Meta-analysis of 49(cid:0)549 individuals imputed with the 1000 Genomes Project reveals an exonic damaging variant in ANGPTL4 determining fasting TG levels
This study illustrates that GWAS with high-scale imputation may still help to unravel the biological mechanism behind circulating lipid levels and identifies more new rare and low-frequency functional variants associated with circulating lipid levels.
New SNPs linked to inflammatory biomarkers in a highly admixed Brazilian population are identified, including a missense variant in an olfactory receptor gene linked to MCP-1, which may be biologically important for inflammation and could affect the risk of cardiometabolic diseases.
J. Leite, G. F. L. Pascoal, G. B. S. Duarte et al.· Frontiers in Immunology· 0 citations
BACKGROUND
Type 1 diabetes (T1D) is a common disease. Although genome-wide association studies (GWASs) have identified hundreds of associated single nucleotide polymorphisms (SNPs), very few T1D GWAS have simultaneously addressed both Asian and European populations.
METHODS
Here, we conducted a large-scale trans-ancestry meta-analysis including 680,539 European individuals (12,525 T1D cases and 668,014 controls) and 133,251 Asian individuals (1,219 T1D cases and 132,032 controls) to identify genetic associations with T1D. Subsequently, fine-mapping and Summary-data-based Mendelian randomization (SMR) analyses were performed to further refine T1D-related genetic signals.
RESULTS
We identified 27 T1D-associated loci, including 8 potentially novel loci (near CDKAL1, NRSN1, FAM65B, LRRC16A, TULP1, SLC17A3, LRIG2, C6orf1). Fine-mapping was performed and helped pinpoint 7 putative causal variants (posterior probability, PP > 0.95) with T1D. Among them, rs9366622 (PP = 0.976) and rs1165190 (PP = 0.996) are located near LRRC16A and SLC17A3, respectively. These two variants are the lead SNPs of identified novel loci. SMR analysis identified a putative risk gene (U91328.19) at the novel locus SLC17A3-rs1165190, whose expression level is causally associated with T1D.
CONCLUSIONS
These findings suggest that, for T1D, increasing ancestral diversity in genetic studies helps identify core genes and provides new insights into pathogenesis.
Genetic and clinical evidence is provided that specific selenoproteins are associated with a decreased risk of AD and highlight the potential role of these proteins in AD pathophysiology and suggest their promise as biomarkers or therapeutic targets, warranting further investigation.
Pei-Xin Jiang, Si-Bo Peng, Yan-Ling Huang et al.· Journal of Alzheimer's Disea...· 0 citations
Bladder cancer is the ninth most common cancer worldwide, caused by genetic and environmental risk factors. Here, we report the findings of a multi-population meta-analysis of genome-wide association studies, including 32,470 individuals with and 1,753,462 without bladder cancer. We identify 70 independent risk loci, of which 43 are novel. Using a 70-marker polygenic risk score (HR = 1.63 per standard deviation), we increase the area under the curve from 0.71 (baseline risk model) to 0.75. Integrative analyses reveal the enrichment of the associated variants within accessible chromatin regions, and of the prioritized genes within pathways for xenobiotic metabolism and smoking behavior. Specifically, we show that the 15q25.1 variant rs71581744-ACCCC/A co-localizes with tissue-specific CHRNA3 expression, modulates mRNA stability, and associates with risk of muscle-invasive bladder cancer among current smokers. Together, these findings substantially expand the known genetic architecture of bladder cancer risk and highlight the germline regulation of smoking behavior as a mechanism driving bladder cancer susceptibility. This study integrates genetic data from diverse populations to identify 70 loci linked to bladder cancer risk, including 43 novel, and uses experimental approaches to uncover how inherited variation influences this risk in the context of smoking.
L. Prokunina-Olsson, O. Flórez-Vargas, Michael G. Levin et al.· Nature Communications· 0 citations
The findings suggest that common LPA variation represented by the 15-SNV genetic score may contribute to T2D risk through mechanisms not fully captured by circulating Lp(a) concentration alone.
P. Corredoira, Daniel Bello Álvarez, Itziar Lamiquiz Moneo et al.· Cardiovascular Diabetology· 0 citations
Background Genome-wide aggregated trans-effects (GATE) analysis is a novel method in which trans-effects on gene expression (as transcript or protein) are combined with SNP-trait association data to identify core genes that directly influence the trait. The objective of this study was to identify core genes for blood pressure. Methods We undertook GWASs of mean arterial pressure (MAP) and and body mass index (BMI) in 373,882 individuals aged less than 60 in the Our Future Health (OFH) cohort. Using summary statistics from GWASs of circulating proteins on the SomaScan and Olink platforms, we tested for association of GATE scores (predicted levels of each protein based on trans-effects) with MAP. We confirmed replication of top associations in an independent cohort. Results The strongest GATE score association with MAP was for LPL (lipoprotein lipase). Higher genetically predicted circulating levels of LPL were associated with lower MAP but higher BMI. GATE scores for three other proteins involved in lipid handling – CD300LG, ADIPOQ, TIMP4 – were also associated with lower MAP but higher BMI. GATE scores for all four of these proteins were inversely associated with chylomicron triglyceride (measured as XXL-VLDL-TG by NMR spectroscopy). The associations of GATE scores for ANGPTL3 and ANGPTL4, which regulate LPL, were consistent with a causal role of LPL in lowering XXL-VLDL-TG and MAP. Conclusions These results point to a key role in hypertension for proteins that regulate post-prandial clearance of triglyceride-rich lipoproteins, independently of adiposity.
S. Braichenko, A. Iakovliev, Jay Dyer et al.· bioRxiv· 0 citations
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