Overview of Neuromuscular Disorder Molecular Diagnostic Experience for the Population of Latvia

Discussion

In the past decade, medical care of patients with NMD in Latvia has purposefully shifted toward using DNA diagnostics as the first-line confirmatory test. After essential clinical, electrophysiologic, and biochemical investigations have been performed, all patients with a suspected NMD are referred to clinical geneticists. Larger and more informative tests are preferred over a sequential diagnostics approach. Exceptions include situations when individual tests for facioscapulohumeral muscle dystrophy or myotonic dystrophy are primarily ordered. In this study, we summarize more than 10 years of experience using the current approach.

The profile of the identified disorders combines patients carrying frequent European pathogenic variants of the FKRP, CAPN3, and CLCN1 genes, as well as some ultrarare cases, such as those carrying the MYBPC1 pathogenic variant that causes congenital myopathy and myogenic tremor. The diversity of these results confirms the necessity of approaches using larger gene panels or WES. However, the numbers of identified patients carrying the FKRP gene variant c.826C>A p.(Leu276Ile) (n = 7) and the CLCN1 gene variant c.2680C>T p.(Arg894Ter) (n = 19) warrants a discussion about testing for these single genetic changes before gene panel testing or WES is performed in patients with relevant clinical symptoms or transferring this step in medical care to additionally trained specialists prior to genetic counseling. This suggestion is supported by the identified allelic frequency of the CLCN1 gene variant c.2680C>T p.(Arg894Ter) in the population of Latvia (2.11%), which is higher than that in the non-Finnish European population (0.34%) and the population of Estonia (1.93%), as reported in the gnomAD database.¹² Allelic frequency data in conjunction with the already identified patients led us to hypothesize that congenital myotonia caused by the CLCN1 gene variant c.2680C>T p.(Arg894Ter) is the most frequent NMD in Latvia.

The situation with calpainopathy in our population is complicated by the presence of the frequent allele c.1746-20C>G, with conflicting interpretation of its pathogenicity.¹³ This allele was identified in 3 cases in a trans compound heterozygous state with another pathogenic/likely pathogenic recessive variant. Until further studies are performed to confirm or refute its role in the development of limb girdle muscle dystrophy, patients with this allele require individual case-by-case management by clinical geneticists together with an NMD team. While the high frequencies of the pathogenic variants c.826C>A p.(Leu276Ile) of the FKRP gene and c.550del p.(Thr184fs) of the CAPN3 gene in Latvia are similar to those in other European populations, the frequency of the CAPN3 gene variant c.1746-20C>G is significantly higher at 2.37%. Nevertheless, the current data do not allow us to draw conclusions about its role in the pathogenesis of calpainopathy.

Since 2008, DNA diagnostics have helped to diagnose 37% of our patients with NMD. This detection rate is not directly compatible with those in previous publications because the genetic tests mentioned in those studies have evolved over time. Only small gene panels and limited copy number analysis were available 10 years ago, while WES, enriched with mitochondrial genome analysis, can be the first-line option nowadays. Nevertheless, very similar results were reported by Harris et al. in cohorts of patients with LGMD for whom WES was performed instead of sequential gene panel testing. They were able to genetically diagnose 37% of patients, and although the total diagnostic yield of standard sequential testing was not much lower at 33%, it was less timely.¹⁴

To ascertain the validity of our results, point prevalence was calculated, and the results were compared with those from published studies. Pediatric patients are a priority for genetic counseling and testing. Some of the most common childhood-onset NMDs in our population were SMA and dystrophinopathies, with a birth prevalence of 1.01 per 10,000 and 2.08 per 10,000 (male population), respectively, which are comparable with data published by other countries.^5,15,16 The carrier frequency of the SMN1 exon 7 deletion varies between 1 of 40 and 1 of 100 individuals, depending on geographic origin and ancestry.¹⁷ The carrier frequency in the population of Latvia was 1 of 47 individuals or 2.1%, which matches with the general European genetic landscape. SMA and dystrophinopathies are the most common disorders, and specialists are well-trained to recognize them. Accessibility of gene therapy for these diseases intensifies the pressure for early diagnosis, and the industry offers regular training for specialists to raise awareness of these disorders.

The unavailability of genetic testing on a regular basis for adults before 2015 left this group of patients in a particularly sorrowful situation. This is well represented in our disease prevalence calculations; the number of identified patients with myotonic dystrophy type 1 and FSHD is at least 10 times lower than in published studies from Europe and the USA.^8,18 A possible explanation for this is the complicated stepwise genetic test of the DMPK gene and the difficulties justifying further investigation of cases with inconclusive genetic screening results. Access to myotonic dystrophy type 1 and FSHD confirmatory level tests in national laboratories would facilitate the diagnosis of patients, allowing all involved specialists, cardiologists, ophthalmologists, and, most importantly, neurologists to order these tests directly. The phenotypic variability observed as well as anticipation makes identifying these diseases more difficult.