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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

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Long-Read Sequencing Resolves a Complex Structural Variant in PRKN Parkinson's Disease.

Kensuke Daida^1,2,3, Manabu Funayama^3,4, Kimberley J Billingsley⁵

¹Integrative Neurogenomics Unit, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.

Movement Disorders : Official Journal of the Movement Disorder Society

|November 6, 2023

Summary

This study identified a large 7 Mb inversion in the Parkin gene (PRKN), a common cause of young-onset Parkinson's disease. Long-read sequencing is crucial for detecting these complex structural variants in PD genetic analysis.

Keywords:

PARK2 Parkinson's disease inversion long-read sequencing structural variant

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Published on: December 14, 2017

Area of Science:

Genetics
Neuroscience
Genomic Medicine

Background:

Parkin RBR E3 ubiquitin-protein ligase (PRKN) mutations are the primary cause of young-onset and autosomal recessive Parkinson's disease (PD).
The PRKN gene is located in a common fragile site (FRA6E), making it susceptible to structural variations.
Complex structural variants, like inversions within PRKN, are rarely reported, indicating potential underdiagnosis.

Purpose of the Study:

To identify complex structural variants, specifically inversions, within the PRKN gene using advanced long-read sequencing technology.
To investigate the genetic underpinnings of young-onset Parkinson's disease in cases with unresolved genetic causes.

Main Methods:

Employed a combination of targeted sequencing, whole exome sequencing, multiple ligation probe amplification, and long-read sequencing to analyze monozygotic twins with dystonia-parkinsonism.
Utilized whole-genome sequencing data from large cohorts (UK-Biobank and AMP-PD) to assess the frequency and impact of PRKN inversions.

Main Results:

A novel heterozygous exon 3 deletion in PRKN was detected, alongside a significant 7 Mb inversion encompassing a substantial portion of the PRKN coding sequence.
Diagnosed affected individuals as compound heterozygous carriers of PRKN mutations.
Identified nine potentially damaging inversions in the UK-Biobank and two in the AMP-PD dataset, likely affecting PRKN gene expression.

Conclusions:

This research presents the first description of a large 7 Mb inversion with breakpoints located outside the PRKN gene.
Emphasizes the critical role of long-read sequencing in uncovering complex structural variants for diagnosing unresolved young-onset Parkinson's disease cases.