Whole-genome sequencing reveals an association between small genomic deletions and an increased risk of developing Parkinson's disease

Abstract

Parkinson's disease: genetic risk factors in a Korean populationA whole-genome sequencing study of Korean individuals with Parkinson's disease (PD) has identified several new genetic risk factors, ranging from single nucleotide variations (SNVs) to larger DNA deletions. PD is the second most prevalent neurodegenerative disease globally, but most studies have focused on SNVs in European populations. Using whole-genome sequencing, Ji-Hye Oh at the University of Ulsan, Seoul, South Korea, and co-workers were able to identify genetic differences between PD patients and healthy controls, including deletions, gains, and several new SNVs. In particular, deletions of small non-coding regions that regulate gene expression may be key contributors to PD. These results provide a whole-genome perspective on genetic risk factors for PD in a Korean population, and illuminate how a whole-genome sequencing approach may be helpful in identifying genetic factors underlying other diseases.,Single-nucleotide variants (SNVs) associated with Parkinson's disease (PD) have been investigated mainly through genome-wide association studies. However, other genomic alterations, including copy number variations, remain less explored. In this study, we conducted whole-genome sequencing of primary (310 PD patients and 100 healthy individuals) and independent (100 PD patients and 100 healthy individuals) cohorts from the Korean population to identify high-resolution small genomic deletions, gains, and SNVs. Global small genomic deletions and gains were found to be associated with an increased and decreased risk of PD development, respectively. Thirty significant locus deletions were identified in PD, with most being associated with an increased PD risk in both cohorts. Small genomic deletions in clustered loci located in the GPR27 region had high enhancer signals and showed the closest association with PD. GPR27 was found to be expressed specifically in brain tissue, and GPR27 copy number loss was associated with upregulated SNCA expression and downregulated dopamine neurotransmitter pathways. Clustering of small genomic deletions on chr20 in exon 1 of the GNAS isoform was detected. In addition, we found several PD-associated SNVs, including one in the enhancer region of the TCF7L2 intron, which exhibited a cis-acting regulatory mode and an association with the beta-catenin signaling pathway. These findings provide a global, whole-genome view of PD and suggest that small genomic deletions in regulatory domains contribute to the risk of PD development.,