ArticlePeerJ2014
Associating disease-related genetic variants in intergenic regions to the genes they impact.
Article in PeerJ, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Associations of Genetic Variants at Nongenic Susceptibility Loci with Breast Cancer Risk and Heterogeneity by Tumor Subtype in Southern Han Chinese Women.BioMed research international · 2016Trial
- Genomic architecture of insertion-deletion (indel) variants in beetal goats of India.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Article
- eMIC-AntiKP: Estimating minimum inhibitory concentrations of antibiotics towardsComputational and structural biotechnology journal · 2023Article
- GCNCDA: A new method for predicting circRNA-disease associations based on Graph Convolutional Network Algorithm.PLoS computational biology · 2020Article
- The rs13388259 Intergenic Polymorphism in the Genomic Context of theParkinson's disease · 2018Article
- Semantic prioritization of novel causative genomic variants.PLoS computational biology · 2017Article
- Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine.PLoS computational biology · 2016Article
- Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.Briefings in bioinformatics · 2016Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a method to assist in interpretation of the functional impact of intergenic disease-associated SNPs that is not limited to search strategies proximal to the SNP. The method builds on two sources of external knowledge: the growing understanding of three-dimensional spatial relationships in the genome, and the substantial repository of information about relationships among genetic variants, genes, and diseases captured in the published biomedical literature. We integrate chromatin conformation capture data (HiC) with literature support to rank putative target genes of intergenic disease-associated SNPs. We demonstrate that this hybrid method outperforms a genomic distance baseline on a small test set of expression quantitative trait loci, as well as either method individually. In addition, we show the potential for this method to uncover relationships between intergenic SNPs and target genes across chromosomes. With more extensive chromatin conformation capture data becoming readily available, this method provides a way forward towards functional interpretation of SNPs in the context of the three dimensional structure of the genome in the nucleus.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.