Significant Genetic Variants Research Articles

Associations between daytime napping, sleep duration, and depression and 15 cardiovascular diseases: a Mendelian randomization study.

Numerous studies have documented the effects of daytime napping, sleep duration, and depression on cardiovascular diseases (CVDs). However, the evidence has been gleaned from observational studies that might be riddled with confounding variables and the possibility of reverse causation bias. Therefore, the present study employed a Mendelian randomization (MR) methodology to meticulously explore the relationships between daytime napping, sleep duration, and depression, and the risk profiles of CVDs. Genome-wide significant genetic variants associated with daytime napping, sleep duration, and depression were used as the instrumental variables (IVs). Data on the genetic correlations between these IVs and 15 CVDs were derived from the United Kingdom (UK) Biobank, Finnish Genome Studies, and other large-scale collaborations. We conducted both univariate and multivariate MR analyses to assess the overall effects and mediated relationships after adjusting for potential confounders, including body mass index (BMI), smoking status, and type 2 diabetes. The effect sizes were estimated using inverse variance-weighted (IVW) regression. The MR analysis revealed that an increased risk of heart failure (HF) [odds ratio (OR): 1.366; 95% confidence interval (CI): 1.013-1.842; P=0.04], coronary atherosclerosis (OR: 1.918; 95% CI: 1.257-2.927; P=0.003), myocardial infarction (MI) (OR: 1.505; 95% CI: 1.025-2.211; P=0.04), and coronary artery disease (CAD) (OR: 1.519; 95% CI: 1.130-2.043; P=0.006) was significantly associated with genetically predicted daytime napping. Prolonged sleep duration was found to be related to a reduced risk of HF (OR: 0.995; 95% CI: 0.993-0.998; P=2.69E-04), peripheral vascular disease (PVD) (OR: 0.984; 95% CI: 0.971-0.997; P=0.02), and CAD (OR: 0.997; 95% CI: 0.994-0.999; P=0.006). Additionally, a statistically significant positive relationship was observed between depressive disorders and the occurrence of atrial fibrillation (AF) (OR: 1.298, 95% CI: 1.065-1.583, P=0.01), indicating a heightened susceptibility. The multivariable MR analyses substantiated the reliability of the observed associations between daytime napping and the incidence of HF and CAD, following adjustments for genetically predicted BMI and smoking. The sensitivity analysis did not reveal any evidence of horizontal pleiotropy or heterogeneity, thus supporting the validity of the study's results. This MR investigation posits a potential causal nexus between daytime napping, sleep duration, and depression, and the genesis of CVDs, offering new perspectives on the prevention and management of CVDs.

The role of genetic variants in the prediction of hearing loss due to cisplatin chemoradiotherapy.

Concomitant high-dose cisplatin with radiotherapy is commonly used for treating head and neck squamous cell carcinoma (HNSCC). Cisplatin, often used with radiotherapy, is known for causing irreversible sensorineural hearing loss, with individual variability suggesting a genetic component. This study aims to enhance the predictive ability of the clinical prediction model for cisplatin-induced hearing loss (CIHL) in HNSCC patients, as outlined in Theunissen etal., by incorporating significant genetic variants. Conducted at the Netherlands Cancer Institute, this retrospective study included 74 patients treated between 1997 and 2011. Thirty-one SNPs that were previously associated with CIHL or other cisplatin-induced toxicities were identified and incorporated into the model. The primary outcome measured was the change in decibels at posttreatment 1-2-4 kHz hearing levels per additional minor allele of these SNPs, evaluated using linear mixed-effects regression models. The model's predictive accuracy was determined by the area under the curve (AUC) using 10-fold cross-validation. The rs2289669 SNP in the SLC47A1/MATE1 gene was linked to a significant 2.67 dB increase in hearing loss per allele (95% CI 0.49-4.86, p = 0.017). Incorporating rs2289669 improved the model's AUC from 0.78 to 0.83, a borderline significant improvement (p = 0.073). This study underscores the importance of the rs2289669 SNP in CIHL and demonstrates the potential of combining genetic and clinical data for enhanced predictive models in personalized treatment strategies.

Genome-wide association study for polledness, horn shape, and wool traits in Original Valachian sheep

Abstract. The Original Valachian sheep is an endangered Slovak national breed that is well adapted to high-altitude pastures. The sheep can be horned with various shapes and can have multi-coloured or completely white or black wool. Breeders are interested in learning about the genetic basis of these traits. We conducted a genome-wide association study based on the genomic information of 96 sheep genotyped by the GeneSeek GGP Ovine 50K SNP (single-nucleotide polymorphism) chip and on the following traits: polledness (presence or absence of horns), horn shape, and wool colour (completely white and completely black). The univariate linear mixed model was used to discover genetic variants significantly associated with tested traits. The Bonferroni correction and the false-discovery rate were used as significance thresholds. The RXFP2 gene (chromosome 10, 29.5 Mb) was identified as a strong candidate for polledness. In addition, when compared to animals with sideways-turned horns vs. polled, the region around the ADAMTS3 gene (chromosome 6, 88.47 Mb) was significant. A total of nine significant genomic regions were found when comparing the sideways-turned spiral horns with the backwards-curled horns, the two most frequent horn types in Original Valachian sheep. The RXFP2 may also contribute to the genetic control of horn shape. Genes identified in other regions were involved to osteogenic differentiation and osteoblast proliferation (PCP4, chromosome 1, 260.7 Mb), bone mineral density and mineral content (NKX1-2, chromosome 22, 43.75 Mb). The significant genetic variants close to the region of MC1R (chromosome 14, at 14.2 Mb) were associated with the wool colour of sheep that were fully white or fully black animals. The results of this study will contribute to a better understanding of the phenotypic variability of the Original Valachian sheep, especially regarding traits that are very important for breeders of this endangered breed.

PCSK9 and Lipid Metabolism: Genetic Variants, Current Therapies, and Cardiovascular Outcomes.

Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a crucial role in the modulation of lipid metabolism as a critical negative regulator of hepatic low-density lipoprotein receptor (LDLR) levels and circulating low-density lipoprotein (LDL) clearance. Numerous gain-of-function (GOF) mutations in PCSK9 have been identified as causing familial hypercholesterolemia (FH) by reducing LDLR levels, and loss-of-function (LOF) mutations associated with a hypercholesterolemia phenotype protective against atherosclerosis. PCSK9 represents an example of successful translational research resulting in the identification of PCSK9 as a major drug target for a lipid-lowering therapy. To explore the genetic constitution of PCSK9 and its biologic role, in this review, we summarize the current evidence of clinically significant PCSK9 genetic variants involved in lipid metabolism as well as emphasize the importance of PCSK9 inhibition for the improvement of cardiovascular outcomes by conducting a meta-analysis of the available data on the incidence of cardiovascular disease events.

Novel genome-wide significant germline genetic variants associated with venous thrombo-embolism (VTE) and arterial embolism (ATE) risk in patients with ALK and ROS1 fusion non-small cell lung cancer (NSCLC).

12092 Background: In a recent meta-analysis, non small cell lung cancers (NSCLC) with ALK or ROS1 fusions had higher rates of VTE compared to KRAS or EGFR mutant NSCLC, and were associated with increased ATE risk, particularly around diagnosis. The underlying mechanisms of how these somatic fusions affect thrombosis remain unclear. We examined clinico-demographic and germline genetic factors associated with VTE and ATE in NSCLC patients with ALK/ROS1 fusions in this first comprehensive genome wide association analysis (GWAS). Methods: In this prospective cohort, germline DNA from whole blood was obtained from 150 patients with ALK fusions and 32 with ROS1 fusions at Princess Margaret Cancer Centre (recruited 2014- 2023). Clinico-demographic, treatment and outcome data were collected from electronic medical charts. Overall survival (OS) by VTE or ATE status was assessed via Cox regression, treating ATE and VTE as time-varying covariates. Genotyping utilized the Infinium Global Screening Array (v3.0 Illumina); quality-control removed 3 patients from final analysis. Using linear regression, outcomes were weighted; no VTE/ATE events (0), one VTE/ATE event (1), or multiple ATE/VTEs (>2). Global significance was set at p < 5 x10-8 and adjusted for age, sex, body mass index (BMI), and ethnic/population stratification (top 3 principal components). Results: There were 97 females (54%) and 82 males (46%), mean age was 57.4 years, 70% had stage 4 disease, 96% adenocarcinoma; 35% experienced VTE/ATE at any time; 13% had 2+ VTE/ATE events. For those with VTE, 32 scored 1, 22 scored 2 and 6 scored 3 on Khorana score. Higher BMI was a significant risk factor for VTE/ATE (adjusted odds ratio 1.59 per 5-unit increase, p=0.01). Shorter OS was observed in patients with VTE (Hazard ratio (HR)=3.15, p<0.001) and ATE (HR=2.51, p=0.036), compared to those without. Two novel GWAS gene peaks on the Manhattan plot (previously not reported to be associated with VTE/ATE) had globally significant associations with risk of VTE/ATE: at Chromosome 6q15 (intergenic region between RNGTT and LOC101928936; 5/10 top variants with top risk-allele p=3.594E-09) and at 15p22 ( TLN2 gene; 2/10 top variants p=1.095E-08). TLN2 is a cytoskeletal protein involved in the assembly of actin filaments and linkages with extracellular matrices. Additional identified variants potentially associated with VTE/ATE in ALK/ROS1 fusion patients were found in: CTBP2, NALCN, WDR7, PAX7, ZNF385D, SORBS2, and CSMD1. Conclusions: Two novel globally significant variants, associated with VTE/ATE, are unique to patients with ALK/ROS1 fusion NSCLC. If validated, these biomarkers may help identify ALK/ROS1 patients who are at highest risk of VTE/ATE who may benefit from prophylactic anticoagulation. Further investigation and clinical evaluation are warranted.

Identification of rare genetic variants in the PCDH genetic family in a cohort of transgender women

ObjectiveTo study the identification of rare genetic variants in the PCDH genetic family in a cohort of transgender women and their potential role in gender identity. DesignExome sequencing and functional ontology analysis. SettingAugusta University, including the Equality Clinic of Augusta and the Reproductive Medicine and Infertility Associates Clinic. Patients24 transgender women and 22 cisgender men. InterventionsExome sequencing followed by variant confirmation through Sanger sequencing and functional classification analysis using the Database for Annotation, Visualization and Integrated Discovery (DAVID) tool. Main Outcome MeasuresIdentification of rare, functionally significant genetic variants in the PCDH gene family and their prevalence in transgender women compared to cisgender men. ResultsExome sequencing revealed 38,524 genetic variants, of which 2441 were rare and predicted to be functionally significant. DAVID analysis demonstrated a statistically enriched functional group, “homophilic cell adhesion via plasma membrane adhesion molecules” (Benjamini corrected p-value 1.5 x 10-11), containing 55 genes, including 18 PCDH gene family members. A total of 37 rare variants in 21 PCDH genes were identified, with 36 confirmed by Sanger sequencing. A statistically significant increase in these variants was observed in transgender women compared to cisgender men (Z = 2.08905, p= 0.037). ConclusionsTransgender women exhibited a greater than 3-fold increase in functionally significant PCDH gene variants compared to cisgender men. These findings suggest that the PCDH family may play a role in the genetic pathways associated with gender identity in transgender women.

Evaluation the Application of Karyotype Analysis and Chromosome Microarray in Prenatal Diagnosis.

We aimed to compare the difference of the chromosomal abnormalities using karyotype analysis and chromosomal microarray (CMA) as well as to evaluate their application in different prenatal diagnosis indications. Overall, 3007 pregnant women with prenatal diagnosis indications from Medical Genetics Department of Linyi Women and Children's Health Care Hospital, who underwent standard G-banded karyotype analysis and CMA, were enrolled from 2018-2022. G-banded karyotype analysis and CMA were undergone simultaneously. All fetuses with genetic variants were enrolled for further analyzing. The frequency and differences of chromosomal abnormalities of the two methods were compared in different prenatal diagnosis indications groups. CMA improved 4.09% (123/3007) of genetic changes compared karyotype analysis. CMA is on par with karyotyping for detection of aneuploidies and gross unbalanced rearrangements. Serological screening and ultrasound abnormalities were the main indications of prenatal diagnosis. The detection rate of chromosomal abnormalities was highest in non-invasive prenatal testing (NIPT) abnormal group. In the ultrasound abnormality group, the detection rate of genetic variants in nuchal translucency (NT) increased group was higher than other subgroups and there was statistically significant difference in the detection rate of pCNVs. CMA can detect 5.57% (40/718) more genetic abnormalities in ultrasound abnormality group on the normal karyotype. CMA improved 0.67% (20/3007) of genetic changes with clinically significant compared karyotype, brought 3.42% (103/3007) of variants with uncertain significance (VOUS). CMA identified additional, clinically significant genetic variants on the basis of normal karyotype analysis, brought a proportion of unclear significant variants. All the pregnant women accepted amniocentesis should be informed about their characteristics of karyotype analysis and CMA by genetic counselors.

Comprehensive Analysis of Drug Utilization Patterns, Gender Disparities, Lifestyle Influences, and Genetic Factors: Insights from Elderly Cohort Using g-Nomic® Software.

Polypharmacy is a global healthcare concern, especially among the elderly, leading to drug interactions and adverse reactions, which are significant causes of death in developed nations. However, the integration of pharmacogenetics can help mitigate these risks. In this study, the data from 483 patients, primarily elderly and polymedicated, were analyzed using Eugenomic®'s personalized prescription software, g-Nomic®. The most prescribed drug classes included antihypertensives, platelet aggregation inhibitors, cholesterol-lowering drugs, and gastroprotective medications. Drug-lifestyle interactions primarily involved inhibitions but also included inductions. Interactions were analyzed considering gender. Significant genetic variants identified in the study encompassed ABCB1, SLCO1B1, CYP2C19, CYP2C9, CYP2D6, CYP3A4, ABCG2, NAT2, SLC22A1, and G6PD. To prevent adverse reactions and enhance medication effectiveness, it is strongly recommended to consider pharmacogenetics testing. This approach shows great promise in optimizing medication regimens and ultimately improving patient outcomes.

Structured testing of genetic association with mixed clinical outcomes.

Genetic factors play a fundamental role in disease development. Studying the genetic association with clinical outcomes is critical for understanding disease biology and devising novel treatment targets. However, the frequencies of genetic variations are often low, making it difficult to examine the variants one-by-one. Moreover, the clinical outcomes are complex, including patients' survival time and other binary or continuous outcomes such as recurrences and lymph node count, and how to effectively analyze genetic association with these outcomes remains unclear. In this article, we proposed a structured test statistic for testing genetic association with mixed types of survival, binary, and continuous outcomes. The structured testing incorporates known biological information of variants while allowing for their heterogeneous effects and is a powerful strategy for analyzing infrequent genetic factors. Simulation studies show that the proposed test statistic has correct type I error and is highly effective in detecting significant genetic variants. We applied our approach to a uterine corpus endometrial carcinoma study and identified several genetic pathways associated with the clinical outcomes.

Interpretation of 10years of Alzheimer's disease genetic findings in the perspective of statistical heterogeneity.

Common genetic variants and susceptibility loci associated with Alzheimer's disease (AD) have been discovered through large-scale genome-wide association studies (GWAS), GWAS by proxy (GWAX) and meta-analysis of GWAS and GWAX (GWAS+GWAX). However, due to the very low repeatability of AD susceptibility loci and the low heritability of AD, these AD genetic findings have been questioned. We summarize AD genetic findings from the past 10years and provide a new interpretation of these findings in the context of statistical heterogeneity. We discovered that only 17% of AD risk loci demonstrated reproducibility with a genome-wide significance of P < 5.00E-08 across all AD GWAS and GWAS+GWAX datasets. We highlighted that the AD GWAS+GWAX with the largest sample size failed to identify the most significant signals, the maximum number of genome-wide significant genetic variants or maximum heritability. Additionally, we identified widespread statistical heterogeneity in AD GWAS+GWAX datasets, but not in AD GWAS datasets. We consider that statistical heterogeneity may have attenuated the statistical power in AD GWAS+GWAX and may contribute to explaining the low repeatability (17%) of genome-wide significant AD susceptibility loci and the decreased AD heritability (40-2%) as the sample size increased. Importantly, evidence supports the idea that a decrease in statistical heterogeneity facilitates the identification of genome-wide significant genetic loci and contributes to an increase in AD heritability. Collectively, current AD GWAX and GWAS+GWAX findings should be meticulously assessed and warrant additional investigation, and AD GWAS+GWAX should employ multiple meta-analysis methods, such as random-effects inverse variance-weighted meta-analysis, which is designed specifically for statistical heterogeneity.

Multi-omics analysis provides insight into the genetic basis of proline-derived milk microbiota in buffalo

Understanding the intricate relationship between genetics, metabolites, and microbiota is paramount for unraveling the complexities that define buffalo milk composition. In this study, we employed a multi-omics approach to dissect the genetic and metabolic determinants of buffalo milk traits. Metabolomics analysis of 100 buffalo milk samples revealed a rich profile of 446 metabolites, with a particular emphasis on those associated with amino acid biosynthesis. Metabolite-based Genome-Wide Association Studies (mGWAS) uncovered 13 significant genetic variants, with a pronounced focus on l-Proline. Notably, single nucleotide polymorphisms (SNPs) within the ATG16L1 gene implicated its role in proline production. Concurrently, an in-depth exploration of milk microbiota dynamics highlighted marked differences between buffaloes with high and low proline groups. High proline abundance correlated with increased microbial diversity, dominated by Firmicutes and Proteobacteria. Distinct genera, such as Acinetobacter and Corynebacterium, characterized low and high proline groups, respectively. Functional changes in milk microbiota, especially in amino acid biosynthesis pathways, underscored proline's pivotal role in shaping microbial functions. Correlations between milk microbiota abundance and proline levels emphasized the intricate relationship between host physiology and microbial composition. These findings not only advance our understanding of the genetic basis of metabolic traits in buffalo milk but also present potential biomarkers for targeted breeding strategies. This integrated approach provides a nuanced perspective on milk composition, offering implications for dairy quality and nutritional enhancement.

Abstract P250: Vascular Contributions to Alzheimer's Disease

Introduction: Alzheimer’s disease (AD) is a debilitating neurodegenerative disorder that affects over 50 million people worldwide. The role of vascular risk factors have been described as a contributor to and a major comorbidity of AD pathogenesis; yet there is discordant evidence of this complex relationship between cardiovascular diseases (CVD) and its risk factors (like hypertension, hyperlipidemia, obesity, etc.) with AD pathophysiology and cognitive decline. AD associated Genome-wide association studies (GWAS) and derived polygenic risk scores (AD PRS) have uncovered some significant common genetic variants relating to CVD risk factors; however, we are still yet to unravel the comprehensive impact of these vascular genetic contributions to AD pathogenesis and cognitive decline. Method: In this study, we used 1800 participants from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort spanning the full spectrum of clinical and pathological diagnoses of the AD spectrum, as our target dataset used for polygenic risk score calculation. Thereafter, we obtained GWAS summary statistics for cumulative cardiovascular risk by searching the Polygenic Score (PGS) GWAS Catalog using CVD as the ‘mapped trait” and then calculated cardiovascular-based PRS using HRS-based imputed GWAS data of the ADNI cohort. We conducted association analysis using a multivariate linear regression model with appropriate covariates (age, sex, APOE, education, etc.) between CVD-related polygenic risk score (CVD-PRS) with the different clinical AD diagnoses groups (Cognitively Normal/CN, Significant Memory Concerns/SMC, Mild Cognitive Impairment/MCI, Alzheimer's Disease/AD). We also performed association analysis of this CVD-PRS with white matter hyperintensity (WMHI) values, a vascular biomarker, at baseline using a linear regression model. Furthermore, we extended our analyses of CVD-related PRS with cognitive performance at baseline using composite scores for memory (MEM) and executive functioning (EF). Results and Conclusion: We found significantly strong correlation of CVD-related PRS with only certain AD Diagnoses groups (Significant Memory Concerns: SMC and Alzheimer's: AD) in the AD continuum. Additionally, we found strong associations (p &lt; 0.05) of this cardiovascular based- polygenic risk score with baseline memory as well as White Matter Hyperintensity (WMH) in our sample, specifically the group with a clinical diagnosis of AD. Furthermore, we are performing longitudinal association analysis of CVD-related PRS with longitudinal cognitive decline using a linear mixed effects model. Our findings will help us understand 1) how a cumulative CVD-related PRS associates with different AD diagnoses subgroups as well as vascular biomarkers for AD and 2) how CVD-related PRS associates with cognitive performance and longitudinal cognitive decline.

Algorithmic assessment reveals functional implications of GABRD gene variants linked to idiopathic generalized epilepsy

Objective The primary objective of this study is to address the challenge posed by the increasing number of variants of unknown clinical significance within the GABRD gene, which encodes the δ subunit of γ-Aminobutyric acid type A receptors. The focus is on predicting the most pathogenic GABRD VUS to enhance precision medicine and improve our understanding of relevant pathophysiology. Methods The study employs a combination of in silico algorithms to analyze 82 variants of unknown clinical significance of GABRD gene sourced from the ClinVar database. Initially, separate algorithms based on sequence homology are utilized to assess this variant set. Subsequently, consensus variants predicted as pathogenic undergo further evaluation through a web server employing an algorithm based on structural homology. The resulting 11 variants are then validated using in silico tools that assess variant effects based on genetic and molecular data. The evaluation includes consideration of disease association and protein stability due to amino acid substitutions. Results The study identifies specific variants (L111R, R114C, D123N, G150S, and L243P) in the coding region of the GABRD gene, which are predicted as deleterious by multiple algorithms. These variants are evolutionarily conserved, mapped onto the extracellular domain of the δ subunit, and associated with idiopathic generalized epilepsy. Conclusions The findings suggest structural or functional consequences that lead to pathogenicity, offering valuable insights for wet-lab experimentation. Besides, the findings contribute to the validation of clinically significant genetic variants in the GABRD gene, which is critical for epilepsy precision medicine.

Anti-factor B antibodies in atypical hemolytic uremic syndrome.

The etiology of atypical hemolytic uremic syndrome (aHUS) is unknown in 30-40% of patients. Anti-factor B (FB) antibodies are reported in C3 glomerulopathy (C3G) and immune-complex membranoproliferative glomerulonephritis (IC-MPGN), though not in aHUS. We screened patients < 18-year-old from cohorts of aHUS and C3G/idiopathic IC-MPGN. Anti-FB IgG antibodies were measured by ELISA and confirmed by Western blot. Normative levels were based on antibody levels in 103 healthy blood donors. Prevalence of anti-FB antibodies was 9.7% (95% CI 6.1-14.5%; n = 21) in 216 patients with aHUS, including 11.5% (95% CI 6.4-18.5%; n = 14) in anti-FH associated aHUS and 11.8% (95% CI 4.4-23.9%; n = 6) in patients without a definitive genetic or autoimmune etiology. Patients with significant genetic variants did not show anti-FB antibodies. In patients with concomitant anti-FB and anti-FH antibodies, median anti-FH titers were higher (11,312 AU/mL vs. 4920 AU/mL; P = 0.04). Anti-FB antibody titer correlated with disease severity (hemoglobin and platelets; P < 0.05), declined following plasma exchange and increased during relapse. While 4/64 patients with C3G (6.3%) and 1/17 with IC-MPGN showed anti-FB antibodies, titers were higher in aHUS (544.8 AU/mL vs. 1028.8AU/mL; P = 0.003). Anti-FB antibodies are present in 6-10% of patients with aHUS and C3G/IC-MPGN, with higher titers in the former. The diagnostic and therapeutic implication of anti-FB antibodies in aHUS needs confirmation and further studies. The study shows propensity for autoantibody generation and co-existence of multiple risk factors for aHUS in Indian children.

Delving into the significance of the His289Tyr single-nucleotide polymorphism in the glutamate ionotropic receptor kainate-1 (Grik1) gene of a genetically audiogenic seizure model.

Genetic abnormalities affecting glutamate receptors are central to excitatory overload-driven neuronal mechanisms that culminate in seizures, making them pivotal targets in epilepsy research. Increasingly used to advance this field, the genetically audiogenic seizure hamster from Salamanca (GASH/Sal) exhibits generalized seizures triggered by high-intensity acoustic stimulation and harbors significant genetic variants recently identified through whole-exome sequencing. Here, we addressed the influence of the missense single-nucleotide polymorphism (C9586732T, p.His289Tyr) in the glutamate receptor ionotropic kainate-1 (Grik1) gene and its implications for the GASH/Sal seizure susceptibility. Using a protein 3D structure prediction, we showed a potential effect of this sequence variation, located in the amino-terminal domain, on the stability and/or conformation of the kainate receptor subunit-1 protein (GluK1). We further employed a multi-technique approach, encompassing gene expression analysis (RT-qPCR), Western blotting, and immunohistochemistry in bright-field and confocal fluorescence microscopy, to investigate critical seizure-associated brain regions in GASH/Sal animals under seizure-free conditions compared to matched wild-type controls. We detected disruptions in the transcriptional profile of the Grik1 gene within the audiogenic seizure-associated neuronal network. Alterations in GluK1 protein levels were also observed in various brain structures, accompanied by an unexpected lower molecular weight band in the inferior and superior colliculi. This correlated with substantial disparities in GluK1-immunolabeling distribution across multiple brain regions, including the cerebellum, hippocampus, subdivisions of the inferior and superior colliculi, and the prefrontal cortex. Notably, the diffuse immunolabeling accumulated within perikarya, axonal fibers and terminals, exhibiting a prominent concentration in proximity to the cell nucleus. This suggests potential disturbances in the GluK1-trafficking mechanism, which could subsequently affect glutamate synaptic transmission. Overall, our study sheds light on the genetic underpinnings of seizures and underscores the importance of investigating the molecular mechanisms behind synaptic dysfunction in epileptic neural networks, laying a crucial foundation for future research and therapeutic strategies targeting GluK1-containing kainate receptors.

Identification of heel bone mineral density as a risk factor of Alzheimer’s disease by analyzing large-scale genome-wide association studies datasets

Introduction: Both low bone mineral density (BMD) and Alzheimer’s disease (AD) commonly co_occur in the older adult. Until now, the association between AD and BMD has been widely reported by observational studies. However, Mendelian randomization (MR) studies did not support the causal association between BMD and AD. We think that the lack of significant causal association between AD and BMD identified by recent MR studies may be caused by small number of potential instrumental variables.Methods: We conduct a MR study to evaluate the causal effect of heel BMD on the risk of AD using 1,362 genome-wide significant and independent (p &amp;lt; 5.00E-08) heel BMD genetic variants as the potential instrumental variables, which are identified by a large-scale genome wide association study (GWAS) of heel BMD in 394,929 UK Biobank individuals. Using these 1,362 genome-wide significant and independent heel BMD genetic variants, we extracted their corresponding AD GWAS summary results in IGAP AD GWAS dataset (n = 63,926) and FinnGen AD GWAS dataset (n = 377,277). Five methods including inverse-variance weighted meta-analysis (IVW), weighted median, MR-Egger, MR-PRESSO, and MRlap were selected to perform the MR analysis. 951 of these 1,362 genetic variants are available in AD GWAS dataset.Results: We observed statistically significant causal effect of heel BMD on the risk of AD using IVW in IGAP AD GWAS dataset (OR = 1.048, 95%CI: 1.002–1.095, p = 0.04) and FinnGen AD GWAS dataset (OR = 1.053, 95% CI:1.011–1.098, p = 0.011). Importantly, meta-analysis of IVW estimates from IGAP and FinnGen further supported the causal effect of heel BMD on the risk of AD (OR = 1.051, 95% CI: 1.02–1.083, p = 0.0013).Discussion: Collectively, our current MR study supports heel BMD to be a risk factor of AD by analyzing the large-scale heel BMD and AD GWAS datasets. The potential mechanisms underlying the association between heel BMD and AD should be further evaluated in future.

Neuroimaging Genomics a Predictor of Major Depressive Disorder (MDD).

Depression is a complex psychiatric disorder influenced by various genetic and environmental factors. Strong evidence has established the contribution of genetic factors in depression through twin studies and the heritability rate for depression has been reported to be 37%. Genetic studies have identified genetic variations associated with an increased risk of developing depression. Imaging genetics is an integrated approach where imaging measures are combined with genetic information to explore how specific genetic variants contribute to brain abnormalities. Neuroimaging studies allow us to examine both structural and functional abnormalities in individuals with depression. This review has been designed to study the correlation of the significant genetic variants with different regions of neural activity, connectivity, and structural alteration in the brain as detected by imaging techniques to understand the scope of biomarkers in depression. This might help in developing novel therapeutic interventions targeting specific genetic pathways or brain circuits and the underlying pathophysiology of depression based on this integrated approach can be established at length.

Genome-wide association study of heart failure in a multiethnic south-east asian cohort

Abstract NMRC Heart failure (HF) is a leading cause of morbidity and mortality worldwide (1). While existing genome-wide association studies (GWAS) have yielded many different loci and causal genes, most of such studies has been conducted in European populations (2). There has been little insight into the genetic architecture of complex diseases, especially HF among Asians, despite up to 60% of the world population consisting of Asians. Through this study, we aim to uncover the genomic basis of heart failure in a South-East Asian cohort, with deep phenotyping of cardiovascular, metabolic, immune, and inflammatory traits. We conducted the largest multi-ancestry South-east Asian all-cause HF GWAS (n=2310, 1305 cases and 1005 controls), utilizing whole genome sequencing (WGS) data. Eleven independent loci were found to be associated with HF (P-value = 5e10-8). In-silico and functional studies were interrogated, allowing us to map most of the loci (n=9) to various genes implicated in various metabolic diseases - hypertension (HTN), diabetes mellitus (DM), and coronary artery disease (CAD). We further conducted a phenome-wide association study (PWAS) of significant loci, which revealed that they augment signals related to CAD, atrial fibrillation, DM and HTN, suggesting a shared genetic etiology between these metabolic risk factors and Asian HF. Of note, this the first HF GWAS to implicate the PDE9A gene, which was previously discovered as a potential biomarker for HF with preserved ejection fraction (HFpEF) through its involvement in the cGMP signaling pathways, and is currently being explored as a therapeutic target in the treatment of HFpEF (3). Polygenic risk scores (PRS) were calculated for heart failure in this Asian cohort, which identified that the most optimized model (HF PRS), included 19,431 of the most significant genetic variants (p=0.073). The prediction power of the HF PRS on HF risk was tested in UKB Asian subjects (N=10,016; 413 cases and 9,603 controls). Our results showed that the highest 10% percentile HF PRS risk subjects in UKB Asian were at 1.56-fold risks (95% CI: 1.16-2.08) for HF. This study provides a comprehensive understanding of the genetic architecture, and sheds light on novel biological pathways underlying HF in a south-east Asian population, indicating a highly metabolic underpinnings of this disease. It provides a step towards developing a precision-medicine based approach for risk stratification, prevention, and management of HF among Asians. Furthermore, this study provides evidence for the use of WGS in GWAS, to expand the discovery of novel targets for downstream interrogation, biomarker and drug development for complex diseases.

Phenotypic but not genetically predicted heart rate variability associated with all-cause mortality

Low heart rate variability (HRV) has been widely reported as a predictor for increased mortality. However, the molecular mechanisms are poorly understood. Therefore, this study aimed to identify novel genetic loci associated with HRV and assess the association of phenotypic HRV and genetically predicted HRV with mortality. In a GWAS of 46,075 European ancestry individuals from UK biobank, we identified 17 independent genome-wide significant genetic variants in 16 loci associated with HRV traits. Notably, eight of these loci (RNF220, GNB4, LINCR-002, KLHL3/HNRNPA0, CHRM2, KCNJ5, MED13L, and C160rf72) have not been reported previously. In a prospective phenotypic relationship between HRV and mortality during a median follow-up of seven years, individuals with lower HRV had higher risk of dying from any cause. Genetically predicted HRV, as determined by the genetic risk scores, was not associated with mortality. To the best of our knowledge, the findings provide novel biological insights into the mechanisms underlying HRV. These results also underline the role of the cardiac autonomic nervous system, as indexed by HRV, in predicting mortality.

The novel candidate genes related to live weight trait in southern meat sheep breed revealed by genome-wide genotyping

The study of the local sheep breeds’ genetic architecture is an important step on the way to preserve their gene pool. The aim of our work was to identify candidate genes associated with the live weight trait in adult southern meat breed sheep. This breed has high productivity, but is under threat of a critical decrease in genetic diversity due to a small number. The live weight of farm animals is one of the key breeding indicators. This quantitative trait is polygenic and breed specific as it has been shown by a number of authors. Animals were genotyped on the Illumina Ovine SNP50 Genotyping Bead Chip assay using standard procedures. Results in quality control, statistics and visualization were carried out in Rstudio 2023.03.0 and plink1.9. Genotyped animals were divided into two groups according to the case/control principle with differences in live weight between representatives of groups of 25–30 kg. Significant genetic variants were determined by the fixation indices method. Further analysis of significant variants (in intron positions) was performed in Ensembl genomic browser and revealed candidate genes localized in chromosomes 5, 6, 12, 20. The statistical analysis of live mass showed significant differences of the studied trait in different genotypes on four genes. The candidate genes identified can be recommended for using as genetic markers, their study could improve the productivity of southern meat sheep breed and help to preserve its gene pool.