Progress Update: Improved, accessible, and affordable FSHD diagnostics

Posted by Friends of FSH Research on May 18, 2021

Report by Peter L Jones PhD
See grant: Improved, accessible, and affordable FSHD diagnostics

We have been developing a new molecular genetic diagnostic approach for FSHD that can be performed on any source of human DNA, including the DNA found in one’s saliva. All current methods for FSHD1 diagnostics involve physically measuring the size of the D4Z4 repeats on an FSHD permissive chromosome 4A. These techniques require large and intact genomic DNA and therefore can only be performed on high quality genomic DNA typically isolated from blood. Saliva DNA is too low quality and fragmented for these types of analyses. Alternatively, our technique is based on the distinct epigenetic signatures (using DNA methylation - a chemical mark on the DNA) specific for FSHD1, FSHD2, and healthy individuals, that can be identified using any quality of genomic DNA.

The primary goal of the overall project was to further validate our FSHD epigenetic diagnostic testing and to determine our ability to reach people around the world and provide FSHD testing. A secondary goal was to begin converting our analysis to a less expensive and higher throughput next-generation sequencing (NGS) method. This one year grant provided partial funding for the large project to validate and optimize epigenetic testing for FSHD.

Key points:

1. Enrolled 557 new subjects (268 domestic and 289 international participants) into our epigenetic FSHD research testing project over the funding period.
2. Joined the MOVE FSHD group, provided saliva collection kits to performance sites, and started receiving samples.
3. Initial POC success with transitioning to a more cost-effective an NGS-based method of analysis.

Over the one year period we enrolled 557 individuals into our FSHD epigenetic research testing project. This included participants from across the USA and Canada and around the world with 1) a clinical FSHD diagnosis only, 2) a genetically confirmed FSHD diagnosis, 3) genetically confirmed as not FSHD, and 4) no clinical FSHD diagnosis but FSHD in the family. We have now reached individuals in a total of 47 countries on six continents, showing the high accessibility of our FSHD testing method. Our assay accurately assessed all genetically confirmed cases of FSHD and all but one genetically confirmed case of healthy (or not FSHD), which we had declared inconclusive. The vast majority of individuals fall very clearly within our methylation ranges for FSHD or healthy, however, a few with longer FSHD1-sized repeats (9RUs) or contracted 4AL alleles fell within borderline methylation. This allowed us to refine our criteria incorporating methylation ranges to clarify these initially borderline individuals. We now have a better understanding of the overall methylation profiles for FSHD vs healthy.

In addition, we have started to receive de-identified samples from the MOVE FSHD study. The purpose of participation in this study is to determine if, and to what extent, DNA methylation correlates with FSHD clinical presentation. This is a multi-year study and the results will not be known for a while, but with funding from the Friends of FSH Research we were able to purchase saliva kits and distribute them to the study sites.

Finally, we have started the transition from our original low throughput analysis that takes a lot of time and costs ~$200/individual analyzed to a much more efficient NGS approach that drops the price down to ~$60-70/ individual analyzed. These costs include ~$8 for domestic two-way shipping but do not reflect international shipping costs. Regardless, the $20 saliva collection kit is still the leading expense for this approach. Overall, we believe we have an extremely accurate, accessible, and affordable diagnostic for FSHD.