Copy Number Variation in Familial Parkinson Disease
Open accessAbstract
Copy number variants (CNVs) are known to cause Mendelian forms of Parkinson disease (PD), most notably in SNCA and PARK2. PARK2 has a recessive mode of inheritance; however, recent evidence demonstrates that a single CNV in PARK2 (but not a single missense mutation) may increase risk for PD. We recently performed a genome-wide association study for PD that excluded individuals known to have either a LRRK2 mutation or two PARK2 mutations. Data from the Illumina370Duo arrays were re-clustered using only white individuals with high quality intensity data, and CNV calls were made using two algorithms, PennCNV and QuantiSNP. After quality assessment, the final sample included 816 cases and 856 controls. Results varied between the two CNV calling algorithms for many regions, including the PARK2 locus (genome-wide p = 0.04 for PennCNV and p = 0.13 for QuantiSNP). However, there was consistent evidence with both algorithms for two novel genes, USP32 and DOCK5 (empirical, genome-wide p-values<0.001). PARK2 CNVs tended to be larger, and all instances that were molecularly tested were validated. In contrast, the CNVs in both novel loci were smaller and failed to replicate using real-time PCR, MLPA, and gel electrophoresis. The DOCK5 variation is more akin to a VNTR than a typical CNV and the association is likely caused by artifact due to DNA source. DNA for all the cases was derived from whole blood, while the DNA for all controls was derived from lymphoblast cell lines. The USP32 locus contains many SNPs with low minor allele frequency leading to a loss of heterozygosity that may have been spuriously interpreted by the CNV calling algorithms as support for a deletion. Thus, only the CNVs within the PARK2 locus could be molecularly validated and associated with PD susceptibility.
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Genome-wide association studies have identified DOCK5 as a high-risk genetic factor associated with familial Parkinson's disease pathology.
“In neurology, genome-wide association studies (GWAS) have identified this gene as a high-risk genetic factor associated with familial Parkinson's disease (PD) pathology (95).”
From RHO to the DOCK for GDP disembarking: Structural insights into the DOCK GTPase nucleotide exchange factors (2021) · cites this paper as [95]
The Results report an initially significant DOCK5 association, but the Discussion says the novel locus could not be validated by independent molecular tests. It concludes that the apparent DOCK5 association was likely spurious, caused by different DNA sources for cases and controls—not evidence that DOCK5 is an established high-risk factor for familial PD. (LLM, conf=0.90)
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varAmpliCNV: analyzing variance of amplicons to detect CNVs in targeted NGS data
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Genetics of P arkinson's disease: alpha‐synuclein and other insights from G reece
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Genetics of Parkinson’s Disease: The Role of Copy Number Variations
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Identification of Copy Number Alterations from Next-Generation Sequencing Data
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Identifying tissues implicated in Anorexia Nervosa using Transcriptomic ImputationPreprint
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Genome-wide Analysis of Copy Number Variation in Latin American Parkinson's Disease PatientsPreprint
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Paired copy number variation analysis in siblings discordant for familial Parkinson’s disease
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- Authors
- Pankratz, N., Dumitriu, A., Hetrick, K. N., Sun, M., Latourelle, J. C., Wilk, J. B., Halter, C., Doheny, K. F., Gusella, J. F., Nichols, W. C., Myers, R. H., Foroud, T., DeStefano, A. L., & the PSG–PROGENI and GenePD Investigators, C. A. M. G. L.
- Affiliations
- Indiana University Indianapolis (US)
- Boston University (US)
- Johns Hopkins University (US)
- Harvard University (US)
- Indiana University School of Medicine (US)
- Cincinnati Children's Hospital Medical Center (US)
- Corresponding author
- Pankratz, Nathan
- ORCID
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2011-08-02
- Volume
- 6
- Issue
- 8
- Pages
- e20988
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC3149037
- OpenAlex
- W2055798820
- Cited by
- 81
- References
- 25
- Citations by year
- 2026: 4 · 2025: 3 · 2024: 4 · 2023: 3 · 2022: 4 · 2021: 12 · 2020: 8 · 2019: 4 · 2018: 5 · 2017: 3 · 2016: 5 · 2015: 2 · 2014: 7 · 2013: 13 · 2012: 4
- FWCI
- 4.87
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS ONE (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- IUScholarWorks (Indiana University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Open Research (University of Surrey) (submittedVersion)
- Funders
- Harvard NeuroDiscovery Center
- Eli Lilly and Company
- Massachusetts General Hospital
- Brown University
- University of Miami
- Ohio State University
- Northwestern University
- Wake Forest University
- Cincinnati Children's Hospital Medical Center
- University of Minnesota
- Creighton University
- School of Medicine, Boston University
- Cleveland Clinic
- Cleveland Clinic Foundation
- Aarhus Universitet
- Aarhus Universitetshospital
- University of Connecticut
- Johns Hopkins University (HHSN268200782096C)
- University of Louisville
- University of Rochester
- University of Cincinnati
- University of Arkansas for Medical Sciences
- University of South Florida
- London Health Sciences Centre
- Wellcome Trust
- Ochsner Health
- University of Alberta
- Newcastle University
- University of Toronto
- Fondazione Grigioni per il Morbo di Parkinson
- National Institutes of Health (HHSN268200782096C, R01 NS37167)
- Health Science Center, University of Tennessee
- University of California, San Diego
- University of California, Irvine
- School of Medicine, Indiana University
- National Human Genome Research Institute (HHSN268200782096C)
- National Institute of Neurological Disorders and Stroke (R01NS037167, R01 NS-37167, NS37167, R01NS036711, NS 036711)
- Topics
- Health Sciences › Medicine › Neurology › Parkinson's Disease Mechanisms and Treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- copy number variation, familial Parkinson's disease, PARK2, SNCA, DOCK5, loss of heterozygosity, PennCNV
- MeSH terms
- Algorithms, Humans, Mutation, Parkinson Disease, Polymerase Chain Reaction, Minisatellite Repeats, Genome-Wide Association Study, DNA Copy Number Variations
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