WGAViewer

WGAViewer performs post-whole genome association analysis by automatically annotating, visualizing, and interpreting P-values to identify candidate genetic variants and genomic regions for follow-up.

Key Features:

• Automatic Annotation: Automatically annotates SNPs and genomic loci with functional information and association statistics from WGA studies.
• Visualization Capabilities: Generates visual representations of P-values and genomic context to display relationships and potential functional mechanisms.
• Interpretation Assistance: Highlights possible links between polymorphisms and gene expression to aid biological interpretation of associations.
• Hypothesis Generation: Supports formulation of hypotheses about the biological relevance of genetic variants based on annotated associations.
• Identification of Biologically Relevant Associations: Prioritizes genomic regions and variants that are likely to be biologically significant for downstream validation.
• Candidate Variant Resequencing: Assists selection of specific genomic regions for resequencing to identify candidate causal variants.

Scientific Applications:

• Large-scale WGA projects: Annotation and visualization of numerous P-values to infer functional implications in whole-genome association studies.
• HIV-1 host genetics: Applied in a study of host control of HIV-1 viral load during the asymptomatic set point period to support heuristic annotation of associations.

Methodology:

Computational steps explicitly include automatic annotation of genomic data and SNPs, visualization of P-values within genomic context, interpretation by highlighting links between polymorphisms and gene expression, and assisting selection of regions for candidate variant resequencing.