SavvyCNV

SavvyCNV detects genome-wide copy number variants using off-target reads from exome and targeted sequencing to recover CNVs outside capture regions for clinical and research applications.

Key Features:

• Utilization of Off-Target Reads: Analyzes off-target reads from exome and targeted sequencing, which can constitute up to 70% of generated reads.
• Genome-Wide Detection Capability: Calls CNVs across the genome from off-target and on-target data, enabling detection beyond captured target regions.
• High Precision and Recall: Benchmarking against truth sets from whole-genome sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA) assays shows superior precision and recall compared with five state-of-the-art CNV callers using off-target and on-target reads.
• Clinical Relevance: Recovers clinically relevant CNVs previously undetected in targeted panel sequencing data.

Scientific Applications:

• Genome-wide CNV discovery: Enables identification of CNVs across the genome using existing exome and targeted sequencing datasets.
• Clinical diagnostics: Supports identification of diagnostic CNVs that may be missed by standard targeted analyses.
• Genetic research and variant discovery: Facilitates study of genetic contributions to disease and discovery of novel CNVs associated with specific conditions.

Methodology:

Analyzes off-target reads and compares sequencing read depth across the genome to identify regions with abnormal copy number; benchmarking used whole-genome sequencing-derived truth sets and MLPA assays.