LocusZoom: regional visualization of genome-wide association scan results

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 informatio...

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Bibliographic Details
Published in:Bioinformatics Vol. 26; no. 18; pp. 2336 - 2337
Main Authors: Pruim, Randall J., Welch, Ryan P., Sanna, Serena, Teslovich, Tanya M., Chines, Peter S., Gliedt, Terry P., Boehnke, Michael, Abecasis, Gonçalo R., Willer, Cristen J.
Format: Journal Article
Language:English
Published: Oxford Oxford University Press 15.09.2010
Subjects:
Applications Note
Biological and medical sciences
Computer Graphics
Fundamental and applied biological sciences. Psychology
General aspects
Genome-Wide Association Study
Humans
Internet
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Software
Genome
Visualization
ISSN:1367-4803, 1367-4811, 1460-2059, 1367-4811
Online Access:Get full text
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Summary: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 ∼20 s. Source code and associated databases are available for download and local installation, and full documentation is available online. Contact: cristen@umich.edu
Bibliography:The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
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To whom correspondence should be addressed.
istex:53181865CA683FFB8881D869855273169295D1BE
ArticleID:btq419
ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
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Associate Editor: Dmitrij Frishman
ISSN:1367-4803
1367-4811
1460-2059
1367-4811
DOI:10.1093/bioinformatics/btq419