A comprehensive analysis of deletions, multiplications, and copy number variations in PARK2
Abstract
Objectives: To perform a comprehensive population genetic study of PARK2. PARK2 mutations are associated with juvenile parkinsonism, Alzheimer disease, cancer, leprosy, and diabetes mellitus, yet ironically, there has been no comprehensive study of PARK2 in control subjects; and to resolve controversial association of PARK2 heterozygous mutations with Parkinson disease (PD) in a well-powered study.
Methods: We studied 1,686 control subjects (mean age 66.1 ± 13.1 years) and 2,091 patients with PD (mean onset age 58.3 ± 12.1 years). We tested for PARK2 deletions/multiplications/copy number variations (CNV) using semiquantitative PCR and multiplex ligation-dependent probe amplification, and validated the mutations by real-time quantitative PCR. Subjects were tested for point mutations previously. Association with PD was tested as PARK2 main effect, and in combination with known PD risk factors: SNCA, MAPT, APOE, smoking, and coffee intake.
Results: A total of 0.95% of control subjects and 0.86% of patients carried a heterozygous CNV mutation. CNV mutations found in 16 control subjects were all in exons 1–4, sparing exons that encode functionally critical protein domains. Thirteen patients had 2 CNV mutations, 5 had 1 CNV and 1 point mutation, and 18 had 1 CNV mutation. Mutations found in patients spanned exons 2–9. In whites, having 1 CNV was not associated with increased risk (odds ratio 1.05, p = 0.89) or earlier onset of PD (64.7 ± 8.6 heterozygous vs 58.5 ± 11.8 normal).
Conclusions: This comprehensive population genetic study in control subjects fills the void for a PARK2 reference dataset. There is no compelling evidence for association of heterozygous PARK2 mutations, by themselves or in combination with known risk factors, with PD.
Get full access to this article
View all available purchase options and get full access to this article.
Supplementary Material
REFERENCES
1.
Asakawa S, Tsunematsu K, Takayanagi A, et al. The genomic structure and promoter region of the human parkin gene. Biochem Biophys Res Commun 2001;286:863–868.
2.
Cesari R, Martin ES, Calin GA, et al. Parkin, a gene implicated in autosomal recessive juvenile parkinsonism, is a candidate tumor suppressor gene on chromosome 6q25-q27. Proc Natl Acad Sci USA 2003;100:5956–5961.
3.
Veeriah S, Taylor BS, Meng S, et al. Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies. Nat Genet 2010;42:77–82.
4.
Kitada T, Asakawa S, Hattori N, et al. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Nature 1998;392:605–608.
5.
Mira MT, Alcais A, Nguyen VT, et al. Susceptibility to leprosy is associated with PARK2 and PACRG. Nature 2004;427:636–640.
6.
Glessner JT, Wang K, Cai G, et al. Autism genome-wide copy number variation reveals ubiquitin and neuronal genes. Nature 2009;459:569–573.
7.
Wongseree W, Assawamakin A, Piroonratana T, Sinsomros S, Limwongse C, Chaiyaratana N. Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses. BMC Bioinformatics 2009;10:294.
8.
Burns MP, Zhang L, Rebeck GW, Querfurth HW, Moussa CE. Parkin promotes intracellular Abeta1–42 clearance. Hum Mol Genet 2009;18:3206–3216.
9.
Chien HF, Rohe CF, Costa MD, et al. Early-onset Parkinson's disease caused by a novel parkin mutation in a genetic isolate from north-eastern Brazil. Neurogenetics 2006;7:13–19.
10.
Hedrich K, Marder K, Harris J, et al. Evaluation of 50 probands with early-onset Parkinson's disease for Parkin mutations. Neurology 2002;58:1239–1246.
11.
Lesage S, Lohmann E, Tison F, Durif F, Durr A, Brice A. Rare heterozygous parkin variants in French early-onset Parkinson disease patients and controls. J Med Genet 2008;45:43–46.
12.
Clark LN, Afridi S, Karlins E, et al. Case-control study of the parkin gene in early-onset Parkinson disease. Arch Neurol 2006;63:548–552.
13.
Foroud T, Uniacke SK, Liu L, et al. Heterozygosity for a mutation in the parkin gene leads to later onset Parkinson disease. Neurology 2003;60:796–801.
14.
Pankratz N, Kissell DK, Pauciulo MW, et al. Parkin dosage mutations have greater pathogenicity in familial PD than simple sequence mutations. Neurology 2009;73:279–286.
15.
Sun M, Latourelle JC, Wooten GF, et al. Influence of heterozygosity for parkin mutation on onset age in familial Parkinson disease: the GenePD study. Arch Neurol 2006;63:826–832.
16.
Oliveira SA, Scott WK, Martin ER, et al. Parkin mutations and susceptibility alleles in late-onset Parkinson's disease. Ann Neurol 2003;53:624–629.
17.
Schlitter AM, Kurz M, Larsen JP, et al. Parkin gene variations in late-onset Parkinson's disease: comparison between Norwegian and German cohorts. Acta Neurol Scand 2006;113:9–13.
18.
Khan NL, Scherfler C, Graham E, et al. Dopaminergic dysfunction in unrelated, asymptomatic carriers of a single parkin mutation. Neurology 2005;64:134–136.
19.
Mortiboys H, Thomas KJ, Koopman WJ, et al. Mitochondrial function and morphology are impaired in parkin-mutant fibroblasts. Ann Neurol 2008;64:555–565.
20.
Lincoln SJ, Maraganore DM, Lesnick TG, et al. Parkin variants in North American Parkinson's disease: cases and controls. Mov Disord 2003;18:1306–1311.
21.
Bruggemann N, Mitterer M, Lanthaler AJ, et al. Frequency of heterozygous Parkin mutations in healthy subjects: need for careful prospective follow-up examination of mutation carriers. Parkinsonism Relat Disord 2009;15:425–429.
22.
Kay DM, Moran D, Moses L, et al. Heterozygous parkin point mutations are as common in control subjects as in Parkinson's patients. Ann Neurol 2007;61:47–54.
23.
Gibb W, Lees A. The relevance of the Lewy body to the pathogenesis of idiopathic Parkinson's disease. J Neurol Neurosurg Psychiatry 1988;51:745–752.
24.
Poorkaj P, Nutt JG, James D, et al. Parkin mutation analysis in clinic patients with early-onset Parkinson's disease. Am J Med Genet A 2004;129:44–50.
25.
Lucking CB, Durr A, Bonifati V, et al. Association between early-onset Parkinson's disease and mutations in the parkin gene: French Parkinson's Disease Genetics Study Group. N Engl J Med 2000;342:1560–1567.
26.
Djarmati A, Guzvic M, Grunewald A, et al. Rapid and reliable detection of exon rearrangements in various movement disorders genes by multiplex ligation-dependent probe amplification. Mov Disord 2007;22:1708–1714.
27.
Scarciolla O, Brancati F, Valente EM, et al. Multiplex ligation-dependent probe amplification assay for simultaneous detection of Parkinson's disease gene rearrangements. Mov Disord 2007;22:2274–2278.
28.
Powers K, Kay D, Factor S, et al. Combined effects of smoking, coffee and NSAIDs on Parkinson's disease risk. Mov Disord 2008;23:88–95.
29.
Kay DM, Factor SA, Samii A, et al. Genetic association between alpha-synuclein and idiopathic Parkinson's disease. Am J Med Genet B Neuropsychiatr Genet 2008;147B:1222–1230.
30.
Mata I, Samii A, Factor S, et al. Variation in the 3′ region of the alpha-synuclein gene modifies risk for Parkinson's disease. Mov Disord 2009;24:S145.
31.
Zabetian CP, Hutter CM, Factor SA, et al. Association analysis of MAPT H1 haplotype and subhaplotypes in Parkinson's disease. Ann Neurol 2007;62:137–144.
32.
Available at: http://www.pdgene.org/. Accessed November 29, 2009.
33.
Payami H, Kay DM, Zabetian CP, Schellenberg GD, Factor SA, McCulloch CC. Visualizing disease associations: graphic analysis of frequency distributions as a function of age using moving average plots (MAP) with application to Alzheimer's and Parkinson's disease. Genet Epidemiol 2009;34:92–99.
Information & Authors
Information
Published In
Copyright
© 2010.
Publication History
Published online: September 27, 2010
Published in print: September 28, 2010
Keyword
Authors
Metrics & Citations
Metrics
Citations
Download Citations
If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Select your manager software from the list below and click Download.
Cited By
- The Role of Structural Variants in the Genetic Architecture of Parkinson’s Disease, International Journal of Molecular Sciences, 25, 9, (4801), (2024).https://doi.org/10.3390/ijms25094801
- Polymorphisms within Autophagy-Related Genes as Susceptibility Biomarkers for Multiple Myeloma: A Meta-Analysis of Three Large Cohorts and Functional Characterization, International Journal of Molecular Sciences, 24, 10, (8500), (2023).https://doi.org/10.3390/ijms24108500
- PARK2 Microdeletion or Duplications Have Been Implicated in Different Neurological Disorders Including Early Onset Parkinson Disease, Genes, 14, 3, (600), (2023).https://doi.org/10.3390/genes14030600
- Genetic landscape of Parkinson’s disease and related diseases in Luxembourg, Frontiers in Aging Neuroscience, 15, (2023).https://doi.org/10.3389/fnagi.2023.1282174
- The effect of Parkin gene S/N 167 polymorphism on resting spontaneous brain functional activity in Parkinson's Disease, Parkinsonism & Related Disorders, 113, (105484), (2023).https://doi.org/10.1016/j.parkreldis.2023.105484
- Association between copy number variations in parkin ( PRKN ) and schizophrenia and autism spectrum disorder: A case–control study , Neuropsychopharmacology Reports, 44, 1, (42-50), (2023).https://doi.org/10.1002/npr2.12370
- Long‐Read Sequencing Resolves a Complex Structural Variant in PRKN Parkinson's Disease , Movement Disorders, 38, 12, (2249-2257), (2023).https://doi.org/10.1002/mds.29610
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer’s disease: review, recommendation, implementation and application, Molecular Neurodegeneration, 17, 1, (2022).https://doi.org/10.1186/s13024-022-00517-z
- New therapeutic approaches to Parkinson's disease targeting GBA, LRRK2 and Parkin, Neuropharmacology, 202, (108822), (2022).https://doi.org/10.1016/j.neuropharm.2021.108822
- A very early onset of juvenile parkinsonism, Journal of Neurology, 269, 12, (6661-6663), (2022).https://doi.org/10.1007/s00415-022-11278-6
- See more
Loading...
View Options
Login options
Check if you have access through your login credentials or your institution to get full access on this article.
Personal login Institutional LoginPurchase Options
The neurology.org payment platform is currently offline. Our technical team is working as quickly as possible to restore service.
If you need immediate support or to place an order, please call or email customer service:
- 1-800-638-3030 for U.S. customers - 8:30 - 7 pm ET (M-F)
- 1-301-223-2300 for customers outside the U.S. - 8:30 - 7 pm ET (M-F)
- [email protected]
We appreciate your patience during this time and apologize for any inconvenience.