Category: Parkinson's Disease: Genetics
Objective: Identify complex structural variants in PRKN gene from Parkinson’s disease patients.
Background: PRKN is the most frequent causative gene in young onset Parkinson’s disease (YOPD) and autosomal recessive PD. Biallelic PRKN patients typically present young or juvenile-onset Parkinsonism. The role of heterozygous PRKN variants in sporadic PD is controversial; where some reports show an increased risk of carrying a single damaging variant, and others report no effect. As it is a widespread pathogenic gene in YOPD, PRKN is considered a potential target for gene therapy. Therefore, it is crucial to identify PD patients harboring PRKN variants. PRKN is located in FRA6E, one of the most common fragile sites in the human genome, making this region prone to structural variants. Structural variants are prevalent in PRKN variants, mainly deletions, and duplication. There are patients where only one variant is identified although they fit in the typical PRKN phenotype and have YOPD. We hypothesized complex structural variants of PRKN, which conventional sequencing methods cannot identify, exist as an unrevealed second mutation in such YOPD cases.
Method: To identify the causative variant in PRKN from PD subjects, we used targeted resequencing for PD-related genes, multiplex ligation-dependent probe amplification (MLPA), and/or short-read whole exome sequencing (WES). PD subjects only harbor heterozygous PRKN variants, without other known causative variants in PD-related genes, were performed long read whole genome sequencing. To confirm the identified variants by long-read sequencing, Sanger sequencing was performed.
Results: Long-read sequencing identified large structural variants which MLPA and short-read WES could not determine from YOPD subjects. YOPD subjects with the large structural variant presented typical PRKN-PD presentation; young onset, good response to levodopa, and lower limb dystonia.
Conclusion: This study suggests that PRKN structural variants cannot be identified by conventional short-read sequencing methods but can be identified by long-read sequencing. Long-read sequencing may expand the role of the PRKN gene in PD.
To cite this abstract in AMA style:K. Daida, M. Funayama, A. Miano-Burkhardt, L. Mailik, K. Billingsley, M. Ishiguro, H. Yoshino, K. Ogaki, G. Oyama, R. Nonaka, W. Akamatsu, C. Blauwendraat, N. Hattori. Using Long read sequencing to identify complex structural variants in PRKN-PD [abstract]. Mov Disord. 2023; 38 (suppl 1). https://www.mdsabstracts.org/abstract/using-long-read-sequencing-to-identify-complex-structural-variants-in-prkn-pd/. Accessed September 23, 2023.
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MDS Abstracts - https://www.mdsabstracts.org/abstract/using-long-read-sequencing-to-identify-complex-structural-variants-in-prkn-pd/