SearcHPV

SearcHPV detects and characterizes human papillomavirus (HPV) integration sites in host genomes from targeted capture DNA sequencing data to define viral-host breakpoints and associated structural variation.

Key Features:

• High Sensitivity and Specificity: Demonstrates superior sensitivity and specificity when identifying integration sites from targeted capture DNA sequencing data.
• Junction Contig Assembly: Produces locally assembled contigs for each integration event, reporting one or two contigs that represent the left and right sides of the viral‑host junction to enable precise breakpoint sequence identification.
• Targeted Capture Technology: Leverages targeted capture to enrich HPV sequences and enhance detection of integration sites in low read coverage sequencing data.
• Integration with Genome‑Wide Analysis: Integrates SearcHPV-defined breakpoints with genome-wide linked read sequencing to identify potential structural variations related to HPV integration.

Scientific Applications:

• Cancer Research: Identifies HPV integration sites adjacent to cancer-related genes such as TP63 and MYC to inform studies of molecular mechanisms driving carcinogenesis.
• Structural Variation Analysis: Detects integrations near regions of large structural variation to support analysis of genomic instability associated with HPV.

Methodology:

SearcHPV employs a detection pipeline using targeted capture DNA sequencing, local assembly of junction contigs (one or two per event) to define viral-host breakpoints, and integrated analysis with genome-wide linked read sequencing for identification and validation of associated structural variation, addressing challenges from low read coverage.