Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors.

ABSTRACT:

Background

Large-scale genome-wide association studies (GWAS) have implicated thousands of germline genetic variants in modulating individuals' risk to various diseases, including cancer. At least 25 risk loci have been identified for low-grade gliomas (LGGs), but their molecular functions remain largely unknown.

Methods

We hypothesized that GWAS loci contain causal single nucleotide polymorphisms (SNPs) that reside in accessible open chromatin regions and modulate the expression of target genes by perturbing the binding affinity of transcription factors (TFs). We performed an integrative analysis of genomic and epigenomic data from The Cancer Genome Atlas and other public repositories to identify candidate causal SNPs within linkage disequilibrium blocks of LGG GWAS loci. W

SUBMITTER: Manjunath M 

PROVIDER: S-EPMC8041333 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature