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LocusFocus

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Application of the Simple Sum method for testing co-localization of GWAS with any other SNP-level data (e.g. eQTL data)

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# LocusFocus

# This project has moved. Please visit https://github.com/strug-hub/LocusFocus/ for the latest version of LocusFocus.

## Explore GWAS Results with GTEx's eQTL Association Results

This web application is to enable the exploration and annotation of GWAS results to assess what gene and tissue are the most probable candidates for the GWAS signal via integration with [GTEx eQTL association results](https://gtexportal.org/home/) into a single interactive plot, and application of the [Simple Sum method](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008007) to visualize the results in a heatmap plot.

In addition, users may upload other datasets to test colocalization with. For example, other phenotypic associations (i.e. PheWAS) may be uploaded for assessing pleiotropy, or eQTL data from other sources to obtain a formal colocalization test and visualization of the data.

LD information is calculated using PLINK on the 1000 Genomes Project to enable viewing of LD given a lead SNP. The default lead SNP is the top SNP.

eQTL association results have been stored locally in a MongoDB database.

Full documentation is available at https://locusfocus.readthedocs.io.  
The application may be accessed at https://locusfocus.research.sickkids.ca.

## SS2 Extension Functions

For R functions that extend the Simple Sum functionality as described in the [SS2 paper]("https://") (e.g. the computation of an LD matrix for a meta-analysis study) by Wang et al., you may refer to the [SimpleSum2Colocalization](https://github.com/FanWang0216/SimpleSum2Colocalization) GitHub repository. The SS2 implementation in the current LocusFocus [web application](https://locusfocus.research.sickkids.ca) is via the [getSimpleSumStats.R](https://github.com/naim-panjwani/LocusFocus/blob/master/getSimpleSumStats.R) script, and applies the two stages described in [the SS2 paper]("https://").

LocusFocus

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