Genome STRiP

Genome STRiP detects and genotypes structural variants, emphasizing multiallelic copy-number variants (mCNVs) from whole-genome sequencing to quantify gene-dosage variation.

Key Features:

• Detection of multiallelic CNVs: Identifies large (>5-kb) multiallelic copy-number variants (mCNVs) that vary in copy number across genomes.
• Analysis of gene dosage variation: Quantifies the contribution of mCNVs to gene-dosage variation, reporting that mCNVs account for seven times more variation in gene dosage than deletions and biallelic duplications combined.
• Identification of runaway duplication haplotypes: Detects haplotypes with highly increased gene copy numbers, with examples including HPR and ORM1.
• Support for heterogeneous datasets: Analyzes diverse whole-genome sequencing cohorts and reports reliable results with minimum sample sizes of 20-30 genomes, with accuracy improving as sample size increases.
• Imputation strategies: Provides initial imputation-based approaches and an associated data resource to support mCNV analysis and imputation.

Scientific Applications:

• Gene expression and dosage studies: Characterizes how mCNVs affect gene dosage and thereby impact gene expression.
• Phenotype and disease association: Enables investigation of mechanisms underlying phenotypic diversity and disease susceptibility through mCNV detection and genotyping.
• Genomics, personalized medicine, and evolutionary biology: Supports population-genomic analyses, personalized-medicine investigations, and evolutionary studies that require accurate mCNV identification and genotyping.

Methodology:

Analyzes whole-genome sequencing data from multiple individuals to identify shared structural variations by examining inter- and intra-genomic differences, with analysis supported by an initial data resource for imputation-based studies.