Characterizing a complex CT-rich haplotype in intron 4 of SNCA using large-scale targeted amplicon long-read sequencing

Pilar Alvarez Jerez; Kensuke Daida; Francis P Grenn; Laksh Malik; Abigail Miano-Burkhardt; Mary B Makarious; Jinhui Ding; J Raphael Gibbs; Anni Moore; Xylena Reed; Mike A Nalls; Syed Shah; Medhat Mahmoud; Fritz J Sedlazeck; Egor Dolzhenko; Morgan Park; Hirotaka Iwaki; Bradford Casey; Mina Ryten; Cornelis Blauwendraat; Andrew B Singleton; Kimberley J Billingsley

doi:10.1038/s41531-024-00749-4

Characterizing a complex CT-rich haplotype in intron 4 of SNCA using large-scale targeted amplicon long-read sequencing

NPJ Parkinsons Dis. 2024 Jul 26;10(1):136. doi: 10.1038/s41531-024-00749-4.

Authors

Pilar Alvarez Jerez^{1

2

3}, Kensuke Daida^{1

2}, Francis P Grenn¹, Laksh Malik², Abigail Miano-Burkhardt^{1

2}, Mary B Makarious^{1

3}, Jinhui Ding¹, J Raphael Gibbs¹, Anni Moore¹, Xylena Reed², Mike A Nalls^{1

2

4}, Syed Shah⁴, Medhat Mahmoud⁵, Fritz J Sedlazeck^{5

6}, Egor Dolzhenko⁷, Morgan Park⁸, Hirotaka Iwaki^{1

2

4}, Bradford Casey⁹, Mina Ryten^{10

11

12}, Cornelis Blauwendraat^{1

2}, Andrew B Singleton^{1

2}, Kimberley J Billingsley^{13

14}

Affiliations

¹ Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA.
² Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA.
³ Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, UK.
⁴ DataTecnica LLC, Washington, DC, USA.
⁵ Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA.
⁶ Department of Computer Science, Rice University, Houston, TX, USA.
⁷ Pacific Biosciences, Menlo Park, CA, USA.
⁸ NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
⁹ The Michael J. Fox Foundation for Parkinson's Research, New York, New York, USA.
¹⁰ Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK.
¹¹ Uk Dementia Research Institute at the University of Cambridge and Department of Clinical Neurosciences, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
¹² Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
¹³ Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA. kimberley.billingsley@nih.gov.
¹⁴ Center for Alzheimer's and Related Dementias, National Institute on Aging, Bethesda, MD, USA. kimberley.billingsley@nih.gov.

Abstract

Parkinson's disease (PD) is a common neurodegenerative disorder with a significant risk proportion driven by genetics. While much progress has been made, most of the heritability remains unknown. This is in-part because previous genetic studies have focused on the contribution of single nucleotide variants. More complex forms of variation, such as structural variants and tandem repeats, are already associated with several synucleinopathies. However, because more sophisticated sequencing methods are usually required to detect these regions, little is understood regarding their contribution to PD. One example is a polymorphic CT-rich region in intron 4 of the SNCA gene. This haplotype has been suggested to be associated with risk of Lewy Body (LB) pathology in Alzheimer's Disease and SNCA gene expression, but is yet to be investigated in PD. Here, we attempt to resolve this CT-rich haplotype and investigate its role in PD. We performed targeted PacBio HiFi sequencing of the region in 1375 PD cases and 959 controls. We replicate the previously reported associations and a novel association between two PD risk SNVs (rs356182 and rs5019538) and haplotype 4, the largest haplotype. Through quantitative trait locus analyzes we identify a significant haplotype 4 association with alternative CAGE transcriptional start site usage, not leading to significant differential SNCA gene expression in post-mortem frontal cortex brain tissue. Therefore, disease association in this locus might not be biologically driven by this CT-rich repeat region. Our data demonstrates the complexity of this SNCA region and highlights that further follow up functional studies are warranted.