Polymerase Chain Reaction-restriction Fragment Length Polymorphism Research Articles

Interaction of genetics risk score and fatty acids quality indices on healthy and unhealthy obesity phenotype

BackgroundThe growth in obesity and rates of abdominal obesity in developing countries is due to the dietary transition, meaning a shift from traditional, fiber-rich diets to Westernized diets high in processed foods, sugars, and unhealthy fats. Environmental changes, such as improving the quality of dietary fat consumed, may be useful in preventing or mitigating the obesity or unhealthy obesity phenotype in individuals with a genetic predisposition, although this has not yet been confirmed. Therefore, in this study, we investigated how dietary fat quality indices with metabolically healthy obesity (MHO) or metabolically unhealthy obesity (MUO) based on the Karelis criterion interact with genetic susceptibility in Iranian female adults.MethodsIn the current cross-sectional study, 279 women with overweight or obesity participated. Dietary intake was assessed using a 147-item food frequency questionnaire and dietary fat quality was assessed using the cholesterol-saturated fat index (CSI) and the ratio of omega-6/omega-3 (N6/N3) essential fatty acids. Three single nucleotide polymorphisms-MC4R (rs17782313), CAV-1 (rs3807992), and Cry-1(rs2287161) were genotyped by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique and were combined to produce the genetic risk score (GRS). Body composition was evaluated using a multi-frequency bioelectrical impedance analyzer. Participants were divided into MHO or MUO phenotypes after the metabolic risk assessment based on the Karelis criteria.ResultsWe found significant interactions between GRS and N6/N3 in the adjusted model controlling for confounding factors (age, body mass index, energy, and physical activity) (β = 2.26, 95% CI: 0.008 to 4.52, P = 0.049). In addition, we discovered marginally significant interactions between GRS and N6/N3 in crude (β = 1.92, 95% CI: -0.06 to 3.91, P = 0.058) and adjusted (age and energy) (β = 2.00, 95% CI: -0.05 to 4.05, P = 0.057) models on the MUH obesity phenotype. However, no significant interactions between GRS and CSI were shown in both crude and adjusted models.ConclusionThis study highlights the importance of personalized nutrition and recommends further study of widely varying fat intake based on the findings on gene-N6/N3 PUFA interactions.

Genetic Variations in MDM2 Gene Contribute to Renal Cell Carcinoma Susceptibility: A Genotype-Phenotype Correlation Study.

This study aimed to investigate the polymorphic genotypes of MDM2 rs937282, rs937283, rs2279744, and rs769412, as well as the combined effects of MDM2 genotypes and environmental factors on RCC susceptibility. A total of 135 RCC patients and 590 controls were recruited for MDM2 genotyping using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Quantitative PCR was performed to assess MDM2 mRNA levels among 30 healthy individuals and 22 RCC patients. MDM2 rs2279744, but not other polymorphisms, was significantly associated with an increased RCC risk (p = 0.0133). The MDM2 rs2279744 G allele was identified as a risk factor for RCC (odds ratio [OR] = 1.49, 95% confidence interval [CI] = 1.14-1.96, p = 0.0047). Among smokers (p = 0.0070), alcohol drinkers (p = 0.0233), individuals with hypertension (p = 0.0041), diabetes (p = 0.0225), and those with a family history of cancer (p = 0.0020), the MDM2 rs2279744 GT and GG genotypes exhibited increased RCC risks. However, this risk effect was not observed in non-smokers, non-drinkers, or individuals without hypertension, diabetes, or a family cancer history (all p > 0.05). Moreover, MDM2 mRNA levels were significantly higher in RCC patients compared to controls and varied among the rs2279744 genotypes, with GG genotype exhibiting the highest expression levels among both RCC patients and controls. This study highlights the association between MDM2 rs2279744 genotypes and RCC risk, suggesting that genotype-associated MDM2 mRNA levels could contribute to early RCC detection. Further studies are warranted to elucidate the detailed mechanisms underlying the role of MDM2 in RCC development.

Investigation of GSTP1 and PTEN gene polymorphisms and their association with susceptibility to colorectal cancer

Abstract Background This study investigates the association of single nucleotide polymorphism in glutathione S transferase P1 (rs1695 and rs1138272) and phosphatase and TENsin homolog (rs701848 and rs2735343) with the risk of colorectal cancer (CRC). Patients and methods In this case-control study, 250 healthy controls and 200 CRC patients were enrolled. All subjects were divided into 3 groups: healthy control, patients, and overall (control + patients). Genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The demographic information, including age, gender, location, smoking status, cancer stage, and node involvement, were collected. Results The allele frequencies of PTEN rs701848 in overall subjects were 0.78 for C and 0.22 for T. Similarly, in overall individuals, allele frequencies for PTEN rs2735343 were 0.65 and 0.35 for G and C alleles, respectively. The CC genotype or C allele of rs701848 and CG/GG genotype of rs2735343 were observed to be a risk factor for CRC. In overall individuals, a significant (p ≤ 0.05)) association was observed between rs701848 and rs2735343 polymorphisms CRC. Allele frequencies for GSTP1 rs1695 were 0.68 and 0.32 for the A and G alleles, respectively. Allele frequencies for GSTP1 rs1138272 were 0.68 and 0.32 for C and T alleles, respectively. However, a significant (p < 0.05) association was found in males for rs1695, while a non-significant difference was observed for the distribution of any genotypes or alleles at GSTP1 (rs1138272). Conclusions Both SNPs of PTEN rs701848 and rs2735343 polymorphisms were significantly associated with CRC. However, in GSTP1, rs1695 was significantly associated with CRC risk in males, and rs1138272 showed a non-significant association with colorectal cancer risk.

Association of Toll-like Receptor 4 Gene Polymorphisms with Diabetes Type 2 Patients in the Palestinian Population.

Toll-like Receptor 4 (TLR4) plays critical roles in innate immunity and several other pathological responses, including a possible role in the susceptibility to Type 2 Diabetes Mellitus (T2DM). Understanding the relationship between TLR4 polymorphism and T2DM is necessary to evaluate the role of innate immunity in diabetes. This study was conducted to evaluate the potential association between three TLR4 SNPs (SNP ID rs11536858, rs4986790, and rs1927914) and risk susceptibility to T2DM in a crosssection of the Palestinian population. A total of 96 individuals including 50 T2DM patients participated in this study. The data were analyzed according to the TLR4 allelic variation results. DNAs were extracted from blood samples collected from the T2DM patients and their matched healthy controls and used to evaluate possible associations between the TLR4 SNP variations and T2DM. The genotypes of TLR4 polymorphisms were analyzed by the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP). Three allelic variations were detected in the participating individuals. The distribution of alleles between T2DM and healthy controls in the three SNPs did not show significant differences, even though some variations tended to favor certain alleles. To look at potential associations of TLR4 gene polymorphisms with the risk of T2DM development, we analyzed the allelic variation in both T2DM patients and health controls. The rs4986790 TLR4 SNPs showed a significant association with T2DM. There were 20% heterozygous alleles in T2DM patients compared to 4.35% in healthy controls with Odds Ratio (OR) = 5.26 and 95% CI = 1.08, 25.6 (P = 0.0252), indicating the AG allele to be a risk factor. Both rs11536858 and rs1927914 alleles demonstrated a potential association of their allelic variations as either a protective or a highrisk factor. Our data have indicated that TLR4 rs4986790, rs1927914, and rs11536858 may play a potential role in innate immunity and susceptibility risk to diabetes and can be potential targets for therapeutic drugs.

Development of Breed Traceability for Autochthonous Attappady Black Goats of South India

Attappady Black goats, a meat-type breed raised by the tribal communities of the Attappady hill ranges in Kerala, India, play a pivotal role in the region’s economy, heavily contributing to the livelihoods of its socially disadvantaged population. This study aimed to develop and validate a set of breed-specific genetic markers to enable the precise differentiation of Attappady Black goats from Malabari goats. Breed genetic traceability for Attappady Black goats was developed by adopting deterministic approach using breed specific markers. High throughput genome-wide SNP genotypic data of reference goat population (24 each from Attappady Black and Malabari) obtained by Illumina Goat SNP50 BeadChip genotyping was used to identify candidate breed specific markers. Among the 605 numbers of putative Attappady breed specific markers identified in the reference population, nine putative Attappady breed specific markers were selected and were validated for breed specificity by converting them into Polymerase Chain Reaction -restriction fragment length polymorphism (PCR-RFLP) markers and genotyped in large sample goat population of 447 goats (246 Attappady Black and 201 Malabari). On validation, four markers retained their breed specificity with probability of identification (Pi) ranging from 0.24 to 0.66. Panel of four Attappady Black breed specific markers yielded Pi of 0.92 with a probability of misjudgement (Pm) of 0.04. These breed-specific markers hold significant potential for facilitating breed traceability thus ensuring their conservation and enhancing the socioeconomic status of the tribal communities that rely on them. Future research should focus on the broader application of these markers in routine breed authentication and in marketing niche livestock products.

Analysis of FOXE1 rs3758249, IRF6 rs2235375, MTRR A66G in Non-syndromic Cleft Lip and Palate among Indonesian Deutero-Malay Population

Non-syndromic cleft lip and palate (NS-CLP) is one of the most common orofacial malformations, with an incidence of 1 in 700 live births worldwide. This study aimed to determine the risk factor for NS-CLP among the Indonesian Deutero-Malay population by analyzing the FOXE1 rs3758249, IRF6 rs2235375, and MTRR A66G polymorphisms. It is a case-control study, using 50 samples of NS-CLP patients and 50 samples of control (for FOXE1 rs3758249 and MTRR A66G), 30 samples of NS-CLP patients, and 30 samples of control (for IRF6 rs2235375). After DNA was extracted, polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLPs) were performed by using restriction enzymes of Mscl (FOXE1 rs3758249) and Nde1 (MTRR A66G), and sequencing was performed for IRF6 rs2235375. The study was done in the Molecular Genetic Laboratory, Faculty of Dentistry Universitas Padjadjaran Bandung, from September 2023 to January 2024. The chi-square test was used with the exact Fisher's alternatives. The results showed that in FOXE1 3758249, A allele (mutant) was found more in control (OR=0.744, p>0.05), in MTRR A66G, G allele (mutant) was found more in NS-CLP (OR=1.267, p>0.05) meanwhile in IRF6 rs2235375, G allele (mutant) (OR=1.710, p>0.05) was found more in NS-CLP. This study concluded that FOXE1 rs 3758249, IRF6 rs2235375, and MTRR A66G genes were not the risk factor for NS-CLP in the Indonesian Deutero-Malay population.

The N‐Acetyltransferase 2 Polymorphism and Susceptibility to Inflammatory Bowel Disease: A Case–Control Study

ABSTRACTThe enzyme N‐acetyltransferase 2 (NAT2) plays an important role in metabolism and detoxification of xenobiotics, including carcinogens and medications. We aimed to assess the contribution of the NAT2 polymorphism to susceptibility to inflammatory bowel disease (IBD) in the Polish population. The study involved 101 IBD patients and 100 healthy controls. The NAT2 gene mutations at positions 481T, 803G, 590A, and 857A were identified using the polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) technique on peripheral blood DNA samples. Carriers of the NAT2*5 allele had a greater chance of developing Crohn's disease (CD) (OR = 1.73, 95% CI 1.06–2.83). Also, the NAT2*4/5 genotype was more prevalent in CD patients (OR = 2.77, 95% CI 1.17–6.57). When compared to the control group, the prevalence of the NAT2*4/6 genotype in the IBD patient population was significantly lower (10.9% vs. 30.0%, p < 0.01). In the Polish population, polymorphism in the NAT2 gene may potentially alter susceptibility to IBD.

Influence of CYP2C8*3 and ABCG2 C421A genetic polymorphisms on trough concentration and molecular response of imatinib in Egyptian patients with chronic myeloid leukemia.

The treatment landscape for chronic myeloid leukemia (CML) has been revolutionized by the introduction of imatinib, a tyrosine kinase inhibitor, which has transformed the disease from a fatal condition into a manageable chronic illness for a substantial number of patients. Despite this, some individuals do not respond adequately to the treatment, and others may experience disease progression even with continued therapy. This study examined how CYP2C8*3 (G416A; rs11572080) and ABCG2 C421A (rs2231142) single nucleotide polymorphisms (SNPs) affect the plasma trough concentration and therapeutic response of imatinib in Egyptian CML patients. The study included fifty patients with chronic-phase CML, who were categorized into two groups: responders (n = 26) and non-responders (n = 24), according to their BCR-ABL1 transcription levels after 12 months of imatinib treatment. Genotyping of the CYP2C8*3 and ABCG2 C421A polymorphisms was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), while plasma trough concentrations were determined through high-performance liquid chromatography with ultraviolet-diode array detection (HPLC-UV/DAD). Patients with the CA genotype of ABCG2 C421A showed significantly higher mean plasma trough concentrations of imatinib (CA: 1731 ± 424.7 ng/mL; CC: 1294 ± 381.3 ng/mL; p = 0.0132) and demonstrated a better molecular response compared to those with the CC genotype (p = 0.0395). The ABCG2 C421A polymorphism significantly influenced imatinib plasma trough concentrations and molecular responses in Egyptian chronic-phase CML patients. Genotyping of this polymorphism in these patients could assist in optimizing imatinib therapy, predicting more favorable treatment outcomes, and enabling the development of more personalized treatment plans.

Genetic Polymorphism of Il-16 and Risks of Coronary Artery Disease in Sudan

The inflammatory process in the atherosclerotic artery may lead to increased blood levels of inflammatory cytokines. The aim of this study is to understand the role of inflammatory markers in the development of coronary artery disease. Therefore, a case-control study was conducted amongst coronary artery disease patients who attended the Sudan Heart Institute and healthy controls. Questionnaires were designed to determine the lifestyle and environmental factors for 200 participants (100 cases, 100 controls). Blood samples were collected to measure lipids profiles using enzymatic colorimetric and DNA extraction using the G-spin Kits. Polymerase chain reaction- restriction fragment length polymorphism (PCR-RFLP) was used for IL-6 and IL-16 genotyping. A total of 64% patients were males, 41% were at 51-61 years, and physical activity was common in 60% of the patients. The risk factors for coronary artery disease were hypertension 62%, angina 62%, cigarette smoking 38%, diabetes 33%, tobacco user 31%, drinking alcohol 24% and stroke 2%. Most patients had a family history of stroke 93%, hypertension 36%, diabetes 34%, angina 9%, and heart attack 4%. Total cholesterol and low-density lipoprotein were significantly different (P>0.05) between cases and controls, and they were significantly associated with IL- 16 genotype. All risk factors for coronary artery diseases were strongly associated with IL-6 genotype (P-value < 0.05, OR >1). Whereas, IL-16 homozygous TT genotype was significantly associated with gender and physical activity. Lifestyle, family history, and IL-16 (TT) genotype are risk factors for coronary artery disease in Sudanese patients.

Impact of rs2046045 SNP in PDE8B on TSH Levels: Insights into Genetic Susceptibility to Hypothyroidism.

Hypothyroidism is the most prevalent thyroid disorder and leads to adverse effects on the human body. Serum thyroid stimulating hormone (TSH) values have been related to polymorphisms in multiple genes that may be involved in the regulation of thyroid function. The single nucleotide polymorphism (SNP) rs2046045 is situated in the intron region of the phosphodiesterase 8B (PDE8B) gene, which encodes a high-affinity cyclic adenosine monophosphate (cAMP)-specific phosphodiesterase widely expressed in thyroid tissue. The principal goal of the present study was to investigate the association between the SNP rs2046045 of the PDE8B gene and hypothyroidism. The study was designed as a case-control study, and a total of 160 hypothyroid and 160 healthy controls were involved. Blood samples were drawn from each individual, and deoxyribonuleic acid (DNA) was separated with a suitable DNA isolation kit. For genotyping, the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was employed. The IBM Statistical Package for Social Sciences (SPSS) 25.0 was utilized to analyze the statistical data. Age differences between the patients and controls were not observed in the present study. The genotype frequency of homozygous wild type (TT), homozygous mutate type (GG), and heterozygous (GT) was 45%, 2.5%, and 52.5%, respectively, in control subjects and 27.5%, 11.25%, and 61.25%, respectively, in cases, and showed a significant difference (p = 0.0002). The minor G allele frequency is elevated in hypothyroid patients as compared to healthy control subjects (41.87% vs. 28.75%), p = 0.0005. The presence of the mutant allele G of rs2046045 in the PDE8B gene correlates with elevated serum TSH levels in hypothyroid patients.

Association between TAB2 genetic polymorphisms and the susceptibility to cervical cancer: a case-control study

BackgroundCervical cancer (CC) ranks as the fourth most common cancer and the fourth leading cause of cancer-related deaths among women globally, with declining incidence and mortality rates in recent decades. Previous studies have suggested that the transforming growth factor-beta (TGF-β) activated kinase 1 (TAK1) binding protein 2 (TAB2) can influence the stemness characteristics of squamous CC cells. However, the specific genetic impact of the TAB2 gene on CC remains unclear. This study aimed to evaluate the relationship between TAB2 genetic polymorphisms and susceptibility to CC using a hospital-based retrospective analysis.MethodsA total of 306 CC patients and 309 healthy controls were included in this study. Genetic analysis involved genotyping of subjects using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Statistical analyses were conducted using SNPstats online analysis software and SPSS software.ResultsThe frequency of the G allele of rs521845 polymorphism was significantly higher in CC patients (P = 0.048, OR = 1.26, 95%CI = 1.00-1.59), with GG homozygotes showing an increased susceptibility to CC compared to CC/CG genotype carriers (P = 0.045, OR = 1.57, 95%CI = 1.01–2.45). Additionally, all three tag single nucleotide polymorphisms (SNPs) were associated with lymph node involvement in patients (P = 0.0006, OR = 0.01, 95%CI = 0.00-0.31 for rs237028 GG genotype; P = 0.009, OR = 0.17, 95%CI = 0.04–0.68 for rs521845 GG genotype; and P = 0.004, OR = 0.14, 95%CI = 0.03–0.59 for rs652921 CC genotype, respectively).ConclusionThis study highlighted that TAB2 rs521845 polymorphism was significantly associated with susceptibility to CC, suggesting that the TAB2 gene may play a crucial role in the progression of CC.

Analysis of SMOC2 gene variants in familial and non-familial primary open angle glaucoma Pakistani patients.

To find out the association of secreted protein acidic and rich in cysteine (SPARC)-related modular calcium binding 2 (SMOC2) gene variants rs2255680 and rs13208776 with genotypic and phenotypic characteristics in both familial and non-familial primary open angle glaucoma (POAG) patients. A total of 212 POAG patients, comprising 124 familial and 88 non-familial, were enrolled. For genotyping the SMOC2 variant rs2255680, amplification refractory mutation system (ARMS)-polymerase chain reaction (PCR) method and PCR-restriction fragment length polymorphism (PCR-RFLP) were utilized for analyzing rs13208776 variant. The mean age of familial POAG patients was 50.92±9.12y, with 78 males and 46 females. The mean age of non-familial POAG patients was 53.14±13.44y, with 52 males and 36 females. The SMOC2 gene variant rs13208776 showed the significant association with POAG between familial and non-familial groups. The homozygous G/G variant was frequent among non-familial (60.2%) whereas the heterozygous G/A variant was more frequent in familial POAG patients (46%). There were significant differences in G/A variant between familial and non-familial glaucoma patients, and the risk was decreased to 0.53-fold in non-familial glaucoma patients [odds ratio (OR): 0.53; 95% confidence interval (CI): 0.29-0.94; P=0.033] in codominant model. The risk was further reduced to 0.49-fold (95%CI: 0.28-0.86; P=0.012) in dominant model for non-familial patients. No significant association of SMOC2 gene variant rs2255680 between familial and non-familial glaucoma patients was found in our population. The haplotype analysis showed the decreased risk for TA [OR: 0.48 (95%CI: 0.29-0.79); P=0.004] and an increased risk for TG [OR=2.28 (95%CI: 1.22-4.25); P=0.01] haplotypes. Current findings show significant association of SMOC2 gene variant rs13208776 with POAG between familial and non-familial Pakistani patients.

Incidence of PAX6 single nucleotide polymorphisms in congenital iridofundal coloboma and other congenital ocular abnormalities: a tertiary care hospital experience from central India

Purpose of this study is to identify selected single nucleotide polymorphisms (SNP) of the PAX6 gene and to assess their correlation with congenital iridofundal colobomas and other congenital ocular anomalies.Material and methods. It was a case-control study done on 45 patients aged from 75 days to 58 years (mean age 29.36 ± 14.4 years) with irido-fundal coloboma and 45 healthy controls aged 35.23 ± 13.92 years. Ocular examination was done by using slit-lamp microscopy inspection, fundoscopy and intraocular pressure measurement. Genotyping was done by using the polymerase chain reaction — restriction fragment length polymorphism (PCR-RFLP) method.Results. Two irido — fundal coloboma patients showed CT (+/-) heterozygous genotype of rs667773 SNP and the rest were wild-type CC (-/-) homozygous genotype. All controls showed CC-/- wild-type homozygous genotype. PAX6 SNP rs3026354 showed CC (-/-) wild-type homozygous genotype condition in all patients. Neither CG (+/-) heterozygous nor homozygous GG (+/+) genotype was reported in patients and controls. SNP rs662702, genotype pattern was CC-/- wild type homozygous in all patients and controls. CC genotype frequency was 95.56 and CT genotype was 4.4% while C allele frequency was 97.78 and T allele frequency was 2.22 % in rs667773 C>T SNP. rs3026354C>G SNP had 100 % CC genotype and C allele frequency in both case and control populations. SNP rs 662702C>T showed 100 % CC genotype and C allele frequency in the case and control respectively.Conclusion. The elevated frequency of the CC genotype with C allele was more common in irido fundal patients. Two heterozygous CT genotype of rs667773C>T SNP were reported in two irido-fundal coloboma patients.

Analysis of association of SP-C gene polymorphisms with Neonatal respiratory distress syndrome

To analyze the association between pulmonary surfactant protein C (SP-C) gene polymorphisms and the risk of Neonatal respiratory distress syndrome (NRDS). Clinical data from 168 neonates diagnosed with NRDS (NRDS group) admitted between August 2020 and June 2023 were collected. Additionally, 168 neonates without respiratory distress, born during the same period, were included as the control group. Peripheral venous blood samples (2 mL each) were collected from both groups. PCR-restriction fragment length polymorphism technique was employed to detect the polymorphisms at the SP-C gene loci p.Thr138Asn (rs4715) and p.Ser186Asn (rs1124). Hardy-Weinberg equilibrium tests were conducted for genotyping, and genotypic and allelic frequencies were compared. The association between SP-C gene polymorphisms and NRDS risk was evaluated. Furthermore, genotypic and allelic frequencies at the rs4715 and rs1124 loci were compared among NRDS cases with varying degrees of disease severity. The study was approved by the Medical Ethics Committee of Shangqiu First People's Hospital (Ethics No. 2020-031). The frequency of the variant allele (A) at the rs4715 locus was significantly higher in the NRDS group compared to the control group (32.14% vs. 24.11%, P = 0.001). The frequency of the variant genotype (AA + AC) was also higher in the NRDS group (47.02% vs. 39.29%, P = 0.043). The frequency of the variant allele (A) at the rs1124 locus was higher in the NRDS group compared to the control group (34.23% vs. 23.51%, P = 0.027), with a higher frequency of the variant genotype (AA + AG) in the NRDS group (49.40% vs. 39.29%, P = 0.019). No significant correlation was observed between the rs4715 polymorphism and the severity of NRDS (P > 0.05). Among NRDS children with grade III severity, the frequency of the variant allele (A) at the rs1124 locus was higher than in grade I and grade II children (47.62% vs. 29.22%, P = 0.020). The frequency of the variant genotype (AA + AG) was also higher in grade III children (64.28% vs. 43.84%, P = 0.040). SP-C gene polymorphisms are associated with the susceptibility to NRDS. Neonates carrying the AA genotype and the A allele at the rs1124 locus are at a higher risk of severe NRDS. These findings have provided further evidence for early screening, diagnosis, and treatment of NRDS.

MTHFR Gene Polymorphisms and DNA Methylation in Idiopathic Spontaneous Preterm Birth

Background and Objectives: Preterm birth (PTB) is a complex condition with various contributing factors, including genetic and epigenetic influences such as DNA methylation. Methylenetetrahydrofolate reductase (MTHFR) plays a critical role in DNA methylation and the remethylation of homocysteine. This study aimed to investigate the association between maternal MTHFR C677T and A1298C polymorphisms, LINE-1 DNA methylation levels, and the risk of idiopathic spontaneous preterm birth (SPTB) in Caucasian women from Croatia and Slovenia. Materials and Methods: A total of 50 women with SPTB (<34 weeks of gestation) and 50 control women were included in the study. MTHFR polymorphisms were analyzed using polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP), and LINE-1 DNA methylation levels were quantified using the MethyLight method. Results: The study found no significant differences in MTHFR C677T and A1298C polymorphisms’ genotype or allele frequencies between women with SPTB and controls. Additionally, no statistical significance of LINE-1 DNA methylation was found between the genotypes of the MTHFR polymorphisms analyzed. Conclusions: The study suggests no conclusive association between MTHFR C677T and A1298C polymorphisms, LINE-1 DNA methylation, and SPTB in Croatian and Slovenian women. Considering prior evidence connecting MTHFR polymorphisms, hyperhomocysteinemia, and PTB, the lack of homocysteine measurements and unassessed impact of folate or vitamin B supplementation limit the conclusions.

Correlation between rs7041 and rs4588 polymorphisms in vitamin D binding protein gene and COVID-19-related severity and mortality

BackgroundThe vitamin D binding protein (DBP) plays a critical role in both innate and adaptive immune systems, participating in several clinical conditions, including coronavirus disease 2019 infection severity, and mortality rate. The study aimed to investigate the correlation between rs7041 and rs4588 polymorphisms in the DBP gene and Coronavirus Disease-2019 (COVID-19) severity and mortality, in patients of Suez Canal University Hospitals in Ismailia, Egypt.MethodsA case-control study enrolled 220 individuals; 140 COVID-19 patients and 80 healthy controls. Serum 25(OH) vitamin D levels were determined by the enzyme-linked immunosorbent assay (ELISA), and rs7041 and rs4588 polymorphisms of the DBP gene were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP).ResultsThe study found that both groups had vitamin D deficiency, which was considerably lower in the COVID-19 patients group compared to controls. Among COVID-19 patients, there was a significant difference in vitamin D levels according to the disease severity indicating that vitamin D levels can be used as predictors of COVID-19 severity. Negative significant correlations between genetic variants rs4588 CA genotype and genetic variants rs7041 TT genotype and COVID-19 prevalence (p = 0.006 and 0.009 respectively) were proved. No significant correlations between all the genetic variants of both rs4588 and rs7041 and COVID-19 severity (p > 0.05). Positive significant correlations between both genetic variants rs4588 CA genotype and genetic variants rs7041 TG genotype and COVID-19 mortality (p = 0.029 and 0.031 respectively).Conclusionvitamin D deficiency increased the severity of COVID-19. The DBP polymorphism correlated with vitamin COVID-19 prevalence and mortality.

Direct assessment of hereditary hemochromatosis in preimplantation genetic testing.

Hereditary hemochromatosis (HH) is a common genetic disorder characterized by iron overload, which, if undiagnosed, can lead to severe organ damage. There are 4 types of HH. Type 1 HH, the most common form, is primarily caused by a common variant in Western Europe (p.Cys282Tyr, C282Y, or c.845 G>A). It is generally preventable during invitro fertilization if proper genetic testing is performed before implantation. Here, we demonstrated a direct detection and cost-effective approach using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in preimplantation genetic testing (PGT) settings. We began by validating the assay with genomic deoxyribonucleic acid (DNA) from Coriell cell lines of known HFE C282Y genotypes, followed by testing patients' genomic DNA samples. After establishing the assay on genomic DNA, we extended the assay to whole-genome amplified DNA from embryo biopsies. The subjects include cell line samples and human specimens and human embryo biopsies. Patients and embryos either carried or did not carry the HFE C282Y variant in their genome. No intervention was applied. The readout included the genotype of samples at the HFE C282Y locus and accuracy of PCR-RFLP results. An accuracy of >99% was achieved across 80 cell line samples, 38 patient samples, and 81 embryo biopsies. In this study, we demonstrated the feasibility of using the PCR-RFLP approach to PGT. Specifically, we validated the assay for the HFE C282Y variant, the primary cause of type 1 hemochromatosis. The assay was tested on genomic DNA and DNA resulting from whole-genome amplification, achieving >99% accuracy, sensitivity, precision, and specificity. These results also suggest the possibility for extending the PCR-RFLP approach to cover a broader range of conditions, such as spinal muscular atrophy, to benefit more patients currently ineligible for testing at PGT laboratories.

The Association of Matrix Metalloproteinase-1, -2, -3, -7, and -13 Gene Polymorphisms With Peri-Implantitis in an Iranian Population: A Case-Control Study.

Peri-implantitis (PI) is the most common biological issue surrounding dental implants. According to current knowledge, the aforementioned complication is not equally distributed across different populations, and gene polymorphisms might be one contributing factor. The current study aimed to examine the association between gene polymorphisms of matrix metalloproteinase- (MMP-) 1, -2, -3, -7, and -13 with PI in an Iranian demographic. The study's sample included 50 subjects suffering from PI and 89 healthy controls. From each participant, a venous blood sample of 5 cc was obtained, and DNA was extracted. Gene polymorphisms were investigated using restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR) combined with electrophoresis. Statistical analyses were done using the Pearson chi-square test, odds ratio, and t-test via SPSS version 28. The MMP-3 (-1171 5A/6A) and MMP-7 (-181 A/G) gene polymorphisms were significantly different between the patients with PI and healthy controls (PV < 0.001 and =0.025, respectively). MMP-1 (-1607 1G/2G), MMP-2 (-1306 C/T), and MMP-13 (-77 A/G) gene polymorphisms did not, however, differ in terms of prevalence between the two groups (PV > 0.05). Moreover, the presence of the 6 A allele in the MMP-3 (-1171 5A/6A) genotype resulted in a significant decrease in PI risk (PV < 0.001). Gene polymorphisms in the genotypes of MMP-3 (-1171 5A/6A) and MMP-7 (-181 A/G) were differential when comparing PI patients and healthy controls of the studied population.

The Association Between the rs2200733 SNP and Atrial Fibrillation Among Arabs: A Study from Jordan.

Atrial fibrillation (AFib) is a common disorder featured by an irregular and fast heartbeat. The etiology of AFib is complex and involves genetic and environmental factors. The rs2200733 single nucleotide polymorphism (SNP) is located in close proximity to the promoter of paired-like homeodomain transcription factor 2 (PITX2) which plays a role in heart development. In this study, the association between the rs2200733 SNP and AFib was examined in the Jordanian population. The study included 450 subjects (274 controls and 176 patients with AFib). Patients were recruited from King Abdullah University Hospital based on the European Society of Cardiology criteria. The rs2200733 SNP was genotyped using restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) technique. The mutant T allele of the rs2200733 SNP was common in the studied population with a frequency of 19%. The T allele and CT/TT genotypes were prevalent among patients with AFib compared with the controls (P<0.05, OR [CI]: 1.65 [1.12-2.43]). In addition, body mass index, diabetes, and hypertension were found to be associated with AFib risk. The rs2200733 SNP was associated with AFib among Jordanian patients. The mutant T allele of the rs2200733 SNP might increase the risk of AFib.

Genetic variants of the XRCC3 DNA repair gene: risk implications in breast cancer among Iraqi patients.

Breast cancer is the predominant form of malignancy among women. Polymorphisms in DNA repair genes, such as X-ray repair cross complementing 3 (XRCC3), can influence an individual's capability to repair damaged DNA. This can result in genetic instability and potentially contribute to the development of cancer. This study investigates the correlation between the XRCC3 Thr241Met genetic variants and the risk of breast cancer. This study is considered the first study in Iraq that sheds light on studying the effect of the XRCC3 Thr241Met genotype variants and their relationship with increased risk of breast cancer. The blood of 75 Iraqi women who had been diagnosed with breast cancer was used in this study to extract DNA, in addition to using 50 blood samples from women who appeared to be healthy and without a family history of any other cancer, as a control group. Genotyping of the XRCC3 Thr241Met gene was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The single nucleotide polymorphism (SNP) genotypes were determined in all participants. The findings of this study demonstrated that the Met/Met allele occurred more frequently in patients than controls (OR = 3.3, 95% CI: 1.8-6.04; p = 0.0001), particularly in patients with positive lymph node metastases, grade II and III, and stages III/IV. These findings established the association of the Thr241Met genotype with breast cancer among Iraqi women; specifically, the homozygous (Met/Met) genotype appeared to be correlated with risk of breast cancer and cancer prognosis. This genotype was notably more prevalent among women diagnosed with high-grade tumours, as well as advanced stage and metastatic breast cancer.