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To elucidate variants associated with MSA, we have been conducting short-read-based whole-genome sequence analysis. In the process of the association studies, we initially focused on <jats:italic>GBA1<\/jats:italic>, a previously proposed susceptibility gene for MSA, to evaluate whether <jats:italic>GBA1<\/jats:italic> variants can be efficiently identified despite its extraordinarily high homology with its pseudogene, <jats:italic>GBA1LP<\/jats:italic>. To accomplish this, we conducted a short-read whole-genome sequence analysis with alignment to GRCh38 as well as Sanger sequence analysis and compared the results. We identified five variants with inconsistencies between the two pipelines, of which three variants (p.L483P, p.A495P\u2013p.V499V, p.L483_M489delinsW) were the results of misalignment due to minor alleles in <jats:italic>GBA1P1<\/jats:italic> registered in GRCh38. The miscalling events in these variants were resolved by alignment to GRCh37 as the reference genome, where the major alleles are registered. In addition, a structural variant was not properly identified either by short-read or by Sanger sequence analyses. Having accomplished correct variant calling, we identified three variants pathogenic for Gaucher disease (p.S310G, p.L483P, and p.L483_M489delinsW). Of these variants, the allele frequency of p.L483P (0.003) in the MSA cases was higher than that (0.0011) in controls. The meta-analysis incorporating a previous report demonstrated a significant association of p.L483P with MSA with an odds ratio of 2.85 (95% CI; 1.05 \u2013 7.76, <jats:italic>p<\/jats:italic> = 0.0400).<\/jats:p>","DOI":"10.1038\/s10038-024-01266-1","type":"journal-article","created":{"date-parts":[[2024,7,18]],"date-time":"2024-07-18T03:33:48Z","timestamp":1721273628000},"page":"613-621","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Association study of GBA1 variants with MSA based on comprehensive sequence analysis -Pitfalls in short-read sequence analysis depending on the human reference 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