STRipy

STRipy genotypes pathogenic short tandem repeats (STRs) from high-throughput sequencing (HTS) data to detect and quantify disease-associated repeat expansions across over 50 known disease loci.

Key Features:

• Comprehensive locus coverage: Targets all known disease-causing STRs implicated in over 50 diseases from HTS data.
• Mitigation of read/fragment length limitations: Addresses underestimation of maximum repeat lengths caused by read or fragment length constraints that can prevent genotypes from reaching pathogenic thresholds.
• Pathogenic-threshold-aware genotyping: Produces genotypes with attention to pathogenic thresholds for disease-associated STR expansions.
• Population reference data: Provides population-wide distributions derived from testing on over two thousand five hundred samples to aid interpretation.

Scientific Applications:

• Disease-associated STR genotyping: Detection and quantification of pathogenic STR expansions across known disease loci using HTS data.
• Interpretation of pathogenicity: Use of population-wide distributions to contextualize repeat lengths relative to pathogenic thresholds.
• Research on STR-related diseases: Comparative analysis of STR expansion spectra across multiple loci implicated in disease.

Methodology:

Genotypes STRs from high-throughput sequencing (HTS) data and computes population-wide distribution statistics based on analysis of over two thousand five hundred samples.