Related Experiment Video
Updated: May 8, 2026

Generation of High Quality Chromatin Immunoprecipitation DNA Template for High-throughput Sequencing (ChIP-seq)
Published on: April 19, 2013
Secondary analysis of publicly available data reveals superoxide and oxygen radical pathways are enriched for
Mojgan Yazdanpanah1, Chuhua Chen, Jinko Graham
1British Columbia Clinical Genomics Network, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada; Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada.
Abstract:
Genome-wide association studies explain at most 5%-10% of the heritable components of type 2 diabetes. Some of the "missing type 2 diabetes heritability" could be explained by low-frequency variants. We examined the associations between low-frequency variants and type 2 diabetes, using data from 2538 diabetic and 2977 nondiabetic subjects in the publicly available database of Genotypes and Phenotypes. We applied two approaches. First, we combined information from all low-frequency (1%-5%) variants at a locus in a gene-centric analysis of associations with diabetes. Next, we searched for gene ontology (GO) biological processes that were enriched for gene-centric associations, after correcting for multiple testing to control the false discovery rate (FDR). We found three GO biological processes that were significantly enriched for associations to diabetes: "response to superoxide" (FDR-adjusted p=2.7×10(-3)), "response to oxygen radical" (FDR-adjusted p=2.7×10(-3)), and "heart contraction" (FDR-adjusted p=2.6×10(-2)). There were three genes that contributed to "response to superoxide" and "oxygen radical" pathways, including the SOD1 gene. Gene-centric tests of association with low-frequency variants, followed by analysis to evaluate which biological pathways are enriched for these associations has the potential to recover, at least some proportion of, the "missing heritability" of type 2 diabetes.
More Related Videos
Related Concept Videos
Type II Diabetes I: Introduction
Type II Diabetes II: Pathophysiology
Type I Diabetes II: Pathophysiology
Diabetes Mellitus: Type 2 and Gestational
Genome-wide Association Studies-GWAS
GWAS does not require the identification of the target gene involved in...
Single Nucleotide Polymorphisms-SNPs

