CRISPR/Cas9 Customization of Electronic Genome Mapping Repeat Expansion Assays

Repeat expansions can be long, repetitive, and GC-rich, which makes them hard to size with PCR and sequencing. Electronic genome mapping (EGM) measures the interval between sequence-specific tags on ultra-long single DNA molecules, so an expansion shows up directly as a longer interval. This study extended the RepX™ Repeat Expansion Analysis pipeline, previously shown for FMR1 and FXN, to DMPK and C9orf72.

Coriell cell lines with known expansions were analyzed on the OhmX™ Platform with the RepX pipeline, which aligns molecules to multiple allele hypotheses, then phases them and counts repeats. The poster compares RepX repeat counts with expected values for each cell line and shows how CRISPR/Cas9 nicking can resize the target interval when a repeat falls in a region that isn't optimal for sizing, with Fragile X as a proof of concept.

Explore how CRISPR/Cas9-customized EGM can extend repeat expansion sizing to new loci in your research.