Update: Epigenetic Analysis and FSHD Research Testing

Report by Dr. Jones
See also Epigenetic Analysis and FSHD Research Testing

We have developed an inexpensive epigenetic diagnostic for FSHD1 and FSHD2 that can be performed on any source of human DNA, including the DNA found in one’s saliva. Other FSHD1 testing (deletion testing) requires a blood draw due to specific quality and isolation requirements followed by processing on highly specialized equipment. The cost of this testing is often prohibitive for those paying out of pocket, despite the promises of the newer deletion testing technology. In contrast, our epigenetic testing can be performed on any source of DNA, including saliva or buccal samples collected through the mail, frozen samples stored for years, and DNAs isolated for other genetic testing procedures. This is particularly useful for young children or anyone who does not have ready access to clinics for blood draws. In addition, our testing can be performed using equipment found in most molecular biology labs or diagnostic labs and is readily scaled to meet the need. Perhaps most importantly, our testing decreases the cost >10-fold compared with current commercial testing for FSHD1, regardless of the technology used (Southern blotting, optical mapping, molecular combing), while also detecting FSHD2 at no additional cost. Thus, our epigenetic testing greatly increases accessibility to FSHD diagnostics.

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. 1) Enrolled 779 new subjects (453 domestic and 326 international participants) into our epigenetic FSHD research testing project.
  2. 2) Further validated our NGS method against or initial method and found it provides the same diagnostic value but with much more certainty. In particular, NGS data has higher confidence for certain haplotypes with unusual epigenetics, mosaic individuals, and otherwise borderline cases.

Over the 1-year period we enrolled 779 individuals into our FSHD epigenetic research testing project as direct enrolls. In addition, we have large collaborative efforts with hospitals in Brazil, Australia, and others around the world. Participants joined with 1) a clinical FSHD diagnosis only, 2) a genetically confirmed FSHD diagnosis, 3) genetically confirmed as not FSHD, or 4) no clinical FSHD diagnosis but FSHD in the family. We have now reached individuals in a total of 68 countries on six continents, showing the high accessibility of our FSHD epigenetic testing method.

Over the course of the past year, we have been able to refine our diagnostic criteria by incorporating additional methylation metrics to clearly identify borderline individuals. It is now more clear that diagnostic levels of methylation are dependent upon certain specific genetic conditions. In addition, our family testing has continued to successfully identify individuals who are mosaic for FSHD1 (a combination of healthy and FSHD1). It is estimated that 1/6 of spontaneous FSHD1 cases are mosaic and these individuals often missed by other testing or not tested due to often being mild or asymptomatic. We now have a better understanding of the methylation profiles for FSHD vs healthy, FSHD1 vs FSHD2, and mosaic FSHD1.

In addition, we have continued to analyze the 450 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. These results will be returned to the participants at the conclusion of the study, if desired.

Overall, our epigenetic testing, first published in 2014, has proven to be an extremely accurate, accessible, and affordable diagnostic for all forms of FSHD. Our recent modifications to the procedure have increased accuracy and greatly decreased cost. Our testing is already accepted in many countries. However, some countries, including the USA, require specific certifications to be considered a clinically relevant testing. Therefore, we are currently making arrangements for our testing to be performed under the appropriate conditions to be considered an official diagnosis in the US and elsewhere.