Repeat Detector: accurate, efficient, and flexible sizing of expanded CAG/CTG repeats from targeted DNA sequencing

Targeted DNA sequencing approaches will improve how the size of short tandem repeats is measured for diagnostic tests and pre-clinical studies. The expansion of these sequences causes dozens of disorders, with longer tracts generally leading to a more severe disease. In addition, interruptions are sometimes present within repeats and can alter disease manifestation. Despite advances in methodologies, determining repeat size and identifying interruptions in targeted sequencing datasets remains a major challenge. This is because standard alignment tools are ill-suited for the repetitive nature of these sequences. To address this, we have developed Repeat Detector (RD), a deterministic profile weighting algorithm for counting repeats in targeted sequencing data. We tested RD using blood-derived DNA samples from Huntington’s disease (HD) and Fuchs endothelial corneal dystrophy patients sequenced using either Illumina MiSeq or Pacific Biosciences single-molecule, real-time sequencing platforms. RD was highly accurate in determining repeat sizes of 609 HD blood-derived samples and did not require prior knowledge of the flanking sequences or their polymorphisms within the patient population. We demonstrate that RD can be used to identify individuals with repeat interruptions and may provide a measure of repeat instability within an individual. RD is therefore highly versatile and may find applications in the diagnosis of expanded repeat disorders and the development of novel therapies. ### Competing Interest Statement LJ is on the scientific advisory boards of LoQus23 Therapeutics and Triplet Therapeutics and a member of the Executive Committee of the European Huntington's Disease Network. Within the last five years DGM has been a scientific consultant and/or received an honoraria/stock options/research contracts from AMO Pharma, Charles River, LoQus23, Small Molecule RNA, Triplet Therapeutics, and Vertex Pharmaceuticals. Within the last 5 years AED has been a scientific consultant for and/or received an honoraria/stock options/research contracts from Triplet Therapeutics, LoQus23 Therapeutics, Design Therapeutics, ProQR Therapeutics and Prime Medicine.