Cited by 2,707Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and AnimalsBioinformatics and Genomic Networks

LocusZoom: regional visualization of genome-wide association scan results

Open access
Pruim, Randall J., Welch, Ryan P., Sanna, Serena, Teslovich, Tanya M., Chines, Peter S., Gliedt, Terry P., Boehnke, Michael, Abecasis, Gonçalo R. +1 more·2010·Bioinformatics

Abstract

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

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  • The Cox model has previously been shown to be applicable to case-control datasets without an elevated type 1 error rate or overestimation of effect sizes.

    “The Cox model has previously been shown to be applicable to case-control datasets without an elevated type 1 error rate nor overestimation in effect sizes73,74.”

    From A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease (2017) · cites this paper as [74]

    The Introduction and Implementation sections describe LocusZoom as a tool for visualizing genome-wide association results, not for evaluating Cox models. Searches for Cox models, case-control datasets, type I error, and effect-size overestimation found no passage addressing the claim. (LLM, conf=0.76)

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Authors
Pruim, R. J., Welch, R. P., Sanna, S., Teslovich, T. M., Chines, P. S., Gliedt, T. P., Boehnke, M., Abecasis, G. R., & Willer, C. J.
Affiliations
National Institutes of Health (US)
Corresponding author
Willer, Cristen J.
Venue
Bioinformatics
Published
2010-07-15
Volume
26
Issue
18
Pages
2336-2337
ISSN
  • 1367-4803 (ISSN-L)
  • 1367-4811
OpenAlex
W2163013660
Cited by
2,707
References
8
Citations by year
2026: 90 · 2025: 128 · 2024: 176 · 2023: 200 · 2022: 225 · 2021: 280 · 2020: 206 · 2019: 195 · 2018: 217 · 2017: 201 · 2016: 200 · 2015: 156 · 2014: 156 · 2013: 126 · 2012: 90
FWCI
49.06
Type
journal article
Language
en
Open access
Locations
  • Bioinformatics (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
  • University of Michigan
  • National Institutes of Health (5k99hl094535-02)
  • College of Pharmacy, University of Michigan
  • National Heart, Lung, and Blood Institute (K99-HL094535)
  • National Institute of Mental Health (MH084698, R01MH084698)
  • National Human Genome Research Institute (R56HG000376, HG005214, HG000040, R01HG002651, R01HG000376, U01HG005214, HG002651, HG000376, Z01HG000040, T32HG000040)
  • National Institute of Diabetes and Digestive and Kidney Diseases (U01DK062370, R56DK062370, DK-062370, R01DK062370)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Keywords
genome-wide association study, linkage disequilibrium, recombination, HapMap, 1000 Genomes Project, genome annotation, genetic loci
MeSH terms
Computer Graphics, Humans, Software, Internet, Genome-Wide Association Study

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