ExpansionHunter

ExpansionHunter genotypes short tandem repeat (STR) regions using sequence graphs to accurately characterize repeat expansions and adjacent variants for genetic research and clinical applications.

Key Features:

• Sequence-Graph-Based Methodology: Uses sequence graphs to model complex genomic regions containing STRs, enabling precise genotyping of repeats adjacent to other variants and imperfect repeats such as polyalanine.
• Targeted Genotyping of Medically Significant Loci: Performs targeted genotyping across a broad class of medically significant loci that contain repeats relevant to repeat-expansion disorders.
• C++ Implementation: Implemented in C++ to provide computational performance for analysis of STR regions.

Scientific Applications:

• Study of repeat-expansion disorders: Used to genotype and investigate genetic disorders linked to repeat expansions, including Huntington's disease and certain muscular dystrophies.
• Genomics research and STR characterization: Provides precise genotyping data for genomics studies that require accurate characterization of STRs and adjacent variation.

Methodology:

Models STR-containing regions using sequence graphs to genotype repeats, including those adjacent to other variants and imperfect repeats such as polyalanine, and is implemented in C++.