Unmasking Compound Heterozygosity in GYG1 Myopathy: Diagnostic Insights From RNA-Seq and Long-Read Genomics

Area of Science:

• Genetics
• Neuromuscular Disorders
• Molecular Biology

Background:

• Polyglucosan body myopathy type 2 (PGBM2) is an autosomal recessive myopathy linked to GYG1 gene variants.
• Characterized by muscle weakness and polyglucosan inclusions, PGBM2 diagnosis can be complex.
• The case involves a 64-year-old woman with progressive proximal weakness and muscle histopathology findings consistent with PGBM2.

Purpose of the Study:

• To report a challenging case of PGBM2 diagnosis in an adult patient.
• To investigate the utility of advanced genomic and transcriptomic techniques for resolving complex variant phasing.
• To confirm the molecular diagnosis and reclassify a deep intronic variant.

Main Methods:

• Whole genome sequencing (GS) identified an initial heterozygous splice-site variant in GYG1.
• Reanalysis of GS data revealed a deep intronic variant.
• RNA sequencing (RNA-seq) confirmed aberrant splicing from both variants.
• Long-read GS was employed to determine variant phasing and confirm compound heterozygosity.

Main Results:

• Two pathogenic GYG1 variants, a splice-site and a deep intronic variant, were identified.
• RNA-seq confirmed that both variants caused aberrant splicing, leading to exon skipping and cryptic exon inclusion.
• Long-read GS definitively established the variants were in trans, confirming compound heterozygosity.
• The deep intronic variant was reclassified as likely pathogenic based on these findings.

Conclusions:

• Complex phasing challenges in adult-onset recessive disorders can be overcome with integrated genomic approaches.
• Long-read GS, RNA-seq, and genome reanalysis are crucial for accurate molecular diagnosis in PGBM2.
• This case underscores the importance of advanced molecular techniques for resolving diagnostic ambiguities in rare genetic myopathies.