Patients with hereditary ALS-FTLD (Lou Gehrig’s disease, marked by frontotemporal lobar degeneration) typically have a hexanucleotide repeat expansion in C9orf72. The size of that repeat expansion can be indicative of age of onset, severity of symptoms, and more, so it’s an important clinical diagnostic tool.
The Sage Science team worked with collaborators at the New York Genome Center to develop and evaluate a simple system for characterizing a person’s repeat expansion length. Unaffected individuals have fewer than 25 repeats, while ALS-FTLD patients might have hundreds or thousands. To gauge the repeat expansion size, we used restriction enzymes to select the genomic region for analysis. That sample was then loaded into the SageELF, which automatically generates 12 consecutive size fractions using gel electrophoresis.
After that process, we used qPCR to identify the size fractions containing the repeat expansion region. The size of the repeat expansion is determined by the size range of the fraction in which it was collected. Since the idea is to eventually deploy this kind of approach for clinical use, an important factor is that the assay can be completed in a single day. We could imagine clinical labs using this method for a quick scan, and following up with deeper analysis techniques for people identified as at risk.
This work was presented recently at the AGBT Precision Health meeting in a poster entitled “A Simple Screening Assay for C9orf72 ALS Repeat Expansions.” As we noted there, “Our assay combines the benefits of Southern blotting for RE sizing, with the sensitivity of PCR, without the need to amplify through the repetitive 100% GC-rich repeat region.” For more information, check out our app note.
This method could be used for repeat expansions of other sizes as well, making it a good fit for diseases like fragile X syndrome, Huntington’s disease, various ataxias, and more.