STRmieHD A Short Tandem Repeat Mapping and Identification Engine for Interruption Aware Genotyping and Somatic Mosaicism Profiling in Huntingtons Disease

Short tandem repeat (STR) expansions in exon 1 of the HTT gene drive Huntingtons disease (HD) pathogenesis and are subject to somatic mosaicism and interruption variation events influencing disease onset and progression. While Next-Generation Sequencing offers the potential for accurate repeat sizing, current computational tools often lack the resolution to capture interruption motifs and allele-specific somatic variations. Here, we present STRmie-HD, an alignment-free de novo approach for interruption-aware genotyping and quantitative assessment of somatic mosaicism at the HTT locus at the single-read level. STRmie-HD processes individual reads and detects uninterrupted CAG tracts, canonical and atypical interruption patterns, and CCG content while providing allele-specific peak calling and per-sample quantification of somatic instability. Benchmarking on independent datasets, including clinically genotyped blood samples, long-read PacBio SMRT-sequenced data, and synthetic reads with predefined repeat sizes and interruption configurations, demonstrated that STRmie-HD achieved high accuracy in allele size prediction and matched or outperformed state-of-the-art tools in clinically relevant scenarios. Furthermore, it uniquely quantifies the proportion of reads carrying interruption variants and provides two metrics for quantifying repeat instability and describing the expansion dynamics. STRmie-HD offers a comprehensive and extensible framework for high-resolution genotyping of repeat expansion loci and supports biologically meaningful assessments of somatic mosaicism in HD.