ArticlePloS one2015
In-silico analysis of inflammatory bowel disease (IBD) GWAS loci to novel connections.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 29 citations in OpenAlex.
- Next-generation non-animal models for inflammatory bowel disease:NAM journal · 2025Review
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- The Role of Ryanodine Receptor 2 Polymorphisms in Oral Squamous Cell Carcinoma Susceptibility and Clinicopathological Features.International journal of molecular sciences · 2024Article
- A broken network of susceptibility genes in the monocytes of Crohn's disease patients.Life science alliance · 2024Article
- Unveiling the Genetic Complexity of Teratozoospermia: Integrated Genomic Analysis Reveals Novel Insights into lncRNAs' Role in Male Infertility.International journal of molecular sciences · 2023Article
- Genotype-protein phenotype characterization ofFrontiers in medicine · 2022Article
- Genome-wide prioritization reveals novel gene signatures associated with cardiotoxic effects of tyrosine kinase inhibitors.Oncology letters · 2021Article
- Epigenome-metabolome-microbiome axis in health and IBD.Current opinion in microbiology · 2020Review
- pCADD: SNV prioritisation in Sus scrofa.Genetics, selection, evolution : GSE · 2020Article
- Mucosal Metabolomic Profiling and Pathway Analysis Reveal the Metabolic Signature of Ulcerative Colitis.Metabolites · 2019Article
- REVEL and BayesDel outperform other in silico meta-predictors for clinical variant classification.Scientific reports · 2019Article
- Differential genetic and functional background in inflammatory bowel disease phenotypes of a Greek population: a systems bioinformatics approach.Gut pathogens · 2019Article
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- The evidence for fungus in Crohn's disease pathogenesis.Clinical journal of gastroenterology · 2018Review
- Functional relevance for central cornea thickness-associated genetic variants by using integrative analyses.BioData mining · 2018Article
- Computational Protein Phenotype Characterization of IL10RA Mutations Causative to Early Onset Inflammatory Bowel Disease (IBD).Frontiers in genetics · 2018Article
- Insights into the pathogenesis of ulcerative colitis from a murine model of stasis-induced dysbiosis, colonic metaplasia, and genetic susceptibility.American journal of physiology. Gastrointestinal and liver physiology · 2016Article
- Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-wide association studies (GWASs) for many complex diseases, including inflammatory bowel disease (IBD), produced hundreds of disease-associated loci-the majority of which are noncoding. The number of GWAS loci is increasing very rapidly, but the process of translating single nucleotide polymorphisms (SNPs) from these loci to genomic medicine is lagging. In this study, we investigated 4,734 variants from 152 IBD associated GWAS loci (IBD associated 152 lead noncoding SNPs identified from pooled GWAS results + 4,582 variants in strong linkage-disequilibrium (LD) (r2 ≥0.8) for EUR population of 1K Genomes Project) using four publicly available bioinformatics tools, e.g. dbPSHP, CADD, GWAVA, and RegulomeDB, to annotate and prioritize putative regulatory variants. Of the 152 lead noncoding SNPs, around 11% are under strong negative selection (GERP++ RS ≥2); and ~30% are under balancing selection (Tajima's D score >2) in CEU population (1K Genomes Project)--though these regions are positively selected (GERP++ RS <0) in mammalian evolution. The analysis of 4,734 variants using three integrative annotation tools produced 929 putative functional SNPs, of which 18 SNPs (from 15 GWAS loci) are in concordance with all three classifiers. These prioritized noncoding SNPs may contribute to IBD pathogenesis by dysregulating the expression of nearby genes. This study showed the usefulness of integrative annotation for prioritizing fewer functional variants from a large number of GWAS markers.
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