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Transcriptome-wide association study to identify susceptibility genes for colorectal cancer

ABSTRACT: Transcriptome-wide association study to identify susceptibility genes for colorectal cancer

PROVIDER: PRJNA807048 | ENA |

REPOSITORIES: ENA

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Transcriptome-wide association study to identify susceptibility genes for colorectal cancer

Project description:Transcriptome-wide association study to identify susceptibility genes for colorectal cancer

| PRJNA807047 | ENA

An Exome-Wide Association Study Identifies New Susceptibility Loci for the Risk of Nicotine Dependence in African-American Populations

Project description:Cigarette smoking is one of the largest causes of preventable death worldwide. Smoking behaviors, including age at smoking initiation (ASI), smoking dependence (SD), and smoking cessation (SC), are all complex phenotypes determined by both genetic and environmental factors as well as their interactions. To identify susceptibility loci for each smoking phenotype, numerous studies have been conducted, with approaches including genome-wide linkage scans, candidate gene-based association analysis, and genome-wide association study (GWAS). Therefore, we conducted an exome-wide association study to identify new susceptibility loci for the risk of nicotine dependence in African-American populations.

2020-04-10 | GSE148375 | GEO

An Exome-Wide Association Study Identifies New Susceptibility Loci for the Risk of Nicotine Dependence in European-American Populations

2020-04-18 | GSE148812 | GEO

Epigenome-wide Association Study of Obesity Susceptibility in Human Twins

Project description:Epigenome-wide Association Study of Obesity Susceptibility in Human Twins

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Integrative genomic analyses revealed colorectal cancer susceptibility genes in risk loci identified in genome-wide association studies

Project description:Genome-wide association studies (GWAS) have identified approximately 50 loci associated with colorectal cancer (CRC) risk. However, the target genes and underlying mechanisms are largely unknown. We conducted a cis-expression quantitative trait loci (cis-eQTL) analysis using data from the Genotype-Tissue Expression (GTEx), The Cancer Genome Atlas (TCGA), and the Colonomics projects. We identified 24 putative target genes for 17 index SNPs at Benjamini-Hochberg adjusted P < 0.05 in at least one of the datasets. By analyzing functional genomic data, our result further indicated that 18 genes (75%) showed evidence of cis-regulation by putative functional SNPs via promoter or enhancer-promoter interactions. We next performed in vitro functional assays for three genes, TMBIM1, AAMP, and CABLES2, and confirmed that they play a vital role in colorectal carcinogenesis via disruption of cell behavior. Furthermore, our results indicate that silencing CABLES2 can promote the PI3K/AKT pathway. Our study reveals new candidate susceptibility genes and provides novel insight into the biological mechanisms for CRC development.

2018-10-23 | GSE121553 | GEO

Enhancer RNA transcriptomics-wide association study reveals an atlas of pan-cancer susceptibility eRNAs

Project description:Increasing evidence has demonstrated that enhancer RNAs (eRNAs) play essential roles in human diseases. However, the complete identification of disease-related subsets of eRNAs remains a major challenge. Here, we construct an atlas of common and rare genetic variants influencing the expression of enhancer RNAs across 49 human tissues. We identify 11,757 eRNA quantitative trait loci (eRNA-QTLs) associated with the expression of 89.75% annotated eRNAs. Mechanically, eRNA-QTLs frequently altered the binding motifs of transcription factors and were further experimentally validated by CRISPR-based base editing. We also observed that 28.48% of cancer signals were co-localized with eRNA-QTLs. Utilizing our newly developed eRNA transcriptome-wide association study (eRNA-TWAS) model, we have effectively identified 259 cancer susceptibility eRNAs spanning 23 distinct cancer types. Notably, among the identified eRNAs, these eRNA-linked cancer susceptibility genes exhibit significant dependence across various cancer cell lines. Interestingly, cancer risk can be significantly influenced by rare functional variants that are linked to eRNAs with transcriptomic outliers. Additionally, we develop a comprehensive and flexible data portal for exploring the genetic underpinnings of eRNAs. Overall, this study reveals a systematic landscape of genetic dependencies on eRNAs across pan-cancers and significantly expands the pool of disease-associated eRNAs.

2025-02-13 | GSE242322 | GEO

Epigenome-wide Association Study of Obesity Susceptibility in Human Twins

Project description:The purpose of the current study was to use an epigenome-wide association approach (EWAS) to identify a potential DNA methylation alterations associated with obesity using twins discordant on obesity status. Buccal cells (from a cheek swab) were used as a purified marker cell for the epigenetic analysis. Analysis of differential DNA methylation regions (DMRs) was used to identify epigenetic associations with metabolic and dietary measures in obesity parameters discordant twins. An edgeR analysis provided a DMR signature with p<1e-04, but a false discovery rate analysis demonstrated a lack of significance due to low sample size and known multivariant origins of obesity.

2023-02-18 | GSE218363 | GEO

Integrative genomic analyses revealed colorectal cancer susceptibility genes in risk loci identified in genome-wide association studies

Project description:Integrative genomic analyses revealed colorectal cancer susceptibility genes in risk loci identified in genome-wide association studies

| PRJNA497782 | ENA

Genome-Wide Association and Transcriptome-Wide Association Studies Identify Novel Susceptibility Genes Contributing to Colorectal Cancer.

Project description:BackgroundColorectal cancer (CRC) is among the most common cancers diagnosed worldwide. Although genome-wide association studies have effectively identified the genetic basis of CRC, there is still unexplained variability in genetic risk. Transcriptome-wide association studies (TWAS) integrate summary statistics from CRC genome-wide association studies (GWAS) with gene expression data to prioritize these GWAS findings and uncover additional gene-trait correlations.MethodsFirst, we carried out a post-GWAS analysis using summary statistics from a large-scale GWAS of CRC (n = 4,562 cases, n = 382,756 controls). Second, combined with the expression weight sets from GTEx (v7), susceptibility genes were identified with the FUSION software. Colocalization, conditional and fine-mapping analyses, phenome-wide association study (pheWAS), and Mendelian randomization were employed to further characterize the observed correlations.ResultsIn the post-GWAS analyses, we first identified new genome-wide significant associations: three genomic risk loci were identified at 8q24.21 (rs6983267, P = 6.98 × 10-12), 15q13.3 (rs58658771, P = 1.40 × 10-10), and 18q21.1 (rs6507874, P = 1.91 × 10-14). In addition, the TWAS also identified four loci statistically significantly associated with CRC risk, largely explained by expression regulation, including six candidate genes (DUSP10, POU5F1B, C11orf53, COLCA1, COLCA2, and GREM1-AS1). We further discovered evidence that low expression of COLCA2 is correlated with CRC risk with Mendelian randomization.ConclusionsWe discovered novel CRC risk loci and candidate functional genes by merging gene expression and GWAS summary data, offering new insight into the molecular processes underlying CRC development. This makes it easier to prioritize potential genes for follow-up functional research in CRC.

| S-EPMC9270168 | biostudies-literature

Enhancer RNA transcriptomics-wide association study reveals an atlas of pan-cancer susceptibility eRNAs

Project description:Enhancer RNA transcriptomics-wide association study reveals an atlas of pan-cancer susceptibility eRNAs

| PRJNA1013097 | ENA