Data Source
This visualization tool contains polygenic score data computed for 37,948 samples from the
Indiana Biobank. All samples have high-quality genotyping data that underwent rigorous
quality control procedures.
Polygenic Scores
We computed polygenic scores using 5,088 scoring files from the
PGS Catalog
,
a comprehensive repository of polygenic scores for human traits and diseases. After quality control
and computational validation, 3,479 scores were retained for analysis.
Quality Control: Scores were filtered based on computational success and population compatibility (variant overlap percentage) to ensure reliable results.
Computation Pipeline
All polygenic scores were computed using the
pgsc_calc pipeline
,
a standardized, reproducible workflow for calculating polygenic scores from genotype data.
Score Normalizations
For each PGS and sample, four different score normalizations are available:
-
SUM
Raw Score: Direct sum of weighted genetic variants
-
Z_MostSimilarPop
Ancestry Normalized: Z-score normalized by most genetically similar population
-
Z_norm1
Continuous Ancestry (Mean): Continuously normalized by ancestry for mean centering
-
Z_norm2
Continuous Ancestry (SD): Z_norm1 further normalized for standard deviation
Available Cohorts
Cohorts are pre-defined groups of samples available for analysis:
- Ancestry-based Cohorts: Computationally inferred ancestry groups (not self-reported)
- User-imported Cohorts: Custom cohorts that have been imported for your specific analyses
User-Specific Features
This tool is designed with user-specific functionality:
- Personal Databases: Upload your own pgsc_calc output using the "Create New Database" button
- Session Management: All your analyses, cohorts, and preferences are tied to your session
- Task Storage: Generated visualizations are stored for 2 weeks before automatic deletion
- Personal Scores: Individual score upload capability Coming Soon
Use Your Own Data: This tool works with any output from the pgsc_calc pipeline.
Simply use the database upload feature to analyze your own polygenic score data.
Citations
PGS Catalog:
Lambert, S.A., Gil, L., Jupp, S. et al. The Polygenic Score Catalog as an open database for reproducibility and systematic evaluation.
Nat Genet 53, 420–425 (2021).
https://doi.org/10.1038/s41588-021-00783-5
pgsc_calc Pipeline:
Rietveld, C.A., Esko, T., Davies, G. et al. pgsc_calc: a standardized workflow for calculating polygenic scores.
Available at:
https://github.com/PGScatalog/pgsc_calc