LocusTrack: Integrated visualization of GWAS results and genomic annotation

Source Code for Biology and Medicine
Gabriel Cuellar-PartidaStuart Macgregor

Abstract

Genome-wide association studies (GWAS) are an important tool for the mapping of complex traits and diseases. Visual inspection of genomic annotations may be used to generate insights into the biological mechanisms underlying GWAS-identified loci. We developed LocusTrack, a web-based application that annotates and creates plots of regional GWAS results and incorporates user-specified tracks that display annotations such as linkage disequilibrium (LD), phylogenetic conservation, chromatin state, and other genomic and regulatory elements. Currently, LocusTrack can integrate annotation tracks from the UCSC genome-browser as well as from any tracks provided by the user. LocusTrack is an easy-to-use application and can be accessed at the following URL: http://gump.qimr.edu.au/general/gabrieC/LocusTrack/. Users can upload and manage GWAS results and select from and/or provide annotation tracks using simple and intuitive menus. LocusTrack scripts and associated data can be downloaded from the website and run locally.

References

Apr 10, 2008·Nature Reviews. Genetics·Mark I McCarthyJoel N Hirschhorn
Nov 1, 2008·Bioinformatics·Andrew D JohnsonPaul I W de Bakker
May 27, 2009·Bioinformatics·Michael LawrenceVincent Carey
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Apr 8, 2014·American Journal of Human Genetics·Joseph K Pickrell

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Citations

Mar 30, 2016·American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics·Erlend J BrevikTetyana Zayats
Jun 7, 2015·Human Molecular Genetics·Gabriel Cuellar-PartidaDavid A Mackey
Oct 26, 2016·Molecular Biology and Evolution·Jullien M FlynnMelania E Cristescu
Jan 18, 2017·Nature Communications·Derrek P HibarM Arfan Ikram
Dec 1, 2017·Nature Communications·Kyoko WatanabeDanielle Posthuma
Mar 15, 2018·Medicine and Science in Sports and Exercise·Xiaochen LinSimin Liu
Sep 26, 2015·PLoS Genetics·Anu LoukolaJaakko Kaprio
Sep 12, 2017·Translational Psychiatry·R GuptaA Loukola
Dec 21, 2019·Bioinformatics·Gittu GeorgeAlex S F Doney
Sep 21, 2019·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Masahiko KumagaiTakeshi Itoh
Nov 7, 2019·Biomechanics and Modeling in Mechanobiology·Giorgio DavicoChristopher P Carty
Mar 7, 2021·Gastroenterology·Rosanna AsseltaPietro Invernizzi

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Software Mentioned

PLINK
SNAP
LocusZoom
UCSC browser
LocusTrack
plot
Bioconductor
R
UCSC genome browser
rtracklayer

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