Documentation for LocusFocus¶
LocusFocus is a web application to facilitate the exploration of a GWAS signal at a particular locus of the genome and its degree of colocalization with any SNP-level association data (e.g. expression quantitative trait loci for genes within +/- 1Mbp in the relevant GTEx tissues selected).
When paired with GTEx data, the aim is to annotate a GWAS (or region-based association) to the most probable gene(s) and tissue(s) that may be driving the observed GWAS signal.
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.
The Simple Sum method is used for assessing the degree of colocalization of any two given datasets. When applied to GTEx, LocusFocus presents the degree of colocalization of genes nearby the GWAS association for all the tissues selected in an interactive heatmap plot.
COLOC2 colocalization testing is also available, and more colocalization methods may be made available in future version releases.
- Quick Start
- Selecting the human coordinate system
- Primary dataset input
- Selecting an LD matrix
- Secondary datasets
- Some important points to consider
- Retrieving a Previous Session
- Example Run, Usage and Interpretation
- Sample Data and Output
- Selecting LD (Linkage Disequilibrium)
- Selecting Secondary Datasets from GTEx
- Selecting Genes of Interest for Colocalization Testing
- Overriding the First-Stage Set-Based P-value Threshold
- Saving and Retrieving Your Session
- Interpreting Data Output
- Local installation of LocusFocus
- MIT License
- Future Directions