ExpansionHunter Denovo

ExpansionHunter Denovo detects novel short tandem repeat (STR) expansions genome-wide from short-read sequencing data to identify pathogenic and non-reference repeat expansions.

Key Features:

• Catalog-Free Detection: Operates genome-wide without relying on predefined repeat catalogs, enabling discovery of novel STR expansions.
• Input Formats and Read Types: Analyzes alignments in BAM/CRAM files derived from short reads (100–200 bp).
• Sensitivity and Coverage: Detects large expansions across diverse pathogenic repeats and identified expansions in 41 of 44 known pathogenic repeats in evaluations.
• Non-Reference Expansion Discovery: Capable of identifying non-reference and recently reported novel expansions, including nine recently reported novel expansions, with performance assessed on real and simulated datasets.

Scientific Applications:

• Monogenic disorder research: Detection of pathogenic STR expansions implicated in monogenic disorders.
• Novel mutation discovery: Genome-wide identification of previously uncharacterized repeat expansions as candidate disease-associated mutations.
• Genomic studies for diagnosis and therapeutics: Supporting studies that map repeat expansions relevant to diagnosis, personalized medicine, and therapeutic development.

Methodology:

Performs catalog-free, genome-wide detection of STR expansions from BAM/CRAM alignments of short reads (100–200 bp) and was evaluated on real and simulated datasets.