Prioritization of Cancer-Related Genomic Variants by SNP Association Network

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dc.contributor.ORCID0000-0001-9344-8493 (Xuan, Z)en_US
dc.contributor.authorLiu, Changningen_US
dc.contributor.authorXuan, Zhenyuen_US
dc.contributor.utdAuthorXuan, Zhenyuen_US
dc.date.accessioned2015-09-01T19:19:59Z
dc.date.available2015-09-01T19:19:59Z
dc.date.created2015-04-01en_US
dc.date.issued2015-04-01en_US
dc.description.abstractWe have developed a general framework to construct an association network of single nucleotide polymorphisms (SNPs) (SNP association network, SAN) based on the functional interactions of genes located in the flanking regions of SNPs. SAN, which was constructed based on protein-protein interactions in the Human Protein Reference Database (HPRD), showed significantly enriched signals in both linkage disequilibrium (LD) and long-range chromatin interaction (Hi-C). We used this network to further develop two methods for predicting and prioritizing disease-associated genes from genome-wide association studies (GWASs). We found that random walk with restart (RWR) using SAN (RWR-SAN) can greatly improve the prediction of lung-cancer-associated genes by comparing RWR with the use of network in HPRD (AUC 0.81 vs 0.66). In a reanalysis of the GWAS dataset of age-related macular degeneration (AMD), SAN could identify more potential AMD-associated genes that were previously ranked lower in the GWAS study. The interactions in SAN could facilitate the study of complex diseases.en_US
dc.identifier.bibliographicCitationLiu, Changning, and Zhenyu Xuan. 2015. "Prioritization of cancer-related genomic variants by SNP association network." Cancer Informatics 14: 57-70.en_US
dc.identifier.issn1176-9351en_US
dc.identifier.urihttp://hdl.handle.net/10735.1/4587
dc.identifier.volume14en_US
dc.publisherLibertas Academicaen_US
dc.relation.urihttp://dx.doi.org/10.4137/CIN.S17288
dc.rightsCC BY-NC 3.0 (Attribution-NonCommercial)en_US
dc.rights©2015 The Authorsen_US
dc.rights.urihttp://creativecommons.org/licenses/by-nc/3.0/en_US
dc.sourceCancer Informatics
dc.subjectGenome-Wide Association Studyen_US
dc.subjectProtein Interaction Mapsen_US
dc.subjectRandom walks (Mathematics)en_US
dc.subjectSingle Nucleotide Polymorphismsen_US
dc.titlePrioritization of Cancer-Related Genomic Variants by SNP Association Networken_US
dc.type.genreArticleen_US

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Xuan, Zhenyu
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