Tayebi N, Lichtenberg J, Hertz E, Sidransky E. Is Gauchian genotyping of
GBA1 variants reliable?
MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.26.23297627. [PMID:
37986861 PMCID:
PMC10659459 DOI:
10.1101/2023.10.26.23297627]
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Abstract
Biallelic mutations in GBA1 result in Gaucher disease (GD), the inherited deficiency of glucocerebrosidase. Variants in GBA1 are also a common genetic risk factor for Parkinson disease (PD). Currently, some PD centers screen for mutant GBA1 alleles to stratify patients who may ultimately benefit from GBA1-targeted therapeutics. However, accurately detecting variants, especially recombinant alleles resulting from a crossover between GBA1 and its pseudogene, is challenging, impacting studies of both GD and GBA1-associated parkinsonism. Recently, the software tool Gauchian was introduced to identify GBA1 variants from whole genome sequencing. We evaluated Gauchian in 90 Sanger-sequenced patients with GD and five GBA1 heterozygotes. While Gauchian genotyped most patients correctly, it missed some rare or de novo mutations due to its limited internal database and over-reliance on intergenic structural variants. This resulted in misreported homozygosity, incomplete genotypes, and undetected recombination events, limiting Gauchian's utility in variant screening and precluding its use in diagnostics.
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