STRIDE-DB

STRIDE-DB provides a comprehensive database for cataloging and analyzing Short Tandem Repeats (STRs) instability and their phenotypic relevance in the human genome.

Key Features:

• Genome-wide STR identification: All STRs in the human reference genome hg19 were identified using RepeatMasker.
• Population frequency annotation: STR loci are annotated with allele frequency data from the 1000 Genomes Project.
• Disease and association annotation: Integration of GWAS and ClinVar associations links STR loci to reported phenotypes and clinical variants.
• Sequence and structural context: Inclusion of Alu loci, haploblocks, and conservation status provides genomic context for each STR.
• Polymorphic STR catalog: A comprehensive catalog of polymorphic STR variation and measures of instability across the genome.

Scientific Applications:

• Forensic analysis: Use of STR variation patterns for human identification and forensic genotyping studies.
• Population genomics: Analysis of population-level STR allele frequencies and polymorphism distributions.
• Clinical genetics: Investigation of STRs in genetic testing and interpretation for neuromuscular and repeat expansion disorders.
• Genotype–phenotype research: Exploration of associations between STR instability and phenotypic outcomes reported in GWAS and ClinVar.

Methodology:

STRs were identified in hg19 using RepeatMasker and annotated with allele frequencies from the 1000 Genomes Project, with additional integration of GWAS, ClinVar, Alu loci, haploblocks, and conservation status.