Complementarity of long-read sequencing and optical genome mapping in Parkinson’s disease Article Swipe
André Fienemann
,
Theresa Lüth
,
Susen Schaake
,
Carolin Gabbert
,
Marius Möller
,
Hauke Busch
,
Katja Lohmann
,
Jonas A. Gustafson
,
Danny E. Miller
,
Kensuke Daida
,
Manabu Funayama
,
Nobutaka Hattori
,
Samia Ben Sassi
,
F. Hentati
,
Matthew J. Farrer
,
Kristian K Ullrich
,
Christine Klein
,
Joanne Trinh
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.08.20.25333965
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.08.20.25333965
Background With third-generation long-read sequencing (LRS) platforms and optical genome mapping technologies (OGM), the ability to detect large and complex structural variants (SVs) is rapidly advancing. This has led to the discovery of novel pathogenic variants, such as large deletions and insertions, in neurodegenerative movement disorders. Thus, we aimed to systematically examine the applicability of the combined application of LRS and OGM in Parkinson’s disease (PD). Methods Ultra-high molecular weight DNA was derived from blood and fibroblast cultures and used for Oxford Nanopore Technologies (ONT) LRS and OGM. We included 19 patients with mostly early-onset PD. Variant calling was performed with the tools Sniffles2 and Spectre for ONT and the Bionano Solve software for OGM. The size distribution of deletions and insertions was compared, and a subsequent analysis pipeline based on AnnotSV, SVAFotate, and needLR was employed to annotate and filter for rare (population allele frequency ≤1%) or potentially pathogenic (CADD-SV >20) variants affecting 134 known movement disorder genes. Results Both methods identified SVs ≥50 kb; however, OGM detected fewer SVs (49,677) with a larger mean size of 25 kb (SD=209 kb) compared to ONT (92,030, mean=17 kb, SD=1.1 Mb). In the size bracket of 50-80 kb, which falls outside the ideal detection range of Sniffles2 and Spectre, OGM detected 384 deletions and insertions, compared to six detected by ONT. OGM detected significantly larger deletions and insertions than ONT (p-value <2.2×10 -16 ). Regarding known movement disorder genes, a heterozygous intergenic deletion (195 kb) near ITPR1 was detected by both methods, and OGM validated a previously published 7 Mb inversion in PRKN . Heterozygous deletions in ATXN2 (1.4 kb), SUCLA2 (1.7 kb), and PNKD (2.6 kb) were detected by OGM and confirmed to be intronic by ONT. Conclusion OGM allows for better detection of large insertions and can serve as a powerful first-line method to detect large pathogenic variants. However, it greatly benefits from a high-resolution sequencing technique like ONT to refine breakpoint positions. Despite certain limitations, ONT proved to be highly capable of detecting large variants independently; thus, it allows for a highly complementary assessment and validation of structural variation in combination with OGM.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1101/2025.08.20.25333965
- https://www.medrxiv.org/content/medrxiv/early/2025/08/21/2025.08.20.25333965.full.pdf
- OA Status
- green
- References
- 63
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4413385839
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
-
https://openalex.org/W4413385839Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1101/2025.08.20.25333965Digital Object Identifier
- Title
-
Complementarity of long-read sequencing and optical genome mapping in Parkinson’s diseaseWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-08-21Full publication date if available
- Authors
-
André Fienemann, Theresa Lüth, Susen Schaake, Carolin Gabbert, Marius Möller, Hauke Busch, Katja Lohmann, Jonas A. Gustafson, Danny E. Miller, Kensuke Daida, Manabu Funayama, Nobutaka Hattori, Samia Ben Sassi, F. Hentati, Matthew J. Farrer, Kristian K Ullrich, Christine Klein, Joanne TrinhList of authors in order
- Landing page
-
https://doi.org/10.1101/2025.08.20.25333965Publisher landing page
- PDF URL
-
https://www.medrxiv.org/content/medrxiv/early/2025/08/21/2025.08.20.25333965.full.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
-
https://www.medrxiv.org/content/medrxiv/early/2025/08/21/2025.08.20.25333965.full.pdfDirect OA link when available
- Concepts
-
Complementarity (molecular biology), Parkinson's disease, Computational biology, Disease, Genetics, Biology, Computer science, Medicine, Internal medicineTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- References (count)
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63Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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