CSVS

CSVS aggregates sequencing data from over 2,000 unrelated Spanish genomes and exomes to provide population-specific allele frequencies and support variant filtering and prioritization for genetic research and personalized medicine.

Key Features:

• Aggregated dataset: Aggregates sequencing data from over 2,000 unrelated Spanish genomes and exomes collected via crowdsourcing from local genomic projects and other scientific endeavors.
• Input data types: Accepts whole-exome sequencing (WES) and whole-genome sequencing (WGS) submissions.
• Variant filtering and gene prioritization: Facilitates prioritization of candidate disease genes by filtering polymorphisms and identifying local variations.
• Disease-category organization: Organizes sequences according to ICD10 upper categories to enable queries that exclude specific disease-related categories.
• Pseudo-control allele frequencies: Generates aggregated allele frequency counts within a pseudo-control Spanish population for variant interpretation.
• Population studies support: Supports population-level analyses such as assessing the prevalence of pharmacogenomic variants.
• Spanish Genome Reference Panel (SGRP1.0): Provides the SGRP1.0 reference panel to facilitate genomic imputation and improve accuracy of genetic analyses within the Spanish context.
• GA4GH Beacon integration: Integrated into the Global Alliance for Genomics and Health (GA4GH) Beacon network for federated querying and data sharing.

Scientific Applications:

• Variant interpretation and prioritization: Use allele frequencies and local variation to prioritize candidate disease genes and interpret variants in the Spanish population.
• Population-specific reference creation: Generate Spanish-specific allele frequency references and pseudo-controls for genetic analyses.
• Genomic imputation: Apply the SGRP1.0 panel to impute genotypes and enhance accuracy of genetic analyses within Spanish cohorts.
• Pharmacogenomics prevalence studies: Assess prevalence and distribution of pharmacogenomic variants in the Spanish population.
• Disease association and genetic research: Support disease-variant discovery and genetic research relevant to personalized medicine in Spain.
• Federated data sharing and discovery: Enable federated querying and international data sharing via the GA4GH Beacon network.

Methodology:

Aggregates WES/WGS sequencing data, filters polymorphisms and identifies local variations, organizes sequences by ICD10 upper categories to allow exclusionary queries, generates aggregated allele frequency counts for a pseudo-control Spanish population, constructs the SGRP1.0 reference panel for genomic imputation, and exposes data via the GA4GH Beacon network.