Recombinant GBA1 alleles presenting as exon-level deletions by short-read NGS in Parkinson disease: Implications for...

Pathogenic variants in GBA1 are a significant genetic risk factor for Parkinson disease (PD). Owing to high sequence homology between GBA1 and its pseudogene GBAP1, short-read NGS (srNGS) is susceptible to read misalignment, particularly in the presence of recombinant alleles. A targeted short-read NGS (srNGS) panel was applied to 175 selected Korean patients with PD, including those with early-onset disease, family history, preoperative assessment, or atypically rapid progression, identifying GBA1 copy-number loss in five patients. Confirmatory testing using MLPA, long-range PCR followed by Sanger sequencing, and long-read sequencing demonstrated that these findings represented recombinant alleles rather than simple deletions in four cases, while confirmatory analysis could not be performed in one case due to insufficient DNA. Thus, recombinant alleles were identified in at least 2.3% (4/175) of patients. We further evaluated whether GBAP1 copy-number analysis could aid interpretation of srNGS findings. GBAP1 copy-number patterns were concordant with confirmatory results in all four cases, indicating gene conversion events; in the remaining case, for which confirmatory testing could not be performed due to insufficient DNA, the pattern was suggestive of a fusion allele. Our findings demonstrate that recombinant alleles may present as exon-level deletions on targeted srNGS. We propose that concurrent GBAP1 copy-number analysis provides a practical interpretive aid for distinguishing recombinant rearrangements from simple copy-number alterations and for guiding confirmatory test selection in routine diagnostics.