<i>FXN</i> gene methylation determines carrier status in Friedreich ataxia.

Abstract

Friedreich ataxia (FRDA) is typically caused by homozygosity for an expanded GAA triplet-repeat (GAA-TRE) in intron 1 of the <i>FXN</i> gene. Some patients are compound heterozygous for the GAA-TRE and another <i>FXN</i> pathogenic variant. Detection of the GAA-TRE in the heterozygous state, occasionally technically challenging, is essential for diagnosing compound heterozygotes and asymptomatic carriers. We explored if the FRDA differentially methylated region (FRDA-DMR) in intron 1, which is hypermethylated in <i>cis</i> with the GAA-TRE, effectively detects heterozygous GAA-TRE. <i>FXN</i> DNA methylation was assayed by targeted bisulfite deep sequencing using the Illumina platform. FRDA-DMR methylation effectively identified a cohort of known heterozygous carriers of the GAA-TRE. In an individual with clinical features of FRDA, commercial testing showed a paternally inherited pathogenic <i>FXN</i> initiation codon variant but no GAA-TRE. Methylation in the FRDA-DMR effectively identified the proband, his mother and various maternal relatives as heterozygous carriers of the GAA-TRE, thus confirming the diagnosis of FRDA. <i>FXN</i> DNA methylation reliably detects the GAA-TRE in the heterozygous state and offers a robust alternative strategy to diagnose FRDA due to compound heterozygosity and to identify asymptomatic heterozygous carriers of the GAA-TRE.