Please use this identifier to cite or link to this item:
Title: ArchiLD: Hierarchical visualization of linkage disequilibrium in human populations
Authors: Melchiotti R.
Rötzschke O.
Poidinger M. 
Keywords: ArchiLD data base
computer program
data base
gene control
gene expression
gene linkage disequilibrium
genetic conservation
single nucleotide polymorphism
Genetic Linkage
Genome, Human
Linkage Disequilibrium
Polymorphism, Single Nucleotide
Issue Date: 2014
Citation: Melchiotti R., Rötzschke O., Poidinger M. (2014). ArchiLD: Hierarchical visualization of linkage disequilibrium in human populations. PLoS ONE 9 (1) : e86761. ScholarBank@NUS Repository.
Rights: Attribution 4.0 International
Abstract: Linkage 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.
Source Title: PLoS ONE
ISSN: 1932-6203
DOI: 10.1371/journal.pone.0086761
Rights: Attribution 4.0 International
Appears in Collections:Staff Publications

Show full item record
Files in This Item:
File Description SizeFormatAccess SettingsVersion 
10_1371_journal_pone_0086761.pdf4.83 MBAdobe PDF




checked on Jan 20, 2021

Page view(s)

checked on Jan 15, 2021

Google ScholarTM



This item is licensed under a Creative Commons License Creative Commons