ArticleBioinformatics (Oxford, England)2016
ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 34 citations in OpenAlex.
- Data simulation to optimize frameworks for genome-wide association studies in diverse populations.Frontiers in genetics · 2025Article
- Whole genome sequencing reveals population diversity and variation in HIV-1 specific host genes.Frontiers in genetics · 2023Article
- Dissecting Generalizability and Actionability of Disease-Associated Genes From 20 Worldwide Ethnolinguistic Cultural Groups.Frontiers in genetics · 2022Article
- Dissecting Meta-Analysis in GWAS Era: Bayesian Framework for Gene/Subnetwork-Specific Meta-Analysis.Frontiers in genetics · 2022Article
- Article
- Insilico Functional Analysis of Genome-Wide Dataset From 17,000 Individuals Identifies Candidate Malaria Resistance Genes Enriched in Malaria Pathogenic Pathways.Frontiers in genetics · 2021Article
- Genetic modifiers of long-term survival in sickle cell anemia.Clinical and translational medicine · 2020Article
- Identifying genetic variants and pathways associated with extreme levels of fetal hemoglobin in sickle cell disease in Tanzania.BMC medical genetics · 2020Article
- Genome-wide association studies of severe P. falciparum malaria susceptibility: progress, pitfalls and prospects.BMC medical genomics · 2019Review
- Exome-wide search and functional annotation of genes associated in patients with severe tick-borne encephalitis in a Russian population.BMC medical genomics · 2019Article
- Post genome-wide association analysis: dissecting computational pathway/network-based approaches.Briefings in bioinformatics · 2019Review
- Human ancestry indentification under resource constraints -- what can one chromosome tell us about human biogeographical ancestry?BMC medical genomics · 2018Article
- Host and Microbiome Genome-Wide Association Studies: Current State and Challenges.Frontiers in genetics · 2018Review
- Development of Bioinformatics Infrastructure for Genomics Research.Global heart · 2017Review
- A Genomic and Protein-Protein Interaction Analyses of Nonsyndromic Hearing Impairment in Cameroon Using Targeted Genomic Enrichment and Massively Parallel Sequencing.Omics : a journal of integrative biology · 2017Article
- A post-GWAS analysis of predicted regulatory variants and tuberculosis susceptibility.PloS one · 2017Article
- Biological Networks for Cancer Candidate Biomarkers Discovery.Cancer informatics · 2016Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
motivationDespite numerous successful Genome-wide Association Studies (GWAS), detecting variants that have low disease risk still poses a challenge. GWAS may miss disease genes with weak genetic effects or strong epistatic effects due to the single-marker testing approach commonly used. GWAS may thus generate false negative or inconclusive results, suggesting the need for novel methods to combine effects of single nucleotide polymorphisms within a gene to increase the likelihood of fully characterizing the susceptibility gene.
resultsWe developed ancGWAS, an algebraic graph-based centrality measure that accounts for linkage disequilibrium in identifying significant disease sub-networks by integrating the association signal from GWAS data sets into the human protein-protein interaction (PPI) network. We validated ancGWAS using an association study result from a breast cancer data set and the simulation of interactive disease loci in the simulation of a complex admixed population, as well as pathway-based GWAS simulation. This new approach holds promise for deconvoluting the interactions between genes underlying the pathogenesis of complex diseases. Results obtained yield a novel central breast cancer sub-network of the human interactome implicated in the proteoglycan syndecan-mediated signaling events pathway which is known to play a major role in mesenchymal tumor cell proliferation, thus providing further insights into breast cancer pathogenesis. AVAILABILITY AND IMPLEMENTATION: The ancGWAS package and documents are available at http://www.cbio.uct.ac.za/~emile/software.html.
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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.