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Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_captureC]

ABSTRACT: We investigated whether intersecting functional genomic data (ATAC-seq + promoter focused Capture C) with increasingly powered publically available GWAS for Body Mass Index and Waist to Hip Ratio could identify additional true postiive subsignficant signals (5x10-8< P value < 5x10-4) without increasing the GWAS sample size

ORGANISM(S): Homo sapiens

PROVIDER: GSE164911 | GEO | 2021/01/16

REPOSITORIES: GEO

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Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_atacseq]

Project description:We investigated whether intersecting functional genomic data (ATAC-seq + promoter focused Capture C) with increasingly powered publically available GWAS for Body Mass Index and Waist to Hip Ratio could identify additional true postiive subsignficant signals (5x10-8< P value < 5x10-4) without increasing the GWAS sample size

2021-01-16 | GSE164745 | GEO

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci.

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-01-15 | GSE164912 | GEO

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci.

Project description:Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci.

| PRJNA692436 | ENA

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_atacseq]

Project description:Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_atacseq]

| PRJNA691887 | ENA

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_captureC]

Project description:Biological constraints on GWAS SNPs at suggestive significance thresholds reveal true BMI loci [hMSC_adipocytes_captureC]

| PRJNA692438 | ENA

Biological constraints on GWAS SNPs at suggestive significance thresholds reveal additional BMI loci.

Project description:To uncover novel significant association signals (p<5×10-8), genome-wide association studies (GWAS) requires increasingly larger sample sizes to overcome statistical correction for multiple testing. As an alternative, we aimed to identify associations among suggestive signals (5 × 10-8≤p<5×10-4) in increasingly powered GWAS efforts using chromatin accessibility and direct contact with gene promoters as biological constraints. We conducted retrospective analyses of three GIANT BMI GWAS efforts using ATAC-seq and promoter-focused Capture C data from human adipocytes and embryonic stem cell (ESC)-derived hypothalamic-like neurons. This approach, with its extremely low false-positive rate, identified 15 loci at p<5×10-5 in the 2010 GWAS, of which 13 achieved genome-wide significance by 2018, including at NAV1, MTIF3, and ADCY3. Eighty percent of constrained 2015 loci achieved genome-wide significance in 2018. We observed similar results in waist-to-hip ratio analyses. In conclusion, biological constraints on sub-significant GWAS signals can reveal potentially true-positive loci for further investigation in existing data sets without increasing sample size.

| S-EPMC7815306 | biostudies-literature

Open chromatin profiling in adipose tissue marks genomic regions with functional roles in cardiometabolic traits

Project description:Identifying the regulatory mechanisms of genome-wide association study (GWAS) loci affecting adipose tissue has been restricted due to limited characterization of adipose transcriptional regulatory elements. We profiled chromatin accessibility in three frozen human subcutaneous adipose tissue needle biopsies and preadipocytes and adipocytes from the Simpson Golabi-Behmel Syndrome (SGBS) cell strain using an assay for transposase-accessible chromatin (ATAC-seq). We identified 68,571 representative accessible chromatin regions (peaks) across adipose tissue samples (FDR<5%). GWAS loci for eight cardiometabolic traits were enriched in these peaks (p<0.005), with the strongest enrichment for waist-hip ratio. Of 110 recently described cardiometabolic GWAS loci colocalized with adipose tissue eQTLs, 59 loci had one or more variants overlapping an adipose tissue peak. Annotated variants at the SNX10 waist-hip ratio locus and the ATP2A1-SH2B1 body mass index locus showed allelic differences in regulatory assays. These adipose tissue accessible chromatin regions elucidate genetic variants that may alter adipose tissue function to impact cardiometabolic traits.

2019-01-01 | GSE110734 | GEO

Ethnic-specific BMI and waist circumference thresholds.

Project description:BMI and waist circumference (WC) are used to identify individuals with elevated obesity-related health risks. The current thresholds were derived largely in populations of European origin. This study determined optimal BMI and WC thresholds for the identification of cardiometabolic risk among white and African-American (AA) adults. The sample included 2096 white women, 1789 AA women, 1948 white men, and 643 AA men aged 18-64 years. Elevated cardiometabolic risk was defined as ≥2 risk factors (blood pressure ≥ 130/85 mm Hg; glucose ≥100 mg/dl; triglycerides ≥150 mg/dl; high-density lipoprotein-cholesterol <40 mg/dl (men) or <50 mg/dl (women)). Receiver Operating Characteristic (ROC) curves were used to identify optimal BMI and WC thresholds in each sex-by-ethnicity group. The optimal BMI thresholds were 30 kg/m2 in white women, 32.9 kg/m2 in AA women, 29.1 kg/m2 white men, and 30.4 kg/m2 in AA men, whereas optimal WC thresholds were 91.9 cm in white women, 96.8 cm in AA women, 99.4 in white men, and 99.1 cm in AA men. The sensitivities at the optimal thresholds ranged from 63.5 to 68.5% for BMI and 68.4 to 71.0% for WC and the specificities ranged from 64.2 to 68.8% for BMI and from 68.5 to 71.0% for WC, respectively. In general, the optimal BMI and WC thresholds approximated currently used thresholds in men and in white women. There are no apparent ethnic differences in men; however, in AA women the optimal BMI and WC values are ~3 kg/m2 and 5 cm higher than in white women.

| S-EPMC3933952 | biostudies-literature

Targeting postsynaptic glutamate receptor scaffolding proteins PSD-95 and PICK1 for obesity treatment

Project description:Human genome-wide association studies (GWAS) suggest a functional role for central glutamate receptor signaling and plasticity in body weight regulation. Here, we utilize UK Biobank GWAS summary statistics of body mass index (BMI) and body fat percentage (BF%) to identify genes encoding for proteins known to interact with postsynaptic AMPA and NMDA receptors. Loci in/near Discs Large Homolog 4 (DLG4) and protein interacting with C kinase 1 (PICK1) reached genome-wide significance (P<5x10-8) for BF% and/or BMI. To further evaluate the functional role of PSD-95 (gene name: DLG4) and PICK1 in energy homeostasis, we used dimeric PDZ-domain-targeting peptides of PSD-95 and PICK1 to demonstrate that pharmacological inhibition of PSD-95 and PICK1 induces prolonged weight-lowering effects in obese mice. Collectively, these data demonstrate that the glutamate receptor scaffolding proteins, PICK1 and PSD-95, are genetically linked to obesity and that pharmacological targeting of their PDZ domains represents a promising new therapeutic avenue for sustained weight loss.

2024-06-16 | PXD047515 | Pride

Evidence for correlations between BMI-associated SNPs and circRNAs.

Project description:Circular RNAs (circRNAs) are regulators of processes like adipogenesis. Their expression can be modulated by SNPs. We analysed links between BMI-associated SNPs and circRNAs. First, we detected an enrichment of BMI-associated SNPs on circRNA genomic loci in comparison to non-significant variants. Analysis of sex-stratified GWAS data revealed that circRNA genomic loci encompassed more genome-wide significant BMI-SNPs in females than in males. To explore whether the enrichment is restricted to BMI, we investigated nine additional GWAS studies. We showed an enrichment of trait-associated SNPs in circRNAs for four analysed phenotypes (body height, chronic kidney disease, anorexia nervosa and autism spectrum disorder). To analyse the influence of BMI-affecting SNPs on circRNA levels in vitro, we examined rs4752856 located on hsa_circ_0022025. The analysis of heterozygous individuals revealed an increased level of circRNA derived from the BMI-increasing SNP allele. We conclude that genetic variation may affect the BMI partly through circRNAs.

| S-EPMC9314347 | biostudies-literature

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