In conclusion, we have successfully applied a novel amplification‐free targeted enrichment method to study the trinucleotide repeat in HTT in clinical HD samples, as well as the three additional loci ATXN10, FMR1, and C9orf72. Our mapping‐independent software allowed us to confidently analyze the unstable HTT repeat and to study repeat sequence variations such as interruptions in the FMR1 repeat. This evidence concerns the gene ATXN10 and Huntington disease.