [95% CI 8.310-46.019] P<.001), GG versus GA+AA genotype (OR=20.444 [95% CI 8.707-48.004] P<.001) and G versus A allele (OR=6.968 [95% CI 3.903-12.440] P<.001) revealed significant association with CL. IL-4 -590 CC versus TT+CT genotype (OR=2.049 [95% CI 1.025-4.096], P=.041) and C versus T allele (OR=2.441 [95% CI 1.355-4.396], P=.002) revealed significant association with CL. Our study indicates that TNF-α 308 G/A and IL-4-590 C/T polymorphisms are significantly associated with susceptibility to CL. Individuals carrying A allele at TNF-α promoter -308 position and T allele at IL-4 promoter -590 position are at a higher risk for CL.

Investigation the Association of the VEGFR-2 and -2578C\A Polymorphism as a Risk Factor for Incidence of Lung Cancer in Babylon Province

Background: VEGF gene polymorphisms can induce either increase or inhibition of VEGF secretion, with altered promoter activity. Aim: We investigated the association of the VEGFR-2 and -2578C\A polymorphism in the VEGF gene with Lung cancer risk in Babylon province. Methodology: VEGFR-2 level was measured by Enzyme Linked Immunoabsorbant Assay ELISA and Genotyping of the VEGF-gene variation (-2578A\C) was performed using the amplification refractory mutation system PCR. We investigated the association of VEGF gene variants with different clinicopathological features of lung cancer patients. Results: No significant difference was seen of the VEGFR-2 levels in lung cancer patients when compared with control group (P=092), the allelic frequency of -2578 A\C VEGF gene no difference was seen in patients lung cancer (p=0.652). Hardy-Weinberg equilibrium showed a significant difference cases group (p=0.016), also revealed A allele exhibits a pathological behavior and it appears in over-dominant model (p=0.05), this proves that there is significant association of -2578A\C VEGF gene in lung cancer patients. Conclusion: Our results showed no significant association of the VEGFR-2 in lung cancer patients while showed a significant association of the VEGF -2578C\A polymorphism with LC susceptibility in Babylon province .The VEGF -2578C\A heterozygote significantly increases the risk and can be useful as a predisposing genetic marker.

Association between IL12A Gene of G/A genotype Polymorphism and Pulmonary Tuberculosis Risk in Baghdad Population

The study included eighty samples. This cases-controlled study was performed including fifty Pulmonary tuberculosis patients, their ages ranged from 12 to 77 year (27 female and 23 male) and thirty controls (healthy), their ages ranged from 19 to 58 year (15 female and 15 male). We confined the frequency of IL12A gene (G/A rs568408 genotype) polymorphism by Tetra-ARMS PCR (Tetra amplification refractory mutation system-polymerase chain reaction) technology. Also, we determined the association of IL12A Gene (G/A rs568408 genotype) polymorphism with Pulmonary tuberculosis patients in Baghdad. Statistical results showed significant difference in genotype frequency of IL12A Gene (G/A rs568408 genotype) polymorphism between Pulmonary tuberculosis patients and control (healthy). The G allele shows high frequency in Pulmonary tuberculosis patients comparison with control (healthy) and present related with etiological fraction risk of Pulmonary tuberculosis patients and its ratio 62% in patients and 51.67% in control (healthy), While A allele shows high frequency in control (healthy) comparison with Pulmonary tuberculosis patients and present related with protective fraction of Pulmonary tuberculosis patients and its ratio 48.33% in control and 38% in Pulmonary tuberculosis patients. The genotypes of GG and AA homozygotes shows high frequency in Pulmonary tuberculosis patients comparison with control (healthy), and its ratio 42% and 18% respectively in Pulmonary tuberculosis patients, while its ratio 3.33% and 0% respectively in control (healthy), also GG and AA genotypes appear related with etiological fraction risk of Pulmonary tuberculosis patients, while the GA heterozygote show high frequency in control (healthy) and its ratio 96%, GA genotypes related with preventive fraction of Pulmonary tuberculosis patients. Our findings demonstrate that the IL12A Gene (G/A rs568408 genotype) polymorphism may represent a significant risk factor for pulmonary tuberculosis patients in Baghdad population.

Identification of three SNPs insmad4gene by tetra‐primer ARMS PCR and analysis of their associations with growth traits in gynogenetic populations ofCulter alburnus

Three single nucleotide polymorphisms, c.1462C > T, c.1663G > T and c.2023G > A, in smad4 gene were isolated and typed in a normal population (meio-G0), a first-generation gynogenetic population (meio-G1) and a second-generation gynogenetic population (meio-G2) in topmouth culter (Culter alburnus) by using the tetra-primer amplification refractory mutation system (ARMS) PCR. The homozygosity of different loci in the three populations was analysed to study the efficiency of gene purification in this fish. Correlation of the three populations to seven growth traits (body length, body weight, body thickness, body height, total length, caudal peduncle length and caudal peduncle height) was estimated. Results showed that homozygosity and homozygosity rates of three SNP loci from meio-G0 to meio-G2 increased obviously, and the average homozygosity of c.1462C > T and c.1663G > T loci was 0.930 and 0.880 in meio-G2 population, which was significantly higher than that in meio-G0 population. In the meio-G1 and meio-G2 populations, correlation of seven growth traits with the CC genotype was significantly higher than that with the TT and TC genotypes in the c.1462C > T locus (p < .05). These results suggested that the CC genotype in the c.1462C > T locus could be an advantage mutation that stably affects the growth of different generations of this fish. It may be used as a potential molecular marker for gene-assisted selection to improve a range of growth traits in topmouth culter.

Distribution of HBB Gene Mutations in the Kurdish Population of Ilam Province, West Iran

β-Thalassemia (β-thal) is one of the most common diseases in Iran. Here, we report the spectrum of HBB gene mutations in 176 Kurdish β-thal carriers from the northern part of Ilam Province, Iran. The amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) technique was used to identify common β-globin gene mutations observed in Iran. Samples negative on ARMS-PCR were analyzed by direct sequencing of the β-globin gene. In total, 12 different mutations were identified on the β-globin gene. The mutations of IVS-II-1 (G>A) (HBB: c.315+1G>A), codons 8/9 (+G) (HBB: c.27_28insG), codons 36/37 (–T) (HBB: c.112delT) and IVS-I-110 (G>A) (HBB: c.93-21G>A), were the most prevalent mutations in our samples, with frequencies of 59.09, 10.80, 7.95 and 7.39%, respectively. In general, the mutation spectrum of the β-globin gene in the northern part of Ilam Province is most similar to that in other western provinces of Iran. On the other hand, due to the high prevalence of carriers and β-thal major (β-TM) patients in this province, our results can be helpful in identifying carriers as well as at-risk fetuses through the prenatal diagnosis program.

The Effect of Adrenergic β2 Receptor Thr164Ile Gene Polymorphism on Asthma Risk, Severity and Response to Β2 Agonists in Egyptian Children

Background: Asthma is a global health problem affecting millions of adults and children. Pathogenesis of asthma is multifactorial and the genetic component is of particular importance. Objectives: To assess the role of ADRB2 Thr164Ile gene polymorphism in asthma risk, severity and response to β2 agonist therapy in Egyptian children. Methodology: The study enrolled 50 asthmatic and 50 control children. Pulmonary function tests and serum levels of IgE of asthmatic children were measured. The Thr164Ile genotypes were detected for all study subjects by Amplification Refractory Mutation System- Polymerase Chain Reaction (ARMS-PCR). Results: Serum IgE levels were significantly higher on comparing mild to moderate and severe cases (P=0.002&amp; 0.02, respectively). The Ile/Ile genotype of Thr164Ile SNP was significantly present in asthmatic subjects (P=0.039). The Thr164Ile SNP was associated with lowered response to β2 agonist inhalation (P&lt;0.001) but there was no association between the studied SNP and asthma severity. Conclusion: The Thr164Ile SNP can be linked to asthma risk and lowered response to β2 agonist treatment but not to asthma severity in asthmatic children.

SNP Scanning in mecA Gene for Methicillin-Resistant Staphylococcus aureus.

Background: Staphylococcus aureus (SA) is known as an important human pathogen, which is responsible for many cases of both hospital and community-acquired infections all over the world. Studying on drug resistance is regarded as an important prevention strategy regarding these types of infections.Objectives: The current study is aimed to assess the association between the single-nucleotide polymorphism (SNP) and resistance to antibiotics in the methicillin-resistant Staphylococcus aureus (MRSA) strains as well as the molecular typing of isolates, collected from the clinical samples.Materials and Methods: We used the disc-diffusion method to test the isolates antibiotic resistance. In addition, the genotypes of staphylococcal cassette chromosome mec (SCCmec) in the Methicillin-resistant Staphylococcus aureus isolates were determined by multiplex -polymerase chain reaction (PCR). SNP was identified in the mecA gene using sequencing and amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) method.Results: The highest resistance was shown against oxacillin, and erythromycin and cephalexin. The most sensitive antibiotic was vancomycin (97%) and resistance to at least three antibiotic classes were identified in all isolates. Eighty six percent of isolates were positive for mecA gene and more than 50% of which were healthcare-acquired methicillin-resistant Staphylococcus aureus (HA-MRSA). Moreover, SCCmec type 3, 1were the predominant strains of the identified MRSA. Also, 23 isolates (23%) were non-typable. By using the ARMS-PCR method, it was found that 10% of the clinical specimens had SNP in the mecA gene.Conclusion: According to the Chi-square test (χ2), it reveals that the association between SNP in the mecA gene and oxacillin, cefoxitin, and erythromycin resistance was confirmed among clinical MRSA. Furthermore, there is a 95%probability of association between SNP and resistance to more than three antibiotics in MRSA strains.

Digital Droplet PCR is a Specific and Sensitive Tool for Detecting IDH2 Mutations in Acute Myeloid LeuKemia Patients.

Isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) interfere with cellular metabolism contributing to oncogenesis. Mutations of IDH2 at R140 and R172 residues are observed in 20% of acute myeloid leukemias (AML), and the availability of the IDH2 inhibitor Enasidenib made IDH2 mutational screening a clinical need. The aim of this study was to set a new quantitative polymerase chain reaction (PCR) technique, the drop-off digital droplet PCR (drop-off ddPCR), as a sensitive and accurate tool for detecting IDH2 mutations. With this technique we tested 60 AML patients. Sanger sequencing identified 8/60 (13.5%) mutated cases, while ddPCR and the amplification refractory mutation system (ARMS) PCR, used as a reference technique, identified mutations in 13/60 (21.6%) cases. When the outcome of IDH2-mutated was compared to that of wild-type patients, no significant difference in terms of quality of response, overall survival, or progression-free survival was observed. Finally, we monitored IDH2 mutations during follow-up in nine cases, finding that IDH2 can be considered a valid marker of minimal residual disease (MRD) in 2/3 of our patients. In conclusion, a rapid screening of IDH2 mutations is now a clinical need well satisfied by ddPCR, but the role of IDH2 as a marker for MRD still remains a matter of debate.

Nutritional Quality's Key Role in the Odds of Overweight in Adults with rs9939609 Polymorphism of FTO Gene- the Role of Manganese and Vitamin D

BackgroundObesity and overweight are the most prevailing problem in most countries. Overweight people are very susceptible to diseases such as diabetes, hypertension, cardiovascular disease, metabolic syndrome, and cancers. Adequate intake of micronutrients along with a quality diet that is varied and balanced plays an important role regarding health and the immune system. Numerous studies have investigated the relationship between the quality of diet and different diseases. Genetics is a risk factor of great importance regarding obesity and overweight. Yet, the role of nutrition in relationship with the underlying mechanisms remains unclear and no specific pathways have been identified for this relation. MethodsA valid food frequency questionnaire was employed to assess dietary intake. We calculated the INQ (Index of Nutritional Quality) of each dietary item using the following formulae: INQ=consumed amount of a nutrient per 1,000 kcal/recommended dietary allowance or adequate intake of that nutrient per 1,000 kcal. In a retrospective chart review, we determined the genotypes of FTO rs9939609 polymorphism (TT/AT/AA) via amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). ResultsModels obtained from the resulting INQs of manganese as a continuous variable in relationship with waist circumference represented a significant association after multivariate adjustment of age, sex, height, fat free mass, weight, body mass index, marital status, TF, fasting blood sugar, low-density lipoproteins, high-density lipoproteins, total cholesterol, insulin resistance, and total energy intake (odds ratio = 0.24, CI = 0.07–0.79). ConclusionsIntake of vitamin D from sunlight and its nutritional sources and adequate intake of Mn from a wide range of vegetables, legumes, seeds, and grains might be solutions for some overweight cases with FTO rs9939609 polymorphism.

Association of TIM-3 (rs1036199) and TIM-4 (rs7700944, rs6882076) gene polymorphisms with susceptibility to systemic lupus erythematosus

BackgroundThe systemic lupus erythematosus (SLE) is a heterogeneous disorder with the involvement of different environmental, immunological, and genetic factors. T-cell immunoglobulin and mucin domain (TIM)-3 and TIM-4 genes are the two members of the TIM gene family with different immunological roles in Th-1 and antigen-presenting cells respectively. Methods131 cases diagnosed with SLE and 131 healthy volunteers as a control group enrolled in the study to investigate the association of rs1036199 of TIM-3, rs7700944 and rs6882076 polymorphisms of TIM-4 gene with susceptibility to SLE using amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) for TIM-3 rs1036199 and TIM-4 rs6882076 polymorphisms and tetra-ARMS PCR for TIM-4 rs7700944 polymorphism. ResultsWhile no association found between TIM-3 rs1036199 polymorphism and SLE, there was a significant difference in the distribution of the G allele among cases and controls for TIM-4 rs7700944 polymorphism (P = .007). Regarding TIM-4 rs6882076 polymorphism, investigations showed that the frequency of the CC genotype was 38.9% in cases and 32.8% in controls (P = .033). ConclusionsThe results suggest that TIM gene family variants, especially TIM-4 gene polymorphisms, may have important roles in the SLE pathogenesis, although further investigations are needed to analyze the precise roles of these polymorphisms in SLE pathogenesis.

KCNB1 gene polymorphisms and related indel as predictor biomarkers of treatment response for colorectal cancer - toward a personalized medicine.

The KCNB1 gene variants were differentially associated with cancers. However, their association with colorectal cancer has not yet been explored. We investigated the contribution of the KCNB1 gene variants rs3331, rs1051295, and indel (insertion/deletion) rs11468831 Polymorphism as predictors of the treatment response in colorectal cancer patients. A retrospective study, which involved 291 Tunisian colorectal cancer patients (aged 60.0 ± 13.1 years), who were stratified into responder and non-responder groups, according to TNM stages and their responsiveness to chemotherapy based on fluorouracil. KCNB1 genotyping was performed with amplification-refractory mutation system-polymerase chain reaction, and was confirmed by Sanger sequencing. Sex-specific response was found and colorectal cancer females are less likely to achieve a positive response during the chemotherapy strategy, compared to males. Weight and body mass index, tumor size, and tumor localization are considered as predictive factors to treatment responsiveness. Carriage of rs11468831 Ins allele was significantly associated with successful therapy achievement (p adjusted < 0.001). Stratification of colorectal cancer patients' response according to tumor localization and TNM stages reveals negative association of rs3331 Major allele to treatment response among the patients with advanced cancer stages (subgroup G2). The presence of rs3331 (homozygous minor) C/C genotype was positively associated with decline in carcino-embryonic antigen (p = 0.043) and CA19-9 (p = 0.014) serum levels. On the other hand, the presence of rs1051295 (homozygous minor) A/A genotype was correlated with marked decline in CA19-9 serum levels. KCNB1 haplotype did not reveal any association between haplotypes and treatment response. The results obtained suggest that gender-specific strategies for screening treatment and prevention protocols as well as KCNB1 variants may constitute an effective model for ongoing personalization medicine.

Biochemical investigation of rs1801282 variations in PPAR-γ gene and its correlation with risk factors of diabetes mellitus in coronary artery disease.

We aimed to investigate the association of single nucleotide polymorphism of Pro/Ala (rs1801282) in peroxisome proliferator-activated receptor-gamma (PPAR-γ) gene with risk factors of diabetes mellitus (DM) in cardiovascular disease (CVD) patients. We recruited 244 participants from Faisalabad Institute of Cardiology and Department of Cardiology, Sargodha District Head Quarter Teaching Hospital, Pakistan. Out of 244 participants, 144 cases were CVD patients and 100 were healthy controls. CVD patients were further divided into 111 coronary artery disease (CAD) and 33 cardiomyopathy (CMP) patients. Assessment of variant specific polymorphism/mutation of Pro/Pro and Pro/Ala genotypes was done through amplification refractory mutation system polymerase chain reaction (ARMS-PCR). Further, serum biomarkers were measured to investigate the association among risk factors of DM and Pro/Ala polymorphism in PPAR-γ gene. About 31.5% Pro/Ala genotype was found in CVD patients out of which 22.5% were CAD patients and 9% were CMP patients. As a result, obesity, hypertension and smoking (35%, 23%, 21%, respectively) were observed to be the most critical risk factors accompanying Pro/Ala mutation in PPAR-γ particularly in CAD patients as compared to that in CMP patients. A similar pattern of association was observed among the elevated levels of glucose, cholesterol, triglyceride and ALT with Pro/Ala mutation in CAD patients. Further, CAD patients using ACE inhibitors (18%) and β-blockers (13%) were found to be the carriers of Pro/Ala genotype and also showed significant increase in glucose level. This study suggests that hyperglycaemia in CAD patients particularly obese, smokers and hypertensives having Pro/Ala polymorphism in PPAR-γ gene are at high risk of developing DM as clearly observed by hyperglycaemia in CAD patients.

Association of rs363598 and rs360932 polymorphisms with autism spectrum disorder in the Bangladeshi children

PurposeAutism spectrum disorder (ASD) is a genetically complicated neuropsychiatric developmental disorder. As the pathogenesis of ASD is not clear till now, we have carried out the present case-control study to validate the association of GRIK1 rs363598 and intergenic rs360932 polymorphisms with ASD in the Bangladeshi children. Methods and materialsWe used Tetra-primer Amplification Refractory Mutation System-Polymerase Chain Reaction (ARMS-PCR) to study 98 ASD children and 112 healthy volunteers from different institutes of Bangladesh. ResultsThe mean CARS score of the ASD children was 41.84 ± 9.28. The rs363598 SNP pretended a significantly higher risk for the progression of ASD with children carrying CC genotype, dominant and recessive models (OR = 4.34, p = .015; OR = 2.07, p = .015 and OR = 3.77, p = .026, respectively). Children with C allele (minor) significantly (p = .002) revealed 2.17 times elevated risk of autism compared to T allele. Again, intergenic rs360932 SNP presented a significantly elevated risk for the development of ASD with AA genotype, dominant and recessive models (OR = 2.34, p = .009; OR = 1.88, p = .026 and OR = 2.25, p = .009, respectively). Children with A allele (minor) had 2.00 times more risk compared to wild allele (p < .05). No significant association was found with heterozygous and overdominant models for both SNPs. ConclusionsThis study concludes that both rs363598 and rs360932 are significantly associated with the risk of ASD in Bangladeshi children. We believe that this case-control study will provide more opportunities to work on these SNPs on a large scale as well as other genes associated with ASD in future investigations.