FXNgene methylation determines carrier status in Friedreich ataxia

BackgroundFriedreich ataxia (FRDA) is typically caused by homozygosity for an expanded GAA triplet-repeat (GAA-TRE) in intron 1 of theFXNgene. Some patients are compound heterozygous for the GAA-TRE and anotherFXNpathogenic variant. Detection of the GAA-TRE in the heterozygous state, occasionally technically challenging, is essential for diagnosing compound heterozygotes and asymptomatic carriers.ObjectiveWe explored if the FRDA differentially methylated region (FRDA-DMR) in intron 1, which is hypermethylated inciswith the GAA-TRE, effectively detects heterozygous GAA-TRE.MethodsFXNDNA methylation was assayed by targeted bisulfite deep sequencing using the Illumina platform.ResultsFRDA-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 pathogenicFXNinitiation 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.ConclusionFXNDNA 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.