SV-HotSpot

SV-HotSpot identifies recurrent structural variant hotspots that impact gene expression by detecting, annotating, and visualizing SVs from whole genome sequencing (WGS) data to link SVs to coding and non-coding genomic elements.

Key Features:

• Integration with Functional Genomic Data: Integrates copy number alterations, gene expression profiles, and genome annotations (genes and regulatory elements) to contextualize structural variants.
• Automated Analysis Pipeline: Automates identification of recurrent structural variants and definition of hotspot regions from WGS-derived SV calls.
• Visualization Capabilities: Provides visualizations that contextualize genomic events within coding and non-coding functional elements to illustrate spatial relationships between SVs and regulatory elements.
• Application in Cancer Research: Has been applied to WGS and transcriptome data from metastatic castration-resistant prostate cancer patients to identify recurrent SVs targeting both coding and non-coding regions.

Scientific Applications:

• Cancer Genomics: Identify structural variants that affect genes involved in cancer progression and metastasis.
• Genomic Medicine: Characterize recurrent SVs that influence gene expression to inform personalized medicine approaches.
• Functional Genomics: Explore impacts of SVs on regulatory elements and non-coding regions using integrated genome annotations.

Methodology:

SV-HotSpot uses bedTools to perform overlapping and counting of genomic features to identify hotspot regions.