Related Experiment Video
Updated: Jun 12, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study
Scott F Saccone1, Raphael Bolze, Prasanth Thomas
1Department of Psychiatry, Washington University, St Louis, MO, USA. ssaccone@wustl.edu
SPOT is a web tool that prioritizes single nucleotide polymorphisms (SNPs) after genome-wide association studies (GWAS). It integrates biological databases using the genomic information network (GIN) method to rank SNPs for further investigation.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Genome-wide association studies (GWAS) identify potential genetic associations with diseases or traits.
- Post-GWAS analysis requires prioritizing significant single nucleotide polymorphisms (SNPs) for further validation.
- Integrating biological information can enhance the selection of biologically relevant SNPs.
Purpose of the Study:
- To introduce the SNP Prioritization Online Tool (SPOT) for prioritizing SNPs after GWAS.
- To provide a user-friendly web interface for implementing the genomic information network (GIN) method.
- To facilitate the selection of biologically relevant SNPs for downstream studies.
Main Methods:
- The SPOT web tool integrates biological databases using the genomic information network (GIN) method.
- Users upload SNP lists and GWAS P-values for prioritization.
- Custom prioritization levels can be set for candidate genes or genomic regions.
Main Results:
- SPOT returns a prioritized list of SNPs based on the GIN method.
- Users can view and interactively explore SNP details, including graphical representations of the GIN method.
- Results are downloadable for further analysis.
Conclusions:
- SPOT is an easily implemented and flexible solution for prioritizing SNPs after GWAS.
- The tool aids investigators in incorporating biological databases into SNP selection strategies.
- SPOT enhances the efficiency of post-GWAS analysis by focusing on biologically relevant variants.
Related Concept Videos
Genome-wide Association Studies-GWAS
GWAS does not require the identification of the target gene involved in...
Single Nucleotide Polymorphisms-SNPs
Comparing Copy Number Variations and SNPs
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Evolutionary Relationships through Genome Comparisons
