LocusZoom: regional visualization of genome-wide association scan results

BioinformaticsPublished 15 July 2010Open access

Randall Pruim, Ryan Welch, Serena Sanna, Tanya M. Teslovich, Peter S. Chines, Terry P. Gliedt

DOI10.1093/bioinformatics/btq419

Source URL

Citations2,968

SJR quartileQ1

SJR score2.45

SNIP1.47

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TL;DR

LocusZoom is a web-based plotting tool that provides fast visual display of GWAS results in a publication-ready format that visually displays regional information such as the strength and extent of the association signal relative to genomic position, local linkage disequilibrium (LD) and recombination patterns and the positions of genes in the region.

Abstract

UNLABELLED: Genome-wide association studies (GWAS) have revealed hundreds of loci associated with common human genetic diseases and traits. We have developed a web-based plotting tool that provides fast visual display of GWAS results in a publication-ready format. LocusZoom visually displays regional information such as the strength and extent of the association signal relative to genomic position, local linkage disequilibrium (LD) and recombination patterns and the positions of genes in the region. AVAILABILITY: LocusZoom can be accessed from a web interface at http://csg.sph.umich.edu/locuszoom. Users may generate a single plot using a web form, or many plots using batch mode. The software utilizes LD information from HapMap Phase II (CEU, YRI and JPT+CHB) or 1000 Genomes (CEU) and gene information from the UCSC browser, and will accept SNP identifiers in dbSNP or 1000 Genomes format. Single plots are generated in approximately 20 s. Source code and associated databases are available for download and local installation, and full documentation is available online.

Keywords

Biochemistry, Genetics and Molecular Biology

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