Progress Update: Improved, accessible, and affordable FSHD diagnostics

See grant: Improved, accessible, and affordable FSHD diagnostics

The primary goal of this project is to further validate our FSHD epigenetic diagnostic testing. To do this, we have been enrolling participants from around the world with 1) a clinical FSHD diagnosis only, 2) a genetic FSHD diagnosis, 3) genetically confirmed as not FSHD, and 4) no FSHD diagnosis but FSHD in the family.

Key points:

  1. Enrolled 247 new subjects into our epigenetic FSHD research testing
  2. Joined the MOVE FSHD group and provided saliva collection kits to performance sites

Domestically, we have enrolled 157 subjects in the past 6 months. These include 30 confirmed FSHD1 subjects, 2 genetically confirmed FSHD2 subjects, 7 clinically diagnosed with no confirmation, 19 genetically confirmed not FSHD/healthy, 24 with self-reported symptoms, and the remaining 75 with FSHD in the family and no self-reported symptoms. Many of this last group are children generally too young to show classic FSHD symptoms but are at risk due to a parent being FSHD1.

On the international front, we have enrolled 90 subjects from 15 countries in the past 6 months, bringing the total to 37 countries, with many more kits still to be returned. As one might expect, the majority of the international subjects do not have a genetic or official clinical diagnosis. The breakdown is 17 genetically confirmed FSHD1, no confirmed FSHD2 cases, 3 additional subjects with clinical FSHD and no testing, 11 self-reporting symptoms, and 56 with FSHD known or suspected in the family.

Overall, the results of the saliva testing have continued to show great specificity. All 47 of the genetically confirmed FSHD1 subjects were found to be FSHD1 and both FSHD2 subjects were confirmed FSHD2 by our assay. It is still difficult to distinguish FSHD2 from FSHD1+2. As for the genetically healthy subjects, our assay correctly identified all 22 participants enrolled the past 6 months. Thus, our direct saliva testing protocol remains 100% accurate when testing subjects with a genetically confirmed FSHD status. However, we have had two instances of not picking up a claimed FSHD determination in genomic DNAs sent to us from a research lab abroad, so a “diagnosis” of healthy/not FSHD is not 100% accurate when all samples tested are included.

In addition, there have been several instances of clinical FSHD being found “not FSHD” and then confirmed later as genetically not FSHD. For example, a recent subject that had tested positive for FSHD1 in the late 1990s enrolled in our study and was found to be 4B/4B, nonpermissive for FSHD. In addition, further analysis showed that they had a contracted 4B chromosome. Clearly, no A/B haplotyping had been performed since this testing was prior to learning about permissive and nonpermissve alleles. Still, to confirm our results we recently had them undergo a blood draw and sent the sample for the Bionano single molecule FSHD testing. They were confirmed to have two 4B chromosomes, one of which was a contracted 4B, and not FSHD. We are now doing exome sequencing to determine what neuromuscular disease they do have.

Another example of an interesting case is a ~40-year old international subject with a clinical diagnosis of FSHD and an onset of disease in their teens. Several other extended family members are similarly affected, but no immediate family members. Our epigenetic testing on saliva samples collected overseas showed no FSHD in the family. We went on to do exome sequencing and found that this subject has compound heterozygous deleterious mutations in the CALPN3 gene, which causes LGMD2A (LGMDR1).

So far, our epigenetic testing has proven to be very accurate in identifying FSHD1, FSHD2, and not FSHD/healthy from saliva collected by mail in the US and around the world. However, we would still benefit from the enrollment of more genetically confirmed subjects, with healthy and FSHD2 subjects needed in particular. We thank you again for your support.