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Bioinformatics. 2018 Mar 1;34(5):887-889. doi: 10.1093/bioinformatics/btx561.

LDassoc: an online tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation.

Abstract

Motivation:

Existing approaches to plot association results from genome-wide association studies (GWAS) are in the form of static Manhattan plots and often lack data integration with rich databases on variant regulatory potential as well as population-specific linkage disequilibrium patterns.

Summary:

We created an intuitive web module for uploading and efficiently exploring GWAS association results. Interactive plots and sortable tables allow researchers to query genomic regions of interest, facilitating the integration of data on linkage disequilibrium, variant regulatory potential and potential target genes. External links allow for visualization of association results in the UCSC genome browser as well as easy access to publically available databases (e.g. dbSNP and RegulomeDB). Through improved visualization and data integration, LDassoc offers genomic researchers a specialized environment to examine association signals and suggests variants for functional investigation.

Availability and implementation:

LDassoc is a free and publically available web tool which can be accessed online at https://analysistools.nci.nih.gov/LDlink/? tab=ldassoc.

Contact:

mitchell.machiela@nih.gov.

PMID:
28968746
PMCID:
PMC6030966
DOI:
10.1093/bioinformatics/btx561
[Indexed for MEDLINE]
Free PMC Article

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