How to Select Tag SNPs in Genetic Association Studies? The CLONTagger Method with Parameter Optimization
dc.contributor.author | Ilhan, Ilhan | |
dc.contributor.author | Tezel, Gulay | |
dc.date.accessioned | 2020-03-26T18:42:07Z | |
dc.date.available | 2020-03-26T18:42:07Z | |
dc.date.issued | 2013 | |
dc.department | Selçuk Üniversitesi | en_US |
dc.description.abstract | Selection of genetic variants is a crucial first step in the rational design of studies aimed at explaining individual differences in susceptibility to complex human diseases or health intervention outcomes; for example, in the emerging fields of pharmacogenomics, nutrigenomics, and vaccinomics. While single nucleotide polymorphisms (SNPs) are frequently employed in these studies, the cost of genotyping a huge number of SNPs remains a limiting factor, particularly in low and middle income countries. Therefore, it is important to detect a subset of SNPs to represent the rest of SNPs with maximum possible accuracy. The present study introduces a new method, CLONTagger with parameter optimization, which uses Support Vector Machine (SVM) to predict the rest of SNPs and Clonal Selection Algorithm (CLONALG) to select tag SNPs. Furthermore, the Particle Swarm Optimization algorithm is preferred for the optimization of C and gamma parameters of the Support Vector Machine. Additionally, using many datasets, we compared the proposed new method with the tag SNP selection algorithms present in literature. Our results suggest that the CLONTagger with parameter optimization can identify tag SNPs with better prediction accuracy than other methods. Application-oriented studies are warranted to evaluate the utility of this method in future research in human genetics and study of the genetic components of variable responses to drugs, nutrition, and vaccines. | en_US |
dc.description.sponsorship | Selcuk University Scientific Research Projects Coordinatorship, Konya, TurkeySelcuk University | en_US |
dc.description.sponsorship | This study is supported by Selcuk University Scientific Research Projects Coordinatorship, Konya, Turkey. The authors would like to thank the OMICS editors and anonymous reviewers of this manuscript for their very helpful suggestions and constructive critique. | en_US |
dc.identifier.doi | 10.1089/omi.2012.0100 | en_US |
dc.identifier.endpage | 383 | en_US |
dc.identifier.issn | 1536-2310 | en_US |
dc.identifier.issn | 1557-8100 | en_US |
dc.identifier.issue | 7 | en_US |
dc.identifier.pmid | 23758474 | en_US |
dc.identifier.scopusquality | Q2 | en_US |
dc.identifier.startpage | 368 | en_US |
dc.identifier.uri | https://dx.doi.org/10.1089/omi.2012.0100 | |
dc.identifier.uri | https://hdl.handle.net/20.500.12395/29556 | |
dc.identifier.volume | 17 | en_US |
dc.identifier.wos | WOS:000321624500002 | en_US |
dc.identifier.wosquality | Q2 | en_US |
dc.indekslendigikaynak | Web of Science | en_US |
dc.indekslendigikaynak | Scopus | en_US |
dc.indekslendigikaynak | PubMed | en_US |
dc.language.iso | en | en_US |
dc.publisher | MARY ANN LIEBERT, INC | en_US |
dc.relation.ispartof | OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY | en_US |
dc.relation.publicationcategory | Makale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı | en_US |
dc.rights | info:eu-repo/semantics/closedAccess | en_US |
dc.selcuk | 20240510_oaig | en_US |
dc.title | How to Select Tag SNPs in Genetic Association Studies? The CLONTagger Method with Parameter Optimization | en_US |
dc.type | Article | en_US |