Nanopore sequencing combined with adaptive sampling and NanoExpansion enables accurate characterization of repeat expansion disorders.

Targeted Nanopore long-read sequencing of native DNA by adaptive sampling, combined with NanoExpansion, a Python-based tool for sizing expanded alleles and detecting sequence interruptions.

The authors evaluate targeted Nanopore long-read sequencing of native DNA by adaptive sampling in 132 participants, including a validation group previously characterised by Southern blot or RP-PCR (DM1, DM2, C9orf72-associated ALS) and a test group (suspected spinocerebellar ataxia, CANVAS, others). They developed NanoExpansion, a Python-based tool that sizes expanded alleles and detects sequence interruptions. All DM1, DM2, ALS, Friedreich ataxia, Huntington's disease and Kennedy disease cases were correctly characterised, and the test group notably yielded eight SCA27B and nine CANVAS cases. Compared with adaptive sampling, long-PCR underestimated alleles exceeding 800 repeats. Interruptions were detected in 27 of 51 DM1 cases (52.9%) and 1 of 10 ALS cases.

Synthesis written by Geno'X. For the full original abstract, please refer to the source publication.

A single assay that replaces Southern blot and RP-PCR while also reading sequence interruptions is real progress for neurogenetics laboratories, especially since interruptions modulate the DM1 phenotype. Validation, however, rests on modest numbers per disorder, and the availability of the NanoExpansion code is not stated in the abstract. It remains to be seen how this targeted approach compares with a full long-read genome that would capture the same loci without preselection.

Analysis by Dr Thibaut Benquey