Please use this identifier to cite or link to this item: https://doi.org/10.1371/journal.pone.0086761
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dc.titleArchiLD: Hierarchical visualization of linkage disequilibrium in human populations
dc.contributor.authorMelchiotti R.
dc.contributor.authorRötzschke O.
dc.contributor.authorPoidinger M.
dc.date.accessioned2019-11-05T02:04:48Z
dc.date.available2019-11-05T02:04:48Z
dc.date.issued2014
dc.identifier.citationMelchiotti R., Rötzschke O., Poidinger M. (2014). ArchiLD: Hierarchical visualization of linkage disequilibrium in human populations. PLoS ONE 9 (1) : e86761. ScholarBank@NUS Repository. https://doi.org/10.1371/journal.pone.0086761
dc.identifier.issn1932-6203
dc.identifier.urihttps://scholarbank.nus.edu.sg/handle/10635/161435
dc.description.abstractLinkage disequilibrium (LD) is an essential metric for selecting single-nucleotide polymorphisms (SNPs) to use in genetic studies and identifying causal variants from significant tag SNPs. The explosion in the number of polymorphisms that can now be genotyped by commercial arrays makes the interpretation of triangular correlation plots, commonly used for visualizing LD, extremely difficult in particular when large genomics regions need to be considered or when SNPs in perfect LD are not adjacent but scattered across a genomic region. We developed ArchiLD, a user-friendly graphical application for the hierarchical visualization of LD in human populations. The software provides a powerful framework for analyzing LD patterns with a particular focus on blocks of SNPs in perfect linkage as defined by r2. Thanks to its integration with the UCSC Genome Browser, LD plots can be easily overlapped with additional data on regulation, conservation and expression. ArchiLD is an intuitive solution for the visualization of LD across large or highly polymorphic genomic regions. Its ease of use and its integration with the UCSC Genome Browser annotation potential facilitates the interpretation of association results and enables a more informed selection of tag SNPs for genetic studies. © 2014 Melchiotti et al.
dc.sourceUnpaywall 20191101
dc.subjectArchiLD data base
dc.subjectarticle
dc.subjectcomputer program
dc.subjectdata base
dc.subjectgene control
dc.subjectgene expression
dc.subjectgene linkage disequilibrium
dc.subjectgenetic conservation
dc.subjectgenomics
dc.subjectgenotype
dc.subjecthuman
dc.subjectsingle nucleotide polymorphism
dc.subjectGenetic Linkage
dc.subjectGenome, Human
dc.subjectGenotype
dc.subjectHumans
dc.subjectLinkage Disequilibrium
dc.subjectPolymorphism, Single Nucleotide
dc.subjectSoftware
dc.typeArticle
dc.contributor.departmentBIOLOGY (NU)
dc.description.doi10.1371/journal.pone.0086761
dc.description.sourcetitlePLoS ONE
dc.description.volume9
dc.description.issue1
dc.description.pagee86761
dc.published.statePublished
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