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Response to: “Is Gauchian genotyping of GBA1 variants reliable?”
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Description
We recently described two methods for GBA1 analysis, which is hampered by the adjacent highly homologous pseudogene: Gauchian, a novel algorithm for analysis of short-read WGS, and targeted long-read sequencing 1. Tayebi et al have applied the former to WGS from 95 individuals, and compared it to Sanger sequencing 2. They report concordant genotypes in 85, while 11 had discrepant calls (we note that this leads to a total of 96). In addition, they report 28 false Gauchian calls in 1000 Genomes Project (1kGP) samples. Gauchian was developed because the homology of the GBA region requires a short read variant caller that does not rely solely on read alignments, and can identify specific variants known to be pathogenic. To understand the cause of these discrepancies, we reviewed their data, and conclude that they are mis-interpreting Gauchian results in 8 of the 11 discrepant samples, and incorrectly using Gauchian to analyze low-coverage 1kGP samples.