Selected Single Nucleotide Polymorphisms Research Articles

Personal history of irradiation and risk of breast cancer: A Mendelian randomisation study.

Studies on the relationship between personal history of irradiation and breast cancer have been reported for a long time. Still, epidemiological studies have not been conclusive, and the causal relationship is unclear. To address this issue, we employed Mendelian randomisation (MR) analysis to examine the association between individual radiation exposure history and breast cancer. We used a series of quality control methods to select single nucleotide polymorphism (SNP) closely related to exposure. Meanwhile, several analysis methods were used to analyse the sample data to make the conclusion more reliable. To evaluate the horizontal pleiotropy, heterogeneity and stability of SNPs for breast cancer, the MR-Egger intercept test, Cochran's Q test and 'leave one' sensitivity analysis were used. Finally, the outlier variation determined by the Mendelian Randomisation Pleiotropy RESidual Sum and Outlier test is gradually eliminated to reduce the influence of heterogeneity and horizontal pleiotropy. After implementing rigorous quality control procedures, we carefully chose 102 qualified instrumental variables closely associated with the selected exposure for sensitivity analysis. This was conducted to evaluate the heterogeneity, level multiplicity, and stability of SNPs in the context of personal radiation history and its correlation with breast cancer. The results of the inverse variance weighted method analysis revealed a positive correlation between personal radiation and a heightened risk of breast cancer (odds ratio (OR) = 1.52; 95% confidence interval (CI) = 1.30-1.77). We also validated on another data set; the results were similar (OR = 1.51; 95% CI = 1.27-1.81). Furthermore, the findings from the sensitivity analysis were consistent. At the genetic level, our research demonstrated that personal radiation exposure is associated with an elevated risk of breast cancer. Using genetic data provides evidence and strengthens the causal link that personal radiation causes breast cancer.

Causal association between common rheumatic diseases and arrhythmia: a Mendelian randomization study.

Observational studies have suggested a link between rheumatic diseases and arrhythmias. However, these studies have been limited by confounding factors and reverse causality, leaving the causal relationship between rheumatic diseases and arrhythmias uncertain. This study addresses this inquiry using genetic evidence. Selected single nucleotide polymorphisms (SNPs) from genome-wide association study (GWAS) data were employed as instrumental variables. Inverse variance weighting (IVW), MR-Egger regression, and the weighted median method were utilized in the two-sample Mendelian randomization analysis. Horizontal pleiotropy was identified and rectified through the MR-PRESSO test and MR-Egger regression. The stability and reliability of the Mendelian randomization results were appraised using the remain-one method, Cochran Q-test, and funnel plot. Odds ratios (OR) were utilized to assess the causal relationship between six rheumatic diseases and five types of arrhythmias. The Inverse Variance Weighted (IVW) method indicated a significant association between rheumatoid arthritis (RA) and an elevated risk of right bundle branch block (RBBB) (OR: 1.10, 95% CI: 1.02-1.18, p = 0.009). Additionally, gout was significantly correlated with an augmented risk of RBBB (OR: 1.28, 95% CI: 1.09-1.51, p = 0.003). Conversely, dermatomyositis (DM) exhibited a negative association with the risk of atrioventricular block (AVB) (OR: 0.94, 95% CI: 0.90-0.99, p = 0.020). No significant associations were observed between other rheumatic diseases and arrhythmias. A two-sample Mendelian Randomization (MR) study provides data indicating that in European populations, a genetically predicted gout or rheumatoid arthritis (RA) may increase the incidence of right bundle branch block (RBBB). To clarify and investigate the processes behind these causal links, more research is necessary. Because racial genetic variability exists, care should be used when interpreting our findings.

Shotgun DNA sequencing for human identification: Dynamic SNP selection and likelihood ratio calculations accounting for errors

Shotgun sequencing is a DNA analysis method that potentially determines the nucleotide sequence of every DNA fragment in a sample, unlike PCR-based genotyping methods that is widely used in forensic genetics and targets predefined short tandem repeats (STRs) or predefined single nucleotide polymorphisms (SNPs). Shotgun DNA sequencing is particularly useful for highly degraded low-quality DNA samples, such as ancient samples or those from crime scenes. Here, we developed a statistical model for human identification using shotgun sequencing data and developed formulas for calculating the evidential weight as a likelihood ratio (LR). The model uses a dynamic set of binary SNP loci and takes the error rate from shotgun sequencing into consideration in a probabilistic manner. To our knowledge, the method is the first to make this possible. Results from replicated shotgun sequencing of buccal swabs (high-quality samples) and hair samples (low-quality samples) were arranged in a genotype-call confusion matrix to estimate the calling error probability by maximum likelihood and Bayesian inference. Different genotype quality filters may be applied to account for genotyping errors. An error probability of zero resulted in the commonly used LR formula for the weight of evidence. Error probabilities above zero reduced the LR contribution of matching genotypes and increased the LR in the case of a mismatch between the genotypes of the trace and the person of interest. In the latter scenario, the LR increased from zero (occurring when the error probability was zero) to low positive values, which allow for the possibility that the mismatch may be due to genotyping errors. We developed an open-source R package, wgsLR, which implements the method, including estimation of the calling error probability and calculation of LR values. The R package includes all formulas used in this paper and the functionalities to generate the formulas.

VEGFA gene variants are associated with breast cancer progression.

Angiogenesis is recognized as a hallmark of cancer, and vascular endothelial growth factor (VEGF) is a key regulator of the angiogenic process and is related to cancer progression. Anti-VEGF therapy has been tried but with limited success and without useful stratification for angiogenesis markers. Further, the landscape of VEGF single nucleotide polymorphisms (SNPs) in breast cancer and their clinical relevance is not well studied, and their relation to tissue-based angiogenesis markers has not been explored. Here, we studied a selection of VEGFA SNPs in nontumor lymph nodes from a population-based breast cancer cohort (n = 544), and their relation to clinicopathologic variables, vascular tissue metrics, and breast cancer-specific survival. Two of the SNP candidates (rs833068GA genotype and rs25648CC genotype) showed associations with angiogenesis tissue markers, and the VEGFA rs833068GA genotype was associated with breast cancer-specific survival among ER-negative cases. We also found trends of association between the rs699947CA genotype and large tumor diameter and ER-negative tumors, and between the rs3025039CC genotype and large tumor diameter. Our findings indicate some associations between certain VEGF SNPs, in particular the rs833068GA genotype, and both vascular metrics and patient survival. These findings and their potential implications need to be validated by independent studies.

IL6 receptor inhibitors: exploring the therapeutic potential across multiple diseases through drug target Mendelian randomization.

High interleukin-6 levels correlate with diseases like cancer, autoimmune disorders, and infections. IL-6 receptor inhibitors (IL-6Ri), used for rheumatoid arthritis and COVID-19, may have wider uses. We apply drug-target Mendelian Randomization (MR) to study IL-6Ri's effects. To simulate the effects of genetically blocking the IL-6R, we selected single nucleotide polymorphisms (SNPs) within or near the IL6R gene that show significant genome-wide associations with C-reactive protein. Using rheumatoid arthritis and COVID-19 as positive controls, our primary research outcomes included the risk of asthma, asthmatic pneumonia, cor pulmonale, non-small cell lung cancer, small cell lung cancer, Parkinson's disease, Alzheimer's disease, ulcerative colitis, Crohn's disease, systemic lupus erythematosus, type 1 diabetes, and type 2 diabetes. The Inverse Variance Weighted (IVW) method served as our principal analytical approach, with the hypotheses of MR being evaluated through sensitivity and colocalization analyses. Additionally, we conducted Bayesian Mendelian Randomization analyses to minimize confounding and reverse causation biases to the greatest extent possible. IL-6 inhibitors significantly reduced the risk of idiopathic pulmonary fibrosis (OR= 0.278, 95% [CI], 0.138-0.558; P <0.001), Parkinson's disease (OR = 0.354, 95% CI, 0.215-0.582; P <0.001), and positively influenced the causal relationship with Type 2 diabetes (OR = 0.759, 95% CI, 0.637-0.905; P = 0.002). However, these inhibitors increased the risk for asthma (OR = 1.327, 95% CI, 1.118-1.576; P = 0.001) and asthmatic pneumonia (OR = 1.823, 95% CI, 1.246-2.666; P = 0.002). The causal effect estimates obtained via the BWMR method are consistent with those based on the IVW approach. Similarly, sIL-6R also exerts a significant influence on these diseases.Diseases such as Alzheimer's disease, Crohn's disease, pulmonary heart disease, systemic lupus erythematosus, Type 1 diabetes, Non-small cell lung cancer and ulcerative colitis showed non-significant associations (p > 0.05) and were excluded from further analysis. Similarly, Small cell lung cancer were excluded due to inconsistent results. Notably, the colocalization evidence for asthmatic pneumonia (coloc.abf-PPH4 = 0.811) robustly supports its association with CRP. The colocalization evidence for Parkinson's disease (coloc.abf-PPH4 = 0.725) moderately supports its association with CRP. IL-6Ri may represent a promising therapeutic avenue for idiopathic pulmonary fibrosis, Parkinson's disease, and Type 2 diabetes.

COPD RISK IN PAKISTANI PUNJABI POPULATION: ROLE OF GATM, PSMA4, AND CHRNA5-A3-B4 GENE VARIANTS

Background: Chronic obstructive pulmonary disease (COPD) is a complex, multifactorial and polygenic disease concerning genetic and environmental factors. Objectives: The selected single nucleotide polymorphisms (SNPs) within or between potential candidate genes were studied to find the association with the onset of COPD disease in the Punjabi population of Pakistan. Methods: 254 COPD patients and 219 control subjects were enrolled for this case-control study. After a literature review and with the help of bioinformatics tools, risk-associated deleterious SNPs residing within or among genes GATM, PSMA4, CHRNA3, CHRNA5, and CHRNB4 were selected to evaluate their association with COPD. Following the mini-sequencing technique, the disease’s association analysis was done using PLINK v1.9 and SHEsis Plus. Results: The mean age of cases was 48.9 ± 9.04 years (N=254), comprising 55.1% males and 44.9% females with 36.6% positive family history of COPD. ‘C’ alleles for rs200551904, rs199547652 and rs1288775 are associated with COPD (p-value 9.70x10-9, 1.14x10-5 and 7.45x10-4 respectively), whereas the ‘CC’ genotype of rs8053 seems to be a protective factor for the disease. The variants rs1288775 and rs199547652 remained associated even with adjusting results for smoking exposure (p-value 0.002 and 1.22 x10-6, respectively). Haplotype analysis for rs1145086, rs1288775, rs8053, rs77994111, rs16969968, rs200551904, rs199547652, rs19968256, and rs181037724 shows that four of the haplotypes H4, H9, H10 and H14, (GATAGGACC; CACAAGACC; CATAGGACC; GACAAGACC respectively), are associated with the disease, while two haplotypes, H1 and H11 (CACAGGCCC and CGCAGGACC respectively), are protective factors against the disease. Conclusion: The association of COPD with chromosome 15 variants in the Punjabi population is reported in this study.

Causality between major depressive disorder and functional dyspepsia: a two-sample Mendelian randomization study.

To investigate the causal relationship between major depression and functional dyspepsia using two-sample Mendelian randomization. Data for major depression and functional dyspepsia were obtained from genome-wide association studies. We selected Single Nucleotide Polymorphisms (SNPs) strongly associated with severe depression. Mendelian randomization analysis was conducted using methods such as Inverse-Variance Weighted (IVW), MR-Egger, and Weighted Median Estimator (WME). Sensitivity analysis was performed to assess the robustness of the results. A total of 31 eligible SNPs were identified as instrumental variables for major depression. IVW analysis indicated a positive causal relationship between the two conditions (β = 0.328; SE = 0.137; p = 0.017), suggesting that severe depression increases the risk of functional dyspepsia (OR = 1.389; 95% CI: 1.062-1.816). Sensitivity tests showed no evidence of heterogeneity or horizontal pleiotropy (p > 0.05). MR analysis had shown that major depressive disorder is associated with an increased risk of functional dyspepsia.

Causal relationships between COVID-19 and venous thromboembolism: A mendelian randomization analysis.

Objective: Observational studies show the correlation between COVID-19 and venous thromboembolism (VTE) risk. However, the causal effects remain uncertain. We aimed to explore the potential causal association between COVID-19 and VTE using Mendelian randomization (MR) design. Methods: Two-sample MR was used to evaluate the potential causality between COVID-19 and VTE by selecting single-nucleotide polymorphisms (SNPs) as instrumental variables (IVs) from genome-wide association studies (GWAS). The weighted median, MR-Egger, simple mode, and weighted mode were employed as supplementary methods for MR estimations, with the inverse-variance weighted (IVW) method serving as the principal analysis. In addition, we took sensitivity analyses, including Cochran's test, MR-Pleiotropy Residual Sum and Outlier (MR-PRESSO), and leave-one-out analysis to ensure that we obtained stable and reliable results. Results: Our study selected 26 COVID-19 severity, 31 COVID-19 hospitalization, and 13 COVID-19 susceptibility SNPs as instrumental variables. The IVW analysis results revealed that there was no causal relationship between COVID-19 severity, hospitalization, or susceptibility and VTE, with odds ratios of 0.974 (95%CI: 0.936-1.013, p = 0.19), 0.976 (95%CI: 0.918-1.039, p = 0.447), and 0.908 (95%CI: 0.775-1.065, p = 0.235), respectively. The IVW approach yielded consistent results with MR-Egger, Weighted Median simple mode, and weighted mode. MR-PRESSO and sensitivity analysis further confirmed the stability and consistency of the MR results. Conclusions: This study did not find evidence to support a causal relationship between COVID-19 and VTE at the genetic level. Further investigation is warranted to determine if the significant association reported in previous observational studies between the two is due to confounding factors.

The role of Immune cells in Alzheimer's disease: a bidirectional Mendelian randomization study.

Alzheimer's disease (AD) is a leading cause of dementia, characterized by the accumulation of amyloid-beta (Aβ) and hyperphosphorylated tau proteins, leading to neuroinflammation and neuronal damage. The role of the immune system in AD pathogenesis is increasingly recognized, prompting an exploration of the causal relationship between immune cells and AD by using Mendelian randomization (MR) approaches. Utilizing genome-wide association study (GWAS) data from European cohorts, we conducted an MR study to investigate the causal links between immune cell phenotypes and AD. We selected single nucleotide polymorphisms (SNPs) associated with immune cell traits at a genome-wide significance threshold and applied various MR methods, including MR Egger, Weighted median, and inverse variance weighted analysis, to assess the causality between 731 immune phenotypes and AD. Our MR analysis identified 15 immune cell types with significant causal relationships to AD pathogenesis. Notably, the absolute count of CD28-CD4-CD8- T cells and the expression of HLA DR on B cells were linked to a protective effect against AD, while 13 other immune phenotypes were identified as contributing to the risk factors for the disease. The causal effects of AD on immunophenotypic traits are predominantly negative, implying that AD may impair the functionality of immune cells. Validation through independent datasets, such as FinnGen and GCST90027158, confirmed the causal association between six specific immune cells and AD. This comprehensive MR study elucidates the intricate network of causal relationships between diverse immunophenotypic traits and AD, providing novel insights into the immunopathogenesis of AD. The findings suggest potential immunological targets that could be leveraged for early diagnosis, disease monitoring, and therapeutic intervention.

Causal relationship between C-reactive protein and ischemic stroke caused by atherosclerosis: A Mendelian randomization study

ObjectivesThis study investigates the association between C-reactive protein (CRP) and ischemic stroke caused by large artery atherosclerosis (LAA). MethodsFive Mendelian Randomization (MR) methodologies were used for two-sample analyses: Inverse Variance Weighting (IVW), MR-Egger regression, Weighted Median (WM), Simple Mode, and Weighted Mode. CRP exposure data were obtained from aggregated summary statistics from a meta-analysis of genome-wide association studies (GWAS) in individuals of European ancestry (n = 343,524; UK Biobank). Stroke data were used as the outcome, with specific dataset details for relevant subtypes (cases = 40,585, controls = 406,111). ResultsIn the CRP GWAS dataset, selected single nucleotide polymorphisms (SNPs) as instrumental variables (IVs) showed genome-wide significance and a causal relationship with CRP, particularly in relation to LAA stroke. IVW indicated a robust causal connection between CRP and LAA stroke (Beta = 0.151, SE = 0.055, P = 0.006). The WM approach supported this relationship (Beta = 0.176, SE = 0.082, P = 0.033). However, MR-Egger regression suggested a potential absence of a causal link (Beta = 0.098, SE = 0.077, P = 0.206), with minimal influence from horizontal pleiotropy (Intercept = 0.0029; P = 0.317). The Simple mode found no significant association (Beta = 0.046, SE = 0.217, P = 0.834), while the Weighted mode revealed a significant causal association (Beta = 0.138, SE = 0.059, P = 0.020) between CRP and LAA stroke. ConclusionsMR analysis provides evidence for a potential causal relationship between CRP and an increased risk of LAA stroke.

CTSG polymorphisms in Chinese children with type 1 diabetes mellitus.

Cathepsin G (CTSG) plays an important role in the regulation of immune processes. Accumulated studies show that CTSG is involved in the onset and development of type 1 diabetes mellitus (T1DM). As the genetic background of T1DM varies widely among populations, we aimed to study the relationship between genetic polymorphisms in CTSG and T1DM susceptibility in Chinese populations. A total of 141 patients with T1DM and 200 healthy controls were enrolled in the study. Serum CTSG expression was detected using enzyme-linked immunosorbent assay (ELISA). Genotyping of two selected single nucleotide polymorphisms (SNPs) (rs2236742 and rs2070697) of CTSG was performed using PCR and Sanger sequencing. CTSG expression in patients with T1DM was significantly higher than in the control group. Alleles C and T of CTSG SNP rs2236742 were increased in T1DM. No significant associations were found for the SNP rs2070697. Our results indicate that the CTSG rs2236742 allele (C/T) is associated with T1DM in Chinese children and may serve as a new biomarker for predicting T1DM susceptibility.

Integrated morphometric and molecular approaches to screen hybrid from wild Labeo rohita and Labeo catla parent populations.

Interspecific hybrids of rohu (Labeo rohita) and catla (Labeo catla) are common, especially in India due to constrained breeding. These hybrids must segregate from their wild parents as part of conservational strategies. This study intended to screen the hybrids from wild rohu and catla parents using both morphometric and molecular approaches. The carp samples were collected from Jharkhand and West Bengal, India. The correlation and regression analysis of morphometric features are considered superficial but could be protracted statistically by clustering analysis and further consolidated by nucleotide variations of one mitochondrial and one nuclear gene to differentiate hybrids from their parents. Out of 21 morphometric features, 6 were used for clustering analysis that exhibited discrete separation among rohu, catla, and their hybrids when the data points were plotted in a low-dimensional 2-D plane using the first 2 principal components. Out of 40 selected single nucleotide polymorphism (SNP) positions of the COX1 gene, hybrid showed 100% similarity with catla. Concerning SNP similarity of the 18S rRNA nuclear gene, the hybrid showed 100% similarity with rohu but not with catla; exhibiting its probable parental inheritance. Along with morphometric analysis, the SNP comparison study together points towards strong evidence of interspecific hybridization between rohu and catla, as these hybrids share both morphological and molecular differences with either parent. However, this study will help screen the hybrids from their wild parents, as a strategy for conservational management.

Serum 25-hydroxyvitamin D levels and dermatomyositis: A 2-sample mendelian randomization study.

Previous studies have reported low serum 25-hydroxyvitamin D [25(OH)D] levels in dermatomyositis (DM) patients, but the exact causal relationship between them remains elusive. Our aim is to confirm the causal relationship between 25(OH)D and DM risk through a Mendelian randomization study. Retrieve genome-wide association study (GWAS) data on 25(OH)D (n = 441 291) and DM (n cases = 201, n controls = 172 834) from the GWAS database (https://gwas.mrcieu.ac.uk/). Select single-nucleotide polymorphisms (SNPs) strongly correlated with 25(OH)D as instrumental variables (IVs). The primary analytical approach involves the use of the inverse-variance weighted method (IVW), supplemented by MR-Egger regression and weighted median methods to enhance the reliability of the results. Heterogeneity and sensitivity analyses were conducted using Cochran's Q and leave-one-out approaches, respectively. The IVW analysis confirmed a positive causal relationship between genetic variation in 25(OH)D levels and DM (OR = 2.36, 95% CI = 1.01-5.52, p = .048). Although not statistically significant (all p > .05), the other methods also suggested a protective effect of 25(OH)D on DM. Based on MR-Egger intercepts and Cochran's Q analysis, the selected SNPs showed no horizontal pleiotropy and heterogeneity. Sensitivity analysis demonstrated the robustness of the results against individual SNPs. We provide the first evidence of a causal relationship between 25(OH)D levels and DM. Our findings support the importance of measuring serum 25(OH)D levels and considering vitamin D supplementation in clinical practice for patients with DM.

Celiac disease and attention-deficit/hyperactivity disorder: a bidirectional Mendelian randomization analysis.

Recent observational research suggests a potential link between celiac disease (CeD) and an increased incidence of attention-deficit/hyperactivity disorder (ADHD). However, the genetic relationship between CeD and ADHD remains unclear. In order to assess the potential genetic causality between these two conditions, we conducted a Mendelian randomization (MR) analysis. We performed a bidirectional MR analysis to investigate the relationship between CeD and ADHD. We carefully selected single nucleotide polymorphisms (SNPs) from publicly available large-scale genome-wide association studies (GWAS) databases, employing rigorous quality screening criteria. MR estimates were obtained using four different methods: fixed-effect inverse variance weighted (fe-IVW), random-effect inverse variance weighting (re-IVW), weighted median (WM), and MR-Egger. The robustness and reliability of our findings were confirmed through sensitivity analyses, assessment of instrumental variable (IV) strength (F-statistic), and statistical power calculations. Our MR analyses did not reveal any significant genetic associations between CeD and ADHD (fe-IVW: OR = 1.003, 95% CI = 0.932-1.079, P = 0.934). Similarly, in the reverse direction analysis, we found no evidence supporting a genetic relationship between ADHD and CeD (fe-IVW: OR = 0.850, 95% CI = 0.591-1.221, P = 0.378). Various MR approaches consistently yielded similar results. Sensitivity analysis indicated the absence of significant horizontal pleiotropy or heterogeneity. However, it's important to note that the limited statistical power of our study may have constrained the causal analysis of the exposure's influence on the outcome. Our findings do not provide compelling evidence for a genetic association between CeD and ADHD within the European population. While the statistical power of our study was limited, future MR research could benefit from larger-scale datasets or datasets involving similar traits. To validate our results in real-world scenarios, further mechanistic studies, large-sample investigations, multicenter collaborations, and longitudinal studies are warranted.

Causal relationship between gut microbiota and intracranial hemorrhage: A two-sample Mendelian randomization study.

Patients with intracranial hemorrhage (ICH) usually have an imbalance in the gut microbiota (GM); however, whether this is a causal correlation remains unclear. This study used summary data from an open genome-wide association study to conduct double-sample Mendelian randomization (MR) to test the causal correlation between GM and ICH. First, we used a cutoff value of P < 10E-5 to select single nucleotide polymorphisms critical for each GM. Inverse variance weighted, weighted median, and MR-PRESSO methods were used to evaluate the strength of this causal association. Finally, functional maps and annotations from genome-wide association studies were used to determine the biological functions of the genes. MR analysis revealed that Rikenellaceae RC9 gut group was significantly positively correlated with ICH risk. For every unit increase in Rikenellaceae RC9 gut group, the relative risk of ICH increased by 34.4%(P = 4.62E-04). Rhodospirillales, Terrisporobacter, Veillonellaceae, Coprococcus 3, unknown genus, Alphaproteobacteria, and Allisonella groups were negatively correlated with the risk of ICH, while Anaerofilum, Eubacteriumbrachy group, Clostridia, Howardella, and Romboutsia were negatively correlated with the risk of ICH. Nonetheless, the specific role of single nucleotide polymorphisms gene enrichment requires further investigation. This study suggests the causal effect on ICH. The discovery of >10 GMs associated with ICH could be used to prevent and treat ICH.

Genetic insights into the gut microbiota, herpes zoster, and postherpetic neuralgia: a bidirectional two-sample Mendelian randomization study

BackgroundAn increasing amount of evidence suggests that gastrointestinal diseases are risk factors for herpes zoster (HZ) and postherpetic neuralgia (PHN). Among them, the gut microbiota may play a crucial role in this process. Therefore, this study aims to explore the potential causal association between the gut microbiota and HZ and PHN.MethodsBidirectional two-sample Mendelian randomization (MR) analysis was used to detect the causal effect between HZ and PHN and the gut microbiota. Gut microbiota data were derived from the MiBioGen consortium, while HZ and PHN data were obtained from the FinnGen database. We selected single-nucleotide polymorphisms (SNPs) as instrumental variables with a threshold of p &amp;lt; 1 × 10⁻⁵ for the association with the gut microbiota in forward MR analysis and p &amp;lt; 5 × 10⁻8 for the association with HZ or PHN in reverse MR analysis and then removed SNPs in linkage disequilibrium (r2 &amp;lt; 0.001) within a distance of 10,000 kb for both the gut microbiota and HZ and PHN. These SNPs were utilized to assess the causal effect between exposures and outcomes using inverse-variance weighting (IVW), MR–Egger, weighted mean, and weighted median tests.ResultsThe class Deltaproteobacteria, order Desulfovibrionales, family Desulfovibrionaceae, and genus Coprococcus 2 were found to reduce the risk of HZ, while the phylum Cyanobacteria, genus Eubacterium rectale group appeared to increase it. The class Coriobacteriia, order Coriobacteriales, family Coriobacteriaceae, genus Lachnospiraceae NK4A136 and genus Ruminococcaceae UCG011 were found to reduce the risk of PHN, while the genus Candidatus Soleaferrea, genus Eubacterium rectale group, and genus Methanobrevibacter appeared to increase it. Moreover, the onset of HZ was found to increase the level of the genus Eubacterium rectale group. These findings remained robust and unaffected by heterogeneity or horizontal pleiotropy among SNPs in both forward and reverse MR analysis.ConclusionThis MR study provided evidence supporting a potential causal relationship between the gut microbiota and HZ and PHN. Moreover, we found that the causal effect between the gut microbiota and HZ is bidirectional. Further studies are required to clarify the biological mechanisms linking the gut microbiota and these conditions.

Causal association between obstructive sleep apnea and amyotrophic lateral sclerosis: a Mendelian randomization study.

Obstructive sleep apnea (OSA) had a high prevalence in the population. Whether OSA increases the risk of amyotrophic lateral sclerosis (ALS) is unknown. Our aim was to clarify this issue using two-sample Mendelian randomization (MR) analysis in a large cohort. Two-sample MR was used to evaluate the potential causality between OSA and ALS by selecting single-nucleotide polymorphisms (SNPs) as instrumental variables (IVs) from genome-wide association studies (GWAS). The inverse-variance weighted (IVW) method was chosen as the primary method to estimate causal association. Weighted median, weighted mode and simple mode methods were used as sensitivity analyses to ensure the robustness of the results. In MR analysis, IVW mode showed genetic liability to OSA was found to be significantly associated with a higher ALS risk (OR, 1.220; 95% confidence interval, 1.031-1.443; p = 0.021). No evidence of heterogeneity and horizontal pleiotropy were suggested. We found potential evidence for a causal effect of OSA on an increased risk of ALS.

Germline polymorphisms of the NOD2 pathway may predict the effectiveness of radioiodine in differentiated thyroid cancer treatment

PurposeDifferentiated thyroid cancer (DTC) presents a complex clinical challenge, especially in patients with distant metastases and resistance to standard treatments. This study aimed to investigate the influence of specific genes and their germline single nucleotide polymorphisms (SNPs) linked to both inflammatory processes and other neoplasms on the clinical and pathological characteristics of DTC, particularly their potential impact on radioiodine (RAI) treatment efficacy.MethodsThis retrospective analysis involved a cohort of 646 patients diagnosed with DTC after thyroidectomy. Study covering 1998–2014, updated in 2023, included 567 women and 79 men (median age: 49; range: 7–83). SNP selection targeted functional significance, while mutational status was assessed by pyrosequencing for comprehensive characterization. Patient genetic profiles were assessed for associations with disease characteristics, RAI response, and cancer pathology.ResultsSignificant correlations emerged between certain SNPs and DTC features. Notably, the NOD2 c.802 T > C variant (rs2066842) was identified as a marker distinguishing between papillary thyroid cancer (PTC) and follicular thyroid cancer (FTC). Moreover, the c.802 T allele was associated with an enhanced response to RAI treatment, indicating a more substantial decrease in posttreatment stimulated thyroglobulin (sTg) concentrations. The NFKB1A allele c.126A (rs696) exhibited connections with lower FTC stages and a reduced probability of multifocality.ConclusionThis study explored the molecular mechanisms of particular SNPs, highlighting the role of NOD2 in innate immunity and the stress response, and its potential impact on RAI efficacy. This research underscores the clinical promise of SNP analysis and contributes to personalized treatment strategies for DTC, emphasizing the relevance of genetic factors in cancer progression and treatment outcomes.

Plasma fatty acids and attention deficit hyperactivity disorder: a Mendelian randomization investigation.

Attention deficit hyperactivity disorder (ADHD) is the most common neurodevelopmental disorder of childhood, and pathogenesis is not fully understood. Observational studies suggest an association between fatty acids abnormalities and ADHD, but there are contradictions and differences between these findings. To address this uncertainty, we employed a two-sample bidirectional Mendelian Randomization (MR) analysis to investigate the causal relationship between fatty acids and ADHD. We conducted a two-sample Mendelian Randomization (MR) study, selecting single nucleotide polymorphisms (SNPs) highly correlated with fatty acid levels from the CHARGE Consortium as our instruments. The outcome data were sourced from the Psychiatric Genomics Consortium (PGC) dataset on ADHD, comprising 225,534 individuals, with 162,384 cases and 65,693 controls. Inverse variance weighting, MR-Egger, and weighted median methods were employed to estimate the causal relationship between fatty acids and ADHD. Cochran's Q-test was used to quantify heterogeneity of instrumental variables. Sensitivity analyses included MR-Egger intercept tests, leave-one-out analyses, and funnel plots. The MR analysis revealed no significant associations between genetically predicted levels of various saturated, monounsaturated, and polyunsaturated fatty acids (including omega-3 and omega-6) and ADHD risk in the CHARGE and PGC cohorts. Notably, an initial association with Dihomo-gamma-linolenic acid (DGLA) (OR = 1.009, p = 0.032 by IVW) did not persist after correction for multiple testing (adjusted p-value = 0.286). Sensitivity analysis supported our findings, indicating robustness. Moreover, there was a lack of evidence supporting a causal link from ADHD to fatty acids. While our study on the basis of genetic data does not provide evidence to support the causal role of fatty acids in ADHD, it does not preclude their potential involvement in reducing the risk of ADHD. Further research is needed to explore this possibility.

Association between genetic polymorphisms and other attributing factors with lipid profiles among statin users: a cross-sectional retrospective study

BackgroundStatins are well known for their efficacy to improve lipid profiles. Their efficacy varies between individuals and can be modified by patient factors such as genetic polymorphisms. This study used a cross-sectional retrospective design to assess the effect of selected single nucleotide polymorphisms (SNPs) and other patient-specific clinical variables on statin-related lipid profile changes in a subgroup of Malaysians. The impact of low and moderate intensity of statin doses (10–40 mg/day for at least six weeks), regardless of statin types, was assessed between SNPs of previously identified genes with clinical relation to statin efficacy and lipid profile changes before (baseline) and after statin treatment; two ranges of treatment durations, i.e. ≤ 6 months and 7–12 months. DNA was extracted from patient's venous blood (3 mL), and SNP genotyping was performed using PCR–RFLP method. Using a dominant genetic model, the association between selected SNPs from six genes of interest (ABCG2, ABCC2, APOE, APOA5, GATM and COQ2) and the patients' lipid profiles was investigated.ResultsA total of 229 statin-treated patients were included. The mean age of the patients was 53 ± 7.16 years, and they were mostly females (53.3%), Malay (96.1%), and were taking atorvastatin and simvastatin (90.4%). Seven SNPs genotyped from six genes investigated were related to different lipid profile before and after statin treatment. At baseline, ABCG2 rs2231142 (P = 0.035) and APOA5 rs662799 (P = 0.007) variants had higher HDL-c levels, while ABCC2 rs717620 variants had higher TC (P = 0.040) and LDL-c levels (P = 0.022). Following statin treatment, ABCC2 rs717620 (lower TG, P = 0.009) and APOA5 rs662799 (higher HDL, P = 0.031; lower TG, P = 0.037) were associated with improved lipid profiles, with the association being substantially related to males carrying minor alleles of the SNPs. None of the investigated SNPs were related to significant statin-related LDL-c lowering effects during statin therapy.ConclusionTo better understand inter-individual heterogeneity in lipid profiles during statin therapy, it would be helpful to take patient genetics and gender into consideration before and after administering statins.