Mutation System-polymerase Chain Reaction Research Articles

TGF-β1 promoter functional gene polymorphism -509 C/T in the maternal susceptibility to recurrent pregnancy loss in South Indian women

Transforming growth factor beta 1 (TGF-β1) is an anti-inflammatory pleiotropic cytokine that regulates implantation and adhesion of trophoblasts to the extracellular matrix. It regulates the balance of Th1/Th2 cytokines and the generation of anti-inflammatory peripheral regulatory T cells (FOXP3 + Tregs), which is necessary for a healthy pregnancy. Single nucleotide polymorphisms (SNP) affecting TGF-β1 production/function may predispose to pregnancy loss. The aim of this study is to evaluate the association between the TGF-β1 -509C/T polymorphism, its serum concentrations, and recurrent pregnancy loss. The study comprised 150 RPL cases and 150 healthy controls for genotyping TGF-β1 -509C/T polymorphism using the Amplification Refractory Mutation System-Polymerase Chain Reaction (ARMS-PCR). Serum concentrations of TGF-β1 protein were estimated by enzyme-linked immunosorbent assay. From our study, women with CT genotype exhibited a protective role against RPL [OR (95 % CI) = 0.48(0.30–0.76), p = 0.002], while women with TT genotype had a significantly higher risk among RPL patients and exhibited twofold increased risk [OR (95 % CI) = 2.34(1.37–4.01), p = 0.002]. Observation of patient’s follow-up data revealed a significant relation with CT genotype of unfavorable pregnancy outcome (CT vs. CC + TT, OR 2.46, 95 % C.I: 1.11–5.43, p = 0.039). Further, variant allele T was significantly elevated in women with unfavorable pregnancy compared with favorable pregnancy outcome, indicating considerable association of T allele in unfavorable pregnancy outcome (T vs. C, OR: 2.68, 95 % C.I: 1.52–4.74, p = <0.001). Serum concentrations of TGF-β1 have shown significant variation between patients and controls, as well as among RPL patients with favorable and unfavorable pregnancy outcome in correspondence to each genotype CC, CT, and TT (p < 0.05). Furthermore, genotype-dependent variation was observed within both the patient and control groups; however, this variation was not observed among RPL women with favorable and unfavorable pregnancy outcome. Our investigation revealed a significant influence of TGF-β1C-509 T polymorphism on RPL risk in South Indian women.

Molecular profiling of BRCA1/BRCA2 gene variants in Pakistani breast cancer patients.

To determine the frequency of genetic variants in breast cancer types 1 and 2 gene in breast cancer Pakistani patients. The case-control study was conducted at the Islamic International Medical College and Pakistan Railway Hospital, Rawalpindi, Pakistan, from October 2022 to August 2023, and comprised females with breast cancer in group A, with an age range of 23-83 years (mean 51.9 ± 10.8 years) and as many healthy, age-matched female controls in group B, with age range of 26-82 years(mean 57.8 ±10.1 years). Peripheral blood samples were taken from all the participants. Allele-specific tetra amplification refractory mutation system-polymerase chain reaction was used to determine the frequency of c.4485G>A, c.4508C>A, c.5278G>C and c.5503C>T genetic variants in breast cancer type 1 gene, and c.92G>A and c.3109C>T genetic variants in breast cancer type 2 gene. Data was analysed using SPSS 27. Of the 336 female participants 168(50%) were in each of the 2 groups. None of the group B controls had genetic variants in breast cancer type 1 and 2 genes. In group A patients, 4(2.3%) had the variant c.4485G>A in breast cancer type 1 gene, while other breast cancer type 1 variants were negative. Also, 9(5.3%) group A patients had variants c.92G>A and c.3109C>T in breast cancer type 2 gene. Cost-effective, polymerase chain reaction-based genetic testing could effectively identify mutant variants of breast cancer types 1 and 2 genes in the Pakistani population.

Genetic Polymorphism of Interferon-Gamma +874T/A as a Risk Factor for Pulmonary Tuberculosis in Cirebon, Indonesia

Background: Tuberculosis (TB) is one of the leading causes of death globally, caused by Mycobacterium tuberculosis. With 10% of all cases worldwide in 2022, Indonesia is the second-largest contributor of tuberculosis cases. IFN-γ gene polymorphism is one of the factors that have been studied extensively for its association with TB. Aims: To analyze IFN-γ +874T/A gene polymorphism as a risk factor for pulmonary tuberculosis in Cirebon. Methods: Observational analysis with case control design was used in this study. Thirty-two tuberculosis patients as cases and 32 healthy controls at RSUD Waled were collected and performed DNA extraction to evaluate the polymorphism by using Amplification-refractory mutation system–polymerase chain reaction (ARMS–PCR). Statistical comparison was performed by using Pearson Chi-square and Kruskal Wallis test. Mann-Whitney U test was done for post hoc test. Odds ratio was calculated to see the risk of the assessed variables, including genotype, allele frequency, and the presence of polymorphism. Results: In the case group, the frequency of TT genotype was 3 (9.4%), TA genotype was 26 (81.3%), AA genotype was 3 (9.4%). In the control group, the frequency of TT genotype was 12 (37.5%), TA genotype was 17 (53.1%), AA genotype was 3 (9.4%). A significant difference (p=0.034) was found among 3 genotype groups. Post hoc test revealed that TT and TA was the pair with significant difference (p=0.007). In addition, TA polymorphism was significantly associated (p=0.004) with tuberculosis (OR=6.614; CI95% = 1.660-26.349). Conclusion: IFN-γ +874 TA gene polymorphism is associated with pulmonary tuberculosis in the population of Cirebon, West Java, Indonesia. Received: 25 September 2024 | Reviewed: 23 October 2024 | Revised: 10 November 2024 | Accepted: 30 November 2024

The Association of Interleukin 6 Receptor Gene Variant (Rs4129267) with Susceptibility to Ankylosing Spondylitis and Soluble IL-6 Receptor Level in Iranian Patients

Objectives: Ankylosing spondylitis (AS) is an axial skeleton-related auto-inflammatory arthritis. Interleukin 6 (IL-6) and its receptor (IL-6R) play a role in the etiopathology of AS. The recent genome-wide association studies (GWASs) revealed that rs4129267; an intrinsic variant of IL6-R is associated with the risk of AS. We aimed to study the rs4129267 IL6R variant in Iranian AS patients and the correlation of this variant with the soluble interleukin-6 receptor (sIL-6R) serum level. Materials and Methods: In this case-control study, we genotyped rs4129267 IL6-R variant in extracted DNA from 498 AS patients and 495 matched healthy controls by Amplification-Refractory Mutation System Polymerase Chain Reaction (ARMS-PCR). The serum level of sIL-6R and IL-6 was also analysed in 39 controls and 42 AS patients by the ELISA method. The correlation between rs4129267 IL-6R variants and patients’ clinical manifestations and sIL-6R level was also investigated. Results: In comparison to the AS individuals, C allele were significantly less prevalent in the healthy control group (OR = 1.23 [1.01 –1.48], P value = .034). Patients had significantly elevated levels of IL-6 serum levels. There was a significant correlation between the presence of the rs4129267 T allele and increased sIL-6R level. Conclusions: Our study confirmed the significant association between the rs4129267 T variant and the protection against AS disease susceptibility. Increased IL-6 level and reduced frequency of sIL-6R rs4129267 T allele in patients which contributes to reduced sIL-6R serum level, highlights the significant role of IL-6 signalling pathway in AS pathogenesis.

Biochemical Investigation of the Association of Apolipoprotein E Gene Allele Variations with Insulin Resistance and Amyloid-β Aggregation in Cardiovascular Disease.

This article investigates the intricate associations between apolipoprotein E (APOE) gene alleles variation, insulin resistance (IR) and amyloid-β aggregation in cardiovascular disease (CVD) patients. A cohort of 250 patients exhibiting the symptoms of CVD and 50 control subjects participated in this study. After applying the stringent inclusion and exclusion criteria, the diseased group was further stratified into three categories: CVD+ (Alzheimer's disease) AD, CVD + (diabetes mellitus) DM and CVD + DM + AD. Blood samples were collected from all recruited participants for the biochemical analyses of lipid profile, glycaemic status, liver function enzymes, inflammatory and oxidative stress biomarkers. Tetra amplification-refractory mutation system-polymerase chain reaction (ARMS-PCR) was employed for APOE gene analysis. Biochemical evaluations revealed the significant elevations in the serum levels of glucose, liver enzymes, interleukin-6 (IL-6), cholesterol, low-density lipoproteins (LDL), triglycerides (TG) and malondialdehyde (MDA) in CVD + DM + AD group. Conversely, the serum levels of insulin, HDL and hexokinase decreased in CVD + DM + AD group compared to the controls and other CVD groups. Tetra ARMS-PCR results indicated a higher percentage of the risk allele in CVD + DM + AD group when compared with the other groups. Our study elucidates the multifaceted cardiovascular risk factors contributing to IR and AD in CVD patients. Age-related risk factors, prevalence of APOE risk alleles and the impact of statin use on AD incidences were identified. These findings underscore the need for tailored preventive measures, particularly in APOEε4 and ε3/ε4 carriers with CVD. Further studies should delve into the knowledge-based protocols to comprehend the underlying mechanisms. Focusing on the therapeutic targets to prevent or delay DM and AD progression in CVDs, especially in APOEε4 carriers, is essential.

Genetic variation in &lt;i&gt;GSTP1&lt;/i&gt; and &lt;i&gt;TBXA2R&lt;/i&gt; genes: influence of Badoush cement factory pollutant

Industrial advancements, while driving economic growth, have simultaneously intensified environmental pollution levels, posing significant health risks to populations residing near industrial hubs. The release of a complex mixture of pollutants, including heavy metals, particulate matter, and volatile organic compounds, has been linked to a range of adverse health outcomes, including respiratory diseases, cardiovascular complications, and cancer. The Badoush Cement Factor in Mosul city, Nineveh, Iraq, a major industrial facility, exemplifies this challenge, emitting substantial quantities of air pollutants capable of long-range transport. This study, therefore, investigated the potential gene-environment interactions focusing on TBXA2R and GSTP1 genes and contributing to respiratory health disparities among 64 employees of the Badoush Cement Factory compared to 10 control subjects. Specifically, the study employed the tetra-primer amplification refractory mutation system-polymerase chain (ARMS-PCR) reaction technique to analyze the role of the TBXA2R gene, known for its involvement in bronchoconstriction and susceptibility to asthma, and the GSTP1 gene, encoding a crucial antioxidant enzyme protecting lung tissue from oxidative stress. By examining these genetic markers within the context of occupational exposure at the Badoush Cement Factory, this research aimed to elucidate the intricate interplay between genetic predisposition and environmental factors in determining respiratory health outcomes. The results indicated that there was no direct correlation between exposure to pollutants and genetic variation in the TBXA2R gene. However, prolonged exposure to pollutants may increase the risk of developing respiratory diseases. No significant association was found between pollutants emitted from the cement plant and genetic variation in the GSTP1 gene.

Association of the Single Nucleotide Polymorphism 19216T/C in the TLR2 Gene (rs3804099) with Entamoeba histolytica/Entamoeba dispar/Entamoeba moshkovskii Infection Among Lebanese Children.

Toll-like receptors (TLRs), particularly the TLR2, take part in the elicitation of immune responses against Entamoeba histolytica. This study aimed to investigate the relationship between a specific polymorphism called rs3804099 in the TLR2 gene and E. histolytica/E. dispar/E. moshkovskii infection among Lebanese children. A case-control study encompassed 180 participants including 68 children with amebiasis and 112 matched controls. Blood samples were collected, and genomic DNA was extracted using the classical proteinase K digestion and phenol-chloroform extraction method. The variant rs3804099 was examined using the Amplification Refractory Mutation System Polymerase Chain Reaction. The accuracy of the genotyping was supported by sequencing 5% of samples. The TLR2 rs3804099 polymorphism was identified in the studied population, and the observed genotypic distributions were consistent with Hardy-Weinberg equilibrium (P > 0.05). The frequency of the rare CC genotype was significantly higher in patients compared to the noninfected group (P < 0.01). In controls, the homozygous TT genotype was less frequent than the heterozygous CT genotype. The rare CC genotype was associated with a higher risk of amebiasis among children (odds ratios = 3.27, P = 0.002). These findings provide evidence supporting the association between the rs3804099 SNP in the TLR2 gene and E. histolytica/E. dispar/E. moshkovskii infection among Lebanese children.

PvuII-ESR1 gene polymorphism in premenstrual dysphoric disorder in South Indian women.

Premenstrual dysphoric disorder (PMDD) is a condition that affects nearly 3-9% of the women in the reproductive age during the luteal phase of each menstrual cycle characterized by symptoms varying in severity and affecting the quality of life. Earlier research studies conducted have reported independent relationships between PvuII-ESR1-polymorphism and psychological traits in PMDD and risk for cognitive, behavioral, and affective symptoms. However, as the studies are few in number and the results are not consistent, there is a need for our study to link between the PvuII-ESR1gene and PMDD. All nonpregnant women aged between 18 and 45 years and attending the OBG or Medicine or Psychiatry OPD for a routine health checkup were recruited into the study. The cross-sectional study recruited 35 samples each in the control and PMDD groups using a validated screening PMDD Assessment Scale Questionnaire (PMDDASQ). Mann-Whitney's U test and Chi-square test were used to calculate P values for the continuous and categorical variables. Tetra-primer-amplification refractory mutation system-polymerase chain reaction was used to identify the PvuII-ESR1gene polymorphism after isolation of genomic DNA from the whole blood. Data-Analysis Pak tool and Med-Calc software were used for data analysis. The PvuII-ESR1 genotype distribution was in Hardy-Weinberg equilibrium in both PMDD and controls. The PMDDASQ scoring showed a significance with P ≤ 0.05. Pearson's Chi-Squared test performed for genotypes and alleles did not show any significant association with the phenotype. PvuII-ESR1 SNP (T/C rs2234693) does not show any association with phenotype between the control and PMDD. However, PMDDAS questionnaire can be used to differentiate the women who are controls from PMDD.

Evaluation of serum IL 18 / IL 18 binding protein ratio and their relation with IL- 18 gene polymorphisms in sample of Iraqi type 2 diabetes mellitus patients. A case control study.

To evaluate the ratio of interleukin18 and interleukin18 binding protein in type 2 diabetes mellitus patients, and its relation with the presence of interleukin18-607C/A and interleukin18-137G/C gene polymorphisms and the type of complications. The case-control study was conducted at the endocrinology clinic of the Madinat Al-Imamin Al-Kazemin Teaching Hospital, Iraq, from September 2020 to July 2021, and comprised diagnosed patients of type 2 diabetes mellitus, and healthy controls matched for age and gender. Blood samples were obtained that were processed for serum separation. Serum interleukin18 and interleukin18 binding protein levels were assessed, and part of the sample was used for deoxyribonucleic acid extraction using tetra-primer amplification refractory mutation system polymerase chain reaction with four specific primers for interleukin18-607C/A and interleukin-18-137G/C gene polymorphisms in both the groups. Data was analysed using SPSS 20. Of the 168 subjects, 86(51.2%) were patients; 67(77.9%) females and 19(22.1%) males with mean age 52±8.97 years. There were 82(48.8%) controls; 56(68.3%) females and 26(31.7%) males with mean age 48±9.44 years (p>0.05). Higher serum level of interleukin18 and lower level of interleukin18 binding protein were seen in type 2 diabetes mellitus group compared to the controls (p<0.001). Interleukin18-137G/C and interleukin18-607C/A mutant alleles had odd ratios 3.52 (confidence interval: 1.91- 6.63) and 3.25 (confidence interval: 1.77-5.83), respectively, as risk factors for the occurrence of type 2 diabetes mellitus. There was an association of interleukin18- 137G/C homozygous mutant genotype with the occurrence of retinopathy among type 2 diabetes mellitus patients (p=0.046), but risk allele C was not associated with retinopathy (p>0.05). The presence of interleukin18-137G/C and interleukin18-607C/A gene polymorphism might be considered a risk factor for type 2 diabetes mellitus.

T315I- a gatekeeper point mutation and its impact on the prognosis of chronic myeloid leukemia.

BCR-ABL kinase domain mutations are an important cause of resistance to tyrosine kinase inhibitors (TKIs) in chronic myeloid leukaemia (CML) of which T315I is the most treatment-resilient. This study aimed to observe the frequency of T315I and its impact on disease prognosis in terms of progression and survival. Patients with a response which categorized them into warning zone/or who failed to respond to their TKI treatment completely as per the European LeukemiaNet (ELN) were labeled as non-responders. They were assessed for T315I mutation using amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) and validated via sequencing. Patients were then longitudinally followed for 96months for the prognostic impact of the mutation. Of the 102 non-responders, T315I mutation was detected in 21.6 % of patients with a female preponderance. Almost 59 % of mutation-harbouring patients were labelled as low Sokal risk at baseline. The disease progression into the blastic phase was reported in 58.8 % of mutation-harbouring patients. Overall survival (study period: 96months) was 81.8 % in patients harbouring T315I mutation. Patients in the blastic phase had significant odds of harbouring T315I mutation. Sub-optimal response or failure to TKI treatment indicates the development of resistance due to the presence of T315I mutation or other mutation(s). Early identification will help redirect the patient's treatment.

Analysis of PIK3CA mutations in the primary and recurrent tumors of hormone receptor positive/human epidermal growth factor receptor 2 negative breast cancer.

Our aim was to compare the PIK3CA mutation status in matched primary and recurrent tumors of hormone receptor positive/human epidermal growth factor receptor 2 negative (HR+/HER2-) breast cancer (BC) to gain insight into the optimization of patient selection and detection time for PIK3CA-targeted therapy. The data were from 3035 patients with BC diagnosed at the Breast Disease Center, Peking University First Hospital, between January 2008 and December 2017. Matched primary and recurrent samples were profiled using amplification-refractory mutation system-polymerase chain reaction covering 11 mutational hotspots in PIK3CA. PIK3CA mutations were detected in 54.3% primary tumors and 48.6% corresponding recurrences. PIK3CA mutation was detected in 37.5% cases in the locoregional recurrent group and 40.0% of distant metastasis, without a statistical difference. Besides, PIK3CA mutations were concordant in 88.6% of the matched pairs. For patients treated with neoadjuvant chemotherapy, 100% concordance was observed. However, PIK3CA mutation was neither correlated with clinicopathological features nor associated with clinical outcomes. Mutations in PIK3CA in HR+/HER2- BC generally progressed to recurrent tumors. The high concordance rate of PIK3CA mutation status between primary tumors and corresponding recurrences suggests that the detection of primary tumors could be a substitute approach when recurrent samples are not easily obtainable.

Genetic polymorphisms in FABP2, CYP2E1, and TP53 genes are potentially associated with colorectal cancer susceptibility

Colorectal cancer (CRC) is among the most prevalent cancers with a high mortality rate. Both genetic and environmental factors contribute to CRC development. This study aimed to assess the association of single nucleotide polymorphisms (SNPs) in the fatty acid binding protein-2 (rs1799883), Cytochrome P450 2E1 (rs3813865), TP53 (rs1042522), and Murine double minute 2 (rs1042522) genes with CRC. A cross-sectional case–control study was conducted at the Institute of Molecular Biology and Biotechnology from May 2020 to March 2021, involving CRC patients (N = 100) and controls (N = 100) recruited from the Multan district in Pakistan. Polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) and tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) were employed to investigate the studied SNPs. The association of SNPs in all genes with CRC was examined either individually or in various combinations. Genotypes at three SNPs, rs1799883 in FABP2, rs3813865 in CYP2E1, and rs1042522 in TP53, were found to be associated with the development of CRC, while rs1042522 in MDM2 was not. Patients who were married, smoked, lacked exercise habits or had a family history of CRC were at a greater risk of acquiring the disease. FABP2 gene rs1799883, CYP2E1 gene rs3813865, and TP53 gene rs1042522 polymorphisms are significant in the development of CRC in Pakistani participants.

Genetic Study for Identifying Beta Thalassemia Trait in Relatives of Children with Beta Thalassemia Major.

The most common inherited illness, thalassemia, is thought to have a detrimental effect on public health, particularly in endemic areas. Children with beta thalassemia disease have several mutations. Prevention and premarital examination are still the most effective measures to lessen the burden of beta thalassemia. This study primarily aimed to determine the beta thalassemia carriers in relatives of beta thalassemia major children, the role of gene study in the confirmation of beta thalassemia trait diagnosis, and to detect the genetic defect in the relatives of beta thalassemia major children. The cross-sectional study was conducted on 109 healthy children, aged between six months and 18 years, who were the relatives (second and fourth degree) of beta thalassemia major cases. Gene screening, using the amplification refractory mutation system (ARMS) polymerase chain reaction (PCR), covered the most common 22 alleles in the Mediterranean region, and was successful in detecting 61.5% of beta-globin chain mutations of studied participants, in addition to high prevalence (34.8%) of beta thalassemia carriers among the relatives of beta thalassemia children. The beta thalassemia carrier rate was found to be highly prevalent among relatives of beta thalassemia major children. Despite the accuracy of gene screening in the detection of beta thalassemia carriers, the use of the most common 22 alleles can only detect 61.5% of carriers; hence, the value of tested gene study is still limited in the detection of carrier rates.

Association between vitamin D metabolism gene polymorphisms and schizophrenia.

Schizophrenia (SZ) is a multifactorial and neurodegenerative disorder that results from the interaction between genetic and environmental factors. Notably, hundreds of single nucleotide polymorphisms (SNPs) are associated with the susceptibility to SZ. Vitamin D (VD) plays an essential role in regulating several genes important for maintaining brain function and health. To the best of the authors' knowledge, no studies have yet been conducted on the association between the VD pathway and patients with SZ. Therefore, the present study aimed to assess the potential association between eight SNPs in genes related to the VD pathway, including CYP2R1, CYP27B1, CYP24A1 and VDR among patients with SZ. A case-control study was conducted, involving a total of 400 blood samples drawn from 200 patients and 200 healthy controls. Genomic DNA was extracted and variants were genotyped using the tetra-amplification refractory mutation system-polymerase chain reaction method. The present study revealed statistically significant differences between patients with SZ and controls regarding the genotypes and allele distributions of three SNPs [CYP2R1 (rs10741657), CYP27B1 (rs10877012) and CYP24A1 (rs6013897) (P<0.0001)]. The AA genotype of rs10741657 was identified to be associated with SZ (P<0.0001) and the frequency of the A allele was higher in patients with SZ (P<0.0001) compared with the control group. Similarly, the TT genotype of rs10877012 was revealed to be associated with SZ (P<0.0001) and the T allele was more frequent in patients with SZ (P<0.0001) than in the control group. Moreover, the AA genotype of rs6013897 was revealed to be associated with SZ (P<0.0001), although no significant difference was detected between the two groups regarding the A allele (P=0.055). VDR (rs2228570, rs1544410, rs731236 and rs7975232) and CYP27B1 (rs4646536) gene polymorphisms did not exhibit a significant association with SZ. While the studied SNPs revealed promising discriminatory capacity between patients with SZ and controls, the rs10741657 SNP exhibited the most optimal area under the curve value at 0.615. A logistic model was applied considering only the significant SNPs and VD levels, which revealed that rs6013897 (T/A) and VD may have protective effects (0.267, P<0.001; 0.888, P<0.001, respectively). Moreover, a low serum VD level was highly prevalent in patients with SZ compared with the controls. Based on this finding, an association between serum 25(OH)D and SZ could be demonstrated. The present study revealed that CYP2R1 (rs10741657), CYP27B1 (rs10877012) and CYP24A1 (rs6013897) gene SNPs may be associated with SZ susceptibility.

Mannose-Binding Lectin Gene Variants as Disease Susceptibility Biomarkers in Rheumatoid Arthritis.

Background: Rheumatoid arthritis (RA) is a chronic, inflammatory autoimmune disease characterized by progressive destruction of peripheral joints. About 1% of the human population worldwide is suffering from this disease. The pathophysiology of RA is largely being influenced by immune dysregulation. Mannose-binding lectin (MBL), an acute-phase protein, has been reported to play an important role in pathogenesis of RA by the activation of complement pathway. Various studies documented the established the role of MBL in pathogenesis of various autoimmune diseases, including RA. MBL protein is encoded by gene MBL2, mapped on chromosome 10q11.2-q21. Objective: Both MBL serum levels and activity are mainly determined genetically by its variants. So considering the putative clinical role of MBL2, this case-control association study was designed to assess its six functional variants in a northwestern Indian cohort. Methods: Genetic typing of six MBL2 variants was done by amplification refractory mutation system-polymerase chain reaction. Data were analyzed using suitable statistical tools. Results: Significant difference has been observed in genotypic and allelic distribution between cases and controls for rs11003125. Comparison of allelic distribution for rs1800450 showed significantly high prevalence of A allele in cases than controls. Conclusion: These results indicate that MBL2 variants may act as plausible marker for susceptibility toward RA. Keeping this in view, it is pertinent to screen these variants in other population groups of India.

Genetic evidence for predisposition to acute leukemias due to a missense mutation (p.Ser518Arg) in ZAP70 kinase: a case-control study

BackgroundThe apparent lack of additional missense mutations data on mixed-phenotype leukemia is noteworthy. Single amino acid substitution by these non-synonymous single nucleotide variations can be related to many pathological conditions and may influence susceptibility to disease. This case-control study aimed to unravel whether the ZAP70 missense variant (rs104893674 (C > A)) underpinning mixed-phenotype leukemia.MethodsThe rs104893674 was genotyped in clients who were mixed-phenotype acute leukemia-, acute lymphoblastic leukemia- and acute myeloid leukemia-positive and matched healthy controls, which have been referred to all major urban hospitals from multiple provinces of country- wide, IRAN, from February 11’ 2019 to June 10’ 2023, by amplification refractory mutation system-polymerase chain reaction method. Direct sequencing for rs104893674 of the ZAP70 gene was performed in a 3130 Genetic Analyzer.ResultsWe found that the AC genotype of individuals with A allele at this polymorphic site (heterozygous variant-type) contribute to the genetic susceptibility to acute leukemia of both forms, acute myeloid leukemia and acute lymphoblastic leukemia as well as with a mixed phenotype. In other words, the ZAP70 missense variant (rs104893674 (C > A)) increases susceptibility of distinct cell populations of different (myeloid and lymphoid) lineages to exhibiting cancer phenotype. The results were all consistent with genotype data obtained using a direct DNA sequencing technique.ConclusionOf special interest are pathogenic missense mutations, since they generate variants that cause specific molecular phenotypes through protein destabilization. Overall, we discovered that the rs104893674 (C > A) variant chance in causing mixed-phenotype leukemia is relatively high.

The Association of Vitamin D Receptor Gene Polymorphism with Polycystic Ovary Syndrome in a Southeast Iranian Population

Background: Polycystic ovary syndrome (PCOS) is a common endocrine disorder among women of reproductive age, characterized by hyperandrogenism, amenorrhea, and polycystic ovaries. Metabolic disorders, including insulin resistance (IR), are common comorbidities of PCOS, with vitamin D receptors playing a crucial role. Objectives: We investigated whether the rs2228570T &gt; C variant of the vitamin D receptor (VDR) gene is associated with the risk of PCOS. Methods: In the current study, 112 women with PCOS and 150 healthy women participated. Genomic DNA was extracted using the standard salting-out method. Genotyping of rs2228570T &gt; C was conducted via amplification-refractory mutation system polymerase chain reaction. Additionally, VD3 levels were measured using the ELISA system. Statistical analysis of genotyping data was performed using the SPSS V.22 package. Results: The statistical analysis showed that the T-allele of rs2228570C/T significantly decreased the risk of PCOS. Moreover, the T-allele in the codominant model significantly eliminated the risk of PCOS in our population. Our results also showed a statistically significant difference in VD3 levels between the CC and TT genotypes. Conclusions: Based on our result, rs228570C/T had a protective role for PCOS risk in our population.

Association of VEGFA polymorphisms with the risk of oesophageal cancer in Punjab, India: A case-control study.

Background & objectives Vascular endothelial growth factor (VEGF) is one of the most important angiogenic factors which stimulates tumour progression induction of endothelial cell migration and division, inhibition of the apoptosis of endothelial cells, induction of serine protease activity and enhancement of vascular permeability. This study aimed to investigate the correlation of VEGF+405G/C,-7C/T and+936C/T polymorphisms with oesophageal cancer risk. Methods DNA samples of 464 subjects (231 sporadic oesophageal cancer affected individuals and 233 controls) were genotyped forVEGF+936C/T,+405G/C and-7C/T polymorphisms. VEGF+936C/T and +405G/C polymorphisms were genotyped by PCR-RFLP method whereas VEGF-7C/T polymorphism was genotyped using Amplification refractory mutation system-polymerase chain reaction (ARMS-PCR). Results CT genotype of VEGF-7C/T polymorphism was significantly associated with reduced risk of oesophageal cancer. VEGF-7C/T polymorphism was significantly associated with reduced risk of oesophageal cancer underdominant, co-dominant, over dominant and log-additive genetic models in total patients and in the female group. C+936G+405T-7 haplotype was significantly associated with decreased risk (P=0.01)of oesophageal cancer in total patients and also in the male group (P=0.02). Interpretation & conclusions In future, replication of the findings of the present study in a larger sample from different ethnic groups, along with functional analysis, may be insightful for the role of VEGFA polymorphisms in the pathogenesis of oesophageal cancer. Identification of the correlation of VEGF variants with specific therapy in oesophageal cancer may help in better selection of patients and monitoring treatment response in VEGF-therapy.

Association between Methylenetetrahydrofolate Reductase (MTHFR) and 5-Methyltetrahydrofolate-Homocysteine Methyltransferase Reductase (MTRR) Polymorphisms in Iraqi Patients with COVID-19.

The methylenetetrahydrofolate reductase (MTHFR) gene is an essential gene in the metabolism of folate-homocysteine. Recently, the level of homocysteine was found to be a significant marker in the follow-up of COVID-19 infection. Thus, this study aimed to detect the effect of genetic polymorphisms for single nucleotide polymorphisms (SNPs) (c.66A>G, c.1298A>C, and c.677CT) on COVID-19 infection. Blood samples were collected from 270 patients with COVID-19 in the medical center of Al-Shifa (Baghdad, Iraq) from November 2020 to March 2021. Tetra-primer amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) technique was used for the detection of genotypes of SNPs. The odds ratio (OR) was used to detect the relationship between SNPs and COVID-19 infections. Haplotype analysis was performed by SHEsis software. There was a significant difference between mild/moderate cases and severe/critical cases for ages (35-45), (46-55), and (56-65) years (P<0.0001, P=0.01, and P=0.006, respectively). The results showed significant differences in the T allele for SNP c.677>C (P<0.0001 and OR=4.58). The C allele for SNP c.1298A>C indicated significant differences (P<0.001 and OR=3.15). Besides, the G allele for SNP c.677C>T showed significant differences (P<0.001 and OR=6.64). Consequently, these SNPs showed a predisposition to the development of COVID-19 infection. With regard to the C-A-A, T-A-A and T-C-G haplotypes indicated significant differences between the control and patient groups. The C-A-A was related to a decreased risk and indicated a protective effect against COVID-19 infection development (P<0.0001 and OR=0.218). The increased risk was associated with T-A-A and T-C-G haplotypes and indicated the risk impact on COVID-19 infection development (P<0.0001, P=0.004, and OR=15.5, OR=6.772, respectively). Furthermore, the linkage disequilibrium (LD) for SNPs was studied, and the complete D' value was 99. The genetic polymorphisms of SNPs (c.66A>G, c.1298A>C, and c.677C>T) in the Iraqi population were associated with COVID-19 infection.

Association of LPP and ZMIZ1 Gene Polymorphism with Celiac Disease in Subjects from Punjab, Pakistan.

Celiac disease (CD) is a complicated autoimmune disease that is caused by gluten sensitivity. It was commonly believed that CD only affected white Europeans, but recent findings show that it is also prevailing in some other racial groups, like South Asians, Caucasians, Africans, and Arabs. Genetics plays a profound role in increasing the risk of developing CD. Genetic Variations in non-HLA genes such as LPP, ZMIZ1, CCR3, and many more influence the risk of CD in various populations. This study aimed to explore the association between LPP rs1464510 and ZMIZ1 rs1250552 and CD in the Punjabi Pakistani population. For this, a total of 70 human subjects were selected and divided into healthy controls and patients. Genotyping was performed using an in-house-developed tetra-amplification refractory mutation system polymerase chain reaction. Statistical analysis revealed a significant association between LPP rs1464510 (χ2 = 4.421, p = 0.035) and ZMIZ1 rs1250552 (χ2 = 3.867, p = 0.049) and CD. Multinomial regression analysis showed that LPP rs1464510 A allele reduces the risk of CD by ~52% (OR 0.48, CI: 0.24-0.96, 0.037), while C allele-carrying subjects are at ~2.6 fold increased risk of CD (OR 3.65, CI: 1.25-10.63, 0.017). Similarly, the ZMIZ1 rs1250552 AG genotype significantly reduces the risk of CD by 73% (OR 0.26, CI: 0.077-0.867, p = 0.028). In summary, Genetic Variations in the LPP and ZMIZ1 genes influence the risk of CD in Punjabi Pakistani subjects. LPP rs1464510 A allele and ZMIZ1 AG genotype play a protective role and reduce the risk of CD.