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Yoshino H, Li Y, Nishioka K, Daida K, Hayashida A, Ishiguro Y, Yamada D, Izawa N, Nishi K, Nishikawa N, Oyama G, Hatano T, Nakamura S, Yoritaka A, Motoi Y, Funayama M, Hattori N, the investigators of Japan Parkinson disease genetic study. Genotype-phenotype correlation of Parkinson's disease with PRKN variants. Neurobiol Aging 2022; 114:117-128. [DOI: 10.1016/j.neurobiolaging.2021.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 12/26/2021] [Accepted: 12/31/2021] [Indexed: 11/16/2022]
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2
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Liu S, Yu T. Kernel density estimation in mixture models with known mixture proportions. Stat Med 2021; 40:6360-6372. [PMID: 34474504 DOI: 10.1002/sim.9187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 06/18/2021] [Accepted: 08/17/2021] [Indexed: 11/11/2022]
Abstract
In this article, we consider the density estimation for data with a mixture structure, where the component densities are assumed unknown, but for each observation, the probabilities of its membership to the subpopulations are known or estimable from other resources. Data of this kind arise from practice and have wide applications. Motivated from the classical kernel density estimation method for a single population, we propose a weighted kernel density estimation method to estimate the component density functions nonparametrically. Within the framework of the EM algorithm, we derive an algorithm that computes our proposed estimates effectively. Via extensive simulation studies, we demonstrate that our methods outperform the existing methods in most occasions. We further compare our methods with existing methods by real data examples.
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Affiliation(s)
- Siyun Liu
- Department of Statistics and Data Science, National University of Singapore, Singapore
| | - Tao Yu
- Department of Statistics and Data Science, National University of Singapore, Singapore
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3
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Day JO, Mullin S. The Genetics of Parkinson's Disease and Implications for Clinical Practice. Genes (Basel) 2021; 12:genes12071006. [PMID: 34208795 PMCID: PMC8304082 DOI: 10.3390/genes12071006] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/21/2021] [Accepted: 06/28/2021] [Indexed: 12/17/2022] Open
Abstract
The genetic landscape of Parkinson’s disease (PD) is characterised by rare high penetrance pathogenic variants causing familial disease, genetic risk factor variants driving PD risk in a significant minority in PD cases and high frequency, low penetrance variants, which contribute a small increase of the risk of developing sporadic PD. This knowledge has the potential to have a major impact in the clinical care of people with PD. We summarise these genetic influences and discuss the implications for therapeutics and clinical trial design.
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Affiliation(s)
- Jacob Oliver Day
- Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK;
| | - Stephen Mullin
- Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK;
- Department of Clinical and Movement Neurosciences, University College London Institute of Neurology, London WC1N 3BG, UK
- Correspondence:
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4
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Yu E, Rudakou U, Krohn L, Mufti K, Ruskey JA, Asayesh F, Estiar MA, Spiegelman D, Surface M, Fahn S, Waters CH, Greenbaum L, Espay AJ, Dauvilliers Y, Dupré N, Rouleau GA, Hassin-Baer S, Fon EA, Alcalay RN, Gan-Or Z. Analysis of Heterozygous PRKN Variants and Copy-Number Variations in Parkinson's Disease. Mov Disord 2020; 36:178-187. [PMID: 32970363 DOI: 10.1002/mds.28299] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/19/2020] [Accepted: 08/30/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Biallelic PRKN mutation carriers with Parkinson's disease (PD) typically have an earlier disease onset, slow disease progression, and, often, different neuropathology compared to sporadic PD patients. However, the role of heterozygous PRKN variants in the risk of PD is controversial. OBJECTIVES Our aim was to examine the association between heterozygous PRKN variants, including single-nucleotide variants and copy-number variations (CNVs), and PD. METHODS We fully sequenced PRKN in 2809 PD patients and 3629 healthy controls, including 1965 late-onset (63.97 ± 7.79 years, 63% men) and 553 early-onset PD patients (43.33 ± 6.59 years, 68% men). PRKN was sequenced using targeted next-generation sequencing with molecular inversion probes. CNVs were identified using a combination of multiplex ligation-dependent probe amplification and ExomeDepth. To examine whether rare heterozygous single-nucleotide variants and CNVs in PRKN are associated with PD risk and onset, we used optimized sequence kernel association tests and regression models. RESULTS We did not find any associations between all types of PRKN variants and risk of PD. Pathogenic and likely-pathogenic heterozygous single-nucleotide variants and CNVs were less common among PD patients (1.52%) than among controls (1.8%, false discovery rate-corrected P = 0.55). No associations with age at onset and in stratified analyses were found. CONCLUSIONS Heterozygous single-nucleotide variants and CNVs in PRKN are not associated with PD. Molecular inversion probes allow for rapid and cost-effective detection of all types of PRKN variants, which may be useful for pretrial screening and for clinical and basic science studies targeting specifically PRKN patients. © 2020 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Eric Yu
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada
| | - Uladzislau Rudakou
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada
| | - Lynne Krohn
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada
| | - Kheireddin Mufti
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada
| | - Jennifer A Ruskey
- Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Farnaz Asayesh
- Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Mehrdad A Estiar
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada
| | - Dan Spiegelman
- Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Matthew Surface
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA
| | - Stanley Fahn
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA
| | - Cheryl H Waters
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Ramat Gan, Israel.,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Ramat Gan, Israel.,Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Alberto J Espay
- UC Gardner Neuroscience Institute and Gardner Family Center for Parkinson's Disease and Movement Disorders, Cincinnati, Ohio, USA
| | - Yves Dauvilliers
- Department of Neurology, National Reference Center for Narcolepsy, Sleep Unit, Gui-de-Chauliac Hospital, CHU Montpellier, University of Montpellier, Montpellier, France
| | - Nicolas Dupré
- Division of Neurosciences, CHU de Québec, Université Laval, Laval, Quebec, Canada.,Department of Medicine, Faculty of Medicine, Université Laval, Laval, Quebec, Canada
| | - Guy A Rouleau
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Sharon Hassin-Baer
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Neurology, Movement Disorders Institute, Sheba Medical Center, Ramat-Gan, Israel
| | - Edward A Fon
- Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Roy N Alcalay
- Department of Neurology, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA.,Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York, USA
| | - Ziv Gan-Or
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Montreal Neurological Institute and Hospital, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
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5
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Pleiotropic effects for Parkin and LRRK2 in leprosy type-1 reactions and Parkinson's disease. Proc Natl Acad Sci U S A 2019; 116:15616-15624. [PMID: 31308240 PMCID: PMC6681704 DOI: 10.1073/pnas.1901805116] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Type-1 reactions (T1R) are pathological immune responses in leprosy and a frequent cause of peripheral nerve damage. Employing a candidate gene approach combined with deep resequencing, we identified amino acid mutations in the E3 ligase Parkin and the polyfunctional kinase LRRK2 that were associated with T1R. This finding directly linked both proteins with the extent of the immune response in an infectious disease. Moreover, amino acids associated with T1R mutations were significantly enriched for mutations found in patients suffering from Parkinson’s disease (PD). These findings confirm Parkin and LRRK2 as 2 key inflammatory regulators and suggest that T1R and PD share overlapping pathways of pathogenesis. Type-1 reactions (T1R) are pathological inflammatory episodes and main contributors to nerve damage in leprosy. Here, we evaluate the genewise enrichment of rare protein-altering variants in 7 genes where common variants were previously associated with T1R. We selected 474 Vietnamese leprosy patients of which 237 were T1R-affected and 237 were T1R-free matched controls. Genewise enrichment of nonsynonymous variants was tested with both kernel-based (sequence kernel association test [SKAT]) and burden methods. Of the 7 genes tested 2 showed statistical evidence of association with T1R. For the LRRK2 gene an enrichment of nonsynonymous variants was observed in T1R-free controls (PSKAT-O = 1.6 × 10−4). This genewise association was driven almost entirely by the gain-of-function variant R1628P (P = 0.004; odds ratio = 0.29). The second genewise association was found for the Parkin coding gene PRKN (formerly PARK2) where 7 rare variants were enriched in T1R-affected cases (PSKAT-O = 7.4 × 10−5). Mutations in both PRKN and LRRK2 are known causes of Parkinson’s disease (PD). Hence, we evaluated to what extent such rare amino acid changes observed in T1R are shared with PD. We observed that amino acids in Parkin targeted by nonsynonymous T1R-risk mutations were also enriched for mutations implicated in PD (P = 1.5 × 10−4). Hence, neuroinflammation in PD and peripheral nerve damage due to inflammation in T1R share overlapping genetic control of pathogenicity.
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6
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Yu T, Li P, Qin J. Maximum smoothed likelihood component density estimation in mixture models with known mixing proportions. Electron J Stat 2019. [DOI: 10.1214/19-ejs1620] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Jankovic MZ, Dobricic V, Kresojevic N, Markovic V, Petrovic I, Svetel M, Pekmezovic T, Novakovic I, Kostic V. Identification of mutations in the PARK2 gene in Serbian patients with Parkinson's disease. J Neurol Sci 2018; 393:27-30. [PMID: 30099245 DOI: 10.1016/j.jns.2018.07.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 04/10/2018] [Accepted: 07/23/2018] [Indexed: 01/03/2023]
Abstract
Mutations in the PARK2 (PRKN) gene are the most common cause of autosomal-recessive (AR) juvenile parkinsonism and young-onset Parkinson's disease (YOPD). >100 different variants have been reported, including point mutations, small indels and single or multiple exon copy number variations. Mutation screening of PARK2 was performed in 225 Serbian PD patients (143 males and 82 females) with disease onset before 50 years and/or positive family history with apparent AR inheritance. All coding regions and their flanking intronic sequences were amplified and directly sequenced. Whole exon multiplications or deletions were detected using Multiple Ligation Probe Amplification (MLPA) method. We identified 12 PD patients with PARK2 mutations (5.3%). Five patients (2.2%) had biallelic mutations and seven (3.1%) were single mutation carriers. Patients with compound heterozygous mutations had earlier onset of the disease compared to non-carriers (p = 0.005) or heterozygotes (p = 0.001). Other clinical features in mutation carriers were not different compared to non-carriers. In our cohort, sequence and dosage variants were equally represented in patients, inducing their first symptoms mainly before the age of 30. For efficient genetic testing strategy, patients with early, especially juvenile onset of PD were strong candidates for both dosage and sequence variants screening of PARK2 gene.
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Affiliation(s)
- M Z Jankovic
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr. Subotica 6, Belgrade, Serbia.
| | - V Dobricic
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr. Subotica 6, Belgrade, Serbia
| | - N Kresojevic
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr. Subotica 6, Belgrade, Serbia
| | - V Markovic
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr. Subotica 6, Belgrade, Serbia
| | - I Petrovic
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr. Subotica 6, Belgrade, Serbia
| | - M Svetel
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr. Subotica 6, Belgrade, Serbia
| | - T Pekmezovic
- Institute for Epidemiology, School of Medicine, University of Belgrade, Visegradska 26, Belgrade, Serbia
| | - I Novakovic
- Institute for Human Genetics, School of Medicine, University of Belgrade, Visegradska 26, Belgrade, Serbia
| | - V Kostic
- Neurology Clinic, Clinical Center of Serbia, School of Medicine, University of Belgrade, Dr. Subotica 6, Belgrade, Serbia
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8
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Kazansky Y, Lai MY, Singh RK, Fushman D. Impact of different ionization states of phosphorylated Serine-65 on ubiquitin structure and interactions. Sci Rep 2018; 8:2651. [PMID: 29422536 PMCID: PMC5805711 DOI: 10.1038/s41598-018-20860-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 01/23/2018] [Indexed: 01/13/2023] Open
Abstract
The covalent attachment of ubiquitin (Ub) or Ub chains to cellular proteins is a versatile post-translational modification involved in a variety of eukaryotic cellular events. Recently, the post-translational modification of Ub itself by phosphorylation has emerged as an important component of the Ub-signaling system. Specifically, Ub phosphorylation at serine-65 was shown to activate parkin-mediated mitochondrial quality control. However, the impact of phosphorylation on Ub structure and interactions is poorly understood. Here we investigate the recently reported structural changes in Ub upon serine-65 phosphorylation, namely, the equilibrium between a native-like and a novel, alternate conformer of phosphorylated Ub (pUb). We show that this equilibrium is pH-dependent, and the two pUb conformers are linked to the different charge states of the phosphate group. We examined pUb binding to a known Ub-receptor and found that the alternate conformer is binding incompetent. Furthermore, serine-65 phosphorylation affects the conformational equilibrium of K48-linked Ub dimers. Lastly, our crystal structure of S65D Ub and NMR data indicate that phosphomimetic mutations do not adequately reproduce the salient features of pUb. Our results suggest that the pH-dependence of the conformations and binding properties of phosphorylated Ub and polyUb could provide an additional level of modulation in Ub-mediated signaling.
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Affiliation(s)
- Yaniv Kazansky
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Ming-Yih Lai
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - Rajesh K Singh
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD, 20742, USA.
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9
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Activation mechanisms of the E3 ubiquitin ligase parkin. Biochem J 2017; 474:3075-3086. [PMID: 28860335 DOI: 10.1042/bcj20170476] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/24/2017] [Accepted: 07/31/2017] [Indexed: 12/31/2022]
Abstract
Monogenetic, familial forms of Parkinson's disease (PD) only account for 5-10% of the total number of PD cases, but analysis of the genes involved therein is invaluable to understanding PD-associated neurodegenerative signaling. One such gene, parkin, encodes a 465 amino acid E3 ubiquitin ligase. Of late, there has been considerable interest in the role of parkin signaling in PD and in identifying its putative substrates, as well as the elucidation of the mechanisms through which parkin itself is activated. Its dysfunction underlies both inherited and idiopathic PD-associated neurodegeneration. Here, we review recent literature that provides a model of activation of parkin in the setting of mitochondrial damage that involves PINK1 (PTEN-induced kinase-1) and phosphoubiquitin. We note that neuronal parkin is primarily a cytosolic protein (with various non-mitochondrial functions), and discuss potential cytosolic parkin activation mechanisms.
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10
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Xu K, Ma Y, Wang Y. Nonparametric distribution estimation in the presence of familial correlation and censoring. Electron J Stat 2017. [DOI: 10.1214/17-ejs1274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Shulskaya MV, Shadrina MI, Fedotova EY, Abramycheva NY, Limborska SA, Illarioshkin SN, Slominsky PA. Second mutation in PARK2 is absent in patients with sporadic Parkinson's disease and heterozygous exonic deletions/duplications in parkin gene. Int J Neurosci 2016; 127:781-784. [DOI: 10.1080/00207454.2016.1255612] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Marina V. Shulskaya
- Department of Molecular Basics of Human Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Maria I. Shadrina
- Department of Molecular Basics of Human Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ekaterina Yu. Fedotova
- Department of Neurogenetics, Federal State Scientific Institution ‘Scientific Center of Neurology’, Moscow, Russia
| | - Nataliya Yu. Abramycheva
- Department of Neurogenetics, Federal State Scientific Institution ‘Scientific Center of Neurology’, Moscow, Russia
| | - Svetlana A. Limborska
- Department of Molecular Basics of Human Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Sergey N. Illarioshkin
- Department of Neurogenetics, Federal State Scientific Institution ‘Scientific Center of Neurology’, Moscow, Russia
| | - Petr A. Slominsky
- Department of Molecular Basics of Human Genetics, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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12
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Wang Y, Liang B, Tong X, Marder K, Bressman S, Orr-Urtreger A, Giladi N, Zeng D. Efficient Estimation of Nonparametric Genetic Risk Function with Censored Data. Biometrika 2015; 102:515-532. [PMID: 26412864 PMCID: PMC4581539 DOI: 10.1093/biomet/asv030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
With an increasing number of causal genes discovered for complex human disorders, it is crucial to assess the genetic risk of disease onset for individuals who are carriers of these causal mutations and compare the distribution of age-at-onset with that in non-carriers. In many genetic epidemiological studies aiming at estimating causal gene effect on disease, the age-at-onset of disease is subject to censoring. In addition, some individuals' mutation carrier or non-carrier status can be unknown due to the high cost of in-person ascertainment to collect DNA samples or death in older individuals. Instead, the probability of these individuals' mutation status can be obtained from various sources. When mutation status is missing, the available data take the form of censored mixture data. Recently, various methods have been proposed for risk estimation from such data, but none is efficient for estimating a nonparametric distribution. We propose a fully efficient sieve maximum likelihood estimation method, in which we estimate the logarithm of the hazard ratio between genetic mutation groups using B-splines, while applying nonparametric maximum likelihood estimation for the reference baseline hazard function. Our estimator can be calculated via an expectation-maximization algorithm which is much faster than existing methods. We show that our estimator is consistent and semiparametrically efficient and establish its asymptotic distribution. Simulation studies demonstrate superior performance of the proposed method, which is applied to the estimation of the distribution of the age-at-onset of Parkinson's disease for carriers of mutations in the leucine-rich repeat kinase 2 gene.
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Affiliation(s)
- Yuanjia Wang
- Department of Biostatistics, Mailman School of Public Health, 722 W168th Street, New York 10032, U.S.A.
| | - Baosheng Liang
- School of Mathematical Sciences, Beijing Normal University, Beijing 100875, China.
| | - Xingwei Tong
- School of Mathematical Sciences, Beijing Normal University, Beijing 100875, China.
| | - Karen Marder
- Department of Neurology and Psychiatry, College of Physicians and Surgeons, Columbia University, New York 10032, U.S.A.
| | - Susan Bressman
- The Alan and Barbara Mirken Department of Neurology, Beth Israel Medical Center, New York, 10003, U.S.A.
| | - Avi Orr-Urtreger
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Nir Giladi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Donglin Zeng
- Department of Biostatistics, CB # 7420, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7420, U.S.A.
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13
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Huttenlocher J, Stefansson H, Steinberg S, Helgadottir HT, Sveinbjörnsdóttir S, Riess O, Bauer P, Stefansson K. Heterozygote carriers for CNVs in PARK2 are at increased risk of Parkinson's disease. Hum Mol Genet 2015; 24:5637-43. [PMID: 26188007 DOI: 10.1093/hmg/ddv277] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Accepted: 07/10/2015] [Indexed: 01/26/2023] Open
Abstract
Together with point mutations, homozygous deletions or duplications in PARK2 are responsible for the majority of autosomal recessive juvenile Parkinsonism. It is debated, however, whether heterozygous carriers of these mutations are at increased risk of Parkinson's disease (PD). Our goal was to determine whether heterozygous carriers of copy number variants (CNVs) affecting exons of the PARK2 gene are at risk of PD that is greater than that of non-carriers. We searched for CNVs affecting exons of PARK2 in a sample of 105 749 genotyped Icelanders. In total, 989 carriers, including 24 diagnosed with PD, were identified. The heterozygous carriers were tested for association in a sample of 1415 PD patients and 40 474 controls ≥65 years of age. PD patients were more often heterozygous carriers of PARK2 CNVs than controls [odds ratio (OR) = 1.69, P = 0.03] and compound heterozygous PD patients for a CNV and a missense mutation were not found. Furthermore, we conducted a meta-analysis of studies reporting on case-control samples screened for heterozygous PARK2 CNVs. Ten studies were included in the final analysis, with 4538 cases and 4213 controls. The pooled OR and P-value for the published and Icelandic results showed significant association between PARK2 CNVs and risk of PD (OR = 2.11, P = 2.54 × 10(-6)). Our analysis shows that heterozygous carriers of CNVs affecting exons of PARK2 have greater risk of PD than non-carriers.
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Affiliation(s)
- Johanna Huttenlocher
- deCODE Genetics/AMGEN, Reykjavik 101, Iceland, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen D-72076, Germany
| | | | | | | | - Sigurlaug Sveinbjörnsdóttir
- Department of Neurology, National University Hospital, Reykjavik 101, Iceland, Department of Neurology, MEHT, Broomfield Hospital, Court Road, Essex CM1 7ET, UK, Neuroscience Department, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK and
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen D-72076, Germany
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen D-72076, Germany
| | - Kari Stefansson
- deCODE Genetics/AMGEN, Reykjavik 101, Iceland, Faculty of Medicine, University of Iceland, Reykjavik IS-101, Iceland
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14
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Marder K, Wang Y, Alcalay RN, Mejia-Santana H, Tang MX, Lee A, Raymond D, Mirelman A, Saunders-Pullman R, Clark L, Ozelius L, Orr-Urtreger A, Giladi N, Bressman S. Age-specific penetrance of LRRK2 G2019S in the Michael J. Fox Ashkenazi Jewish LRRK2 Consortium. Neurology 2015; 85:89-95. [PMID: 26062626 DOI: 10.1212/wnl.0000000000001708] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 03/12/2015] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE Estimates of the penetrance of LRRK2 G2019S vary widely (24%-100%), reflective of differences in ascertainment, age, sex, ethnic group, and genetic and environmental modifiers. METHODS The kin-cohort method was used to predict penetrance in 2,270 relatives of 474 Ashkenazi Jewish (AJ) Parkinson disease (PD) probands in the Michael J. Fox LRRK2 AJ Consortium in New York and Tel Aviv, Israel. Patients with PD were genotyped for the LRRK2 G2019S mutation and at least 7 founder GBA mutations. GBA mutation carriers were excluded. A validated family history interview, including age at onset of PD and current age or age at death for each first-degree relative, was administered. Neurologic examination and LRRK2 genotype of relatives were included when available. RESULTS Risk of PD in relatives predicted to carry an LRRK2 G2019S mutation was 0.26 (95% confidence interval [CI] 0.18-0.36) to age 80 years, and was almost 3-fold higher than in relatives predicted to be noncarriers (hazard ratio [HR] 2.89, 95% CI 1.73-4.55, p < 0.001). The risk among predicted G2019S carrier male relatives (0.22, 95% CI 0.10-0.37) was similar to predicted carrier female relatives (0.29, 95% CI 0.18-0.40; HR male to female: 0.74, 95% CI 0.27-1.63, p = 0.44). In contrast, predicted noncarrier male relatives had a higher risk (0.15, 95% CI 0.11-0.20) than predicted noncarrier female relatives (0.07, 95% CI 0.04-0.10; HR male to female: 2.40, 95% CI 1.50-4.15, p < 0.001). CONCLUSION Penetrance of LRRK2 G2019S in AJ is only 26% and lower than reported in other ethnic groups. Further study of the genetic and environmental risk factors that influence G2019S penetrance is warranted.
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Affiliation(s)
- Karen Marder
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel.
| | - Yuanjia Wang
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel
| | - Roy N Alcalay
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel
| | - Helen Mejia-Santana
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel
| | - Ming-Xin Tang
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel
| | - Annie Lee
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel
| | - Deborah Raymond
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel
| | - Anat Mirelman
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel
| | - Rachel Saunders-Pullman
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel
| | - Lorraine Clark
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel
| | - Laurie Ozelius
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel
| | - Avi Orr-Urtreger
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel
| | - Nir Giladi
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel
| | - Susan Bressman
- From the Departments of Neurology (K.M., R.N.A., H.M.-S., M.-X.T.) and Pathology and Cell Biology (L.C.), and Center for Human Genetics (L.C.), College of Physicians and Surgeons, Columbia University; Taub Institute for Research on Alzheimer's Disease and the Aging Brain (K.M., R.N.A., M.-X.T., L.C.) and Department of Biostatistics, Mailman School of Public Health (Y.W., A.L.), Columbia University, New York; The Alan and Barbara Mirken Department of Neurology (D.R., R.S.-P., S.B.), Beth Israel Medical Center, New York, NY; Movement Disorders Unit, Department of Neurology, Tel Aviv Medical Center (A.M., N.G.), Sackler School of Medicine (A.O.U.), and Sagol School for Neurosciences (A.M., N.G.), Tel Aviv University; School of Health Related Professions (A.M.), Ben Gurion University, Beer Sheba, Israel; Departments of Genetics and Genomic Sciences and Neurology (L.O.), Mount Sinai School of Medicine, New York, NY; and Genetics Institute (A.O.U.), Tel Aviv Sourasky Medical Center, Israel
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15
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Alcalay RN, Dinur T, Quinn T, Sakanaka K, Levy O, Waters C, Fahn S, Dorovski T, Chung WK, Pauciulo M, Nichols W, Rana HQ, Balwani M, Bier L, Elstein D, Zimran A. Comparison of Parkinson risk in Ashkenazi Jewish patients with Gaucher disease and GBA heterozygotes. JAMA Neurol 2014; 71:752-7. [PMID: 24756352 PMCID: PMC4082726 DOI: 10.1001/jamaneurol.2014.313] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
IMPORTANCE Information on age-specific risk for Parkinson disease (PD) in patients with Gaucher disease (GD) and glucocerebrosidase (GBA) heterozygotes is important for understanding the pathophysiology of the genetic association and for counseling these populations. OBJECTIVE To estimate the age-specific risk for PD in Ashkenazi Jewish patients with type 1 GD and in GBA heterozygotes. DESIGN, SETTING, AND PARTICIPANTS The study included patients with GD from 2 tertiary centers, Shaare Zedek Medical Center, Jerusalem, Israel (n = 332) and Mount Sinai School of Medicine, New York, New York (n = 95). GBA noncarrier non-PD spouse control participants were recruited at the Center for Parkinson's Disease at Columbia University, New York (n = 77). All participants were Ashekanzi Jewish and most patients (98.1%) with GD carried at least 1 N370S mutation. MAIN OUTCOMES AND MEASURES The main outcome measure was a diagnosis of PD. Diagnosis was established in patients with GD on examination. We used a validated family history interview that identifies PD with a sensitivity of 95.5% and specificity of 96.2% to identify PD in family members. Kaplan-Meier survival curves were used to estimate age-specific PD risk among patients with GD (n = 427), among their parents who are obligate GBA mutation carriers (heterozygotes, n = 694), and among noncarriers (parents of non-PD, non-GD control participants, n = 154). The age-specific risk was compared among groups using the log-rank test. RESULTS Among those who developed PD, patients with GD had a younger age at onset than GBA heterozygotes (mean, 54.2 vs 65.2 years, respectively; P = .003). Estimated age-specific risk for PD at 60 and 80 years of age was 4.7% and 9.1% among patients with GD, 1.5% and 7.7% among heterozygotes, and 0.7% and 2.1% among noncarriers, respectively. The risk for PD was higher in patients with GD than noncarriers (P = .008, log-rank test) and in heterozygotes than noncarriers (P = .03, log-rank test), but it did not reach statistical significance between patients with GD and GBA heterozygotes (P = .07, log-rank test). CONCLUSIONS AND RELEVANCE Patients with GD and GBA heterozygotes have an increased age-specific risk for PD compared with control individuals, with a similar magnitude of PD risk by 80 years of age; however, the number of mutant alleles may play an important role in age at PD onset.
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Affiliation(s)
- Roy N. Alcalay
- Department of Neurology and the Taub Institute, Columbia University Medical Center, New York, NY
| | - Tama Dinur
- Gaucher Clinic, Shaare Zedek Medical Center, Jerusalem, affiliated with the Hebrew University – Hadassah Medical School, Ein Karem, Israel
| | - Timothy Quinn
- Department of Neurology and the Taub Institute, Columbia University Medical Center, New York, NY
| | - Karina Sakanaka
- Department of Neurology and the Taub Institute, Columbia University Medical Center, New York, NY
| | - Oren Levy
- Department of Neurology and the Taub Institute, Columbia University Medical Center, New York, NY
| | - Cheryl Waters
- Department of Neurology and the Taub Institute, Columbia University Medical Center, New York, NY
| | - Stanley Fahn
- Department of Neurology and the Taub Institute, Columbia University Medical Center, New York, NY
| | - Tsvyatko Dorovski
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
| | - Wendy K Chung
- Departments of Pediatrics and Medicine Columbia University Medical Center, New York, NY, USA
| | - Michael Pauciulo
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - William Nichols
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Huma Q. Rana
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY
| | - Manisha Balwani
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY
| | - Louise Bier
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY
| | - Deborah Elstein
- Gaucher Clinic, Shaare Zedek Medical Center, Jerusalem, affiliated with the Hebrew University – Hadassah Medical School, Ein Karem, Israel
| | - Ari Zimran
- Gaucher Clinic, Shaare Zedek Medical Center, Jerusalem, affiliated with the Hebrew University – Hadassah Medical School, Ein Karem, Israel
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16
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Qin J, Garcia TP, Ma Y, Tang MX, Marder K, Wang Y. COMBINING ISOTONIC REGRESSION AND EM ALGORITHM TO PREDICT GENETIC RISK UNDER MONOTONICITY CONSTRAINT. Ann Appl Stat 2014; 8:1182-1208. [PMID: 25404955 DOI: 10.1214/14-aoas730] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In certain genetic studies, clinicians and genetic counselors are interested in estimating the cumulative risk of a disease for individuals with and without a rare deleterious mutation. Estimating the cumulative risk is difficult, however, when the estimates are based on family history data. Often, the genetic mutation status in many family members is unknown; instead, only estimated probabilities of a patient having a certain mutation status are available. Also, ages of disease-onset are subject to right censoring. Existing methods to estimate the cumulative risk using such family-based data only provide estimation at individual time points, and are not guaranteed to be monotonic, nor non-negative. In this paper, we develop a novel method that combines Expectation-Maximization and isotonic regression to estimate the cumulative risk across the entire support. Our estimator is monotonic, satisfies self-consistent estimating equations, and has high power in detecting differences between the cumulative risks of different populations. Application of our estimator to a Parkinson's disease (PD) study provides the age-at-onset distribution of PD in PARK2 mutation carriers and non-carriers, and reveals a significant difference between the distribution in compound heterozygous carriers compared to non-carriers, but not between heterozygous carriers and non-carriers.
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Affiliation(s)
- Jing Qin
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, 6700B Rockledge Drive, MSC 7609, Bethesda, MD 20892-7609
| | - Tanya P Garcia
- Department of Epidemiology and Biostatistics, Texas A&M University Health Science Center, TAMU 1266, College Station, TX 77843-1266
| | - Yanyuan Ma
- Department of Statistics, Texas A&M University, TAMU 3143, College Station, TX 77843-3143
| | - Ming-Xin Tang
- Department of Biostatistics, Columbia University, 630 West 168th Street, New York, New York 10032
| | - Karen Marder
- Department of Biostatistics, Columbia University, 630 West 168th Street, New York, New York 10032
| | - Yuanjia Wang
- Department of Biostatistics, Columbia University, 630 West 168th Street, New York, New York 10032
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17
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Chai C, Lim KL. Genetic insights into sporadic Parkinson's disease pathogenesis. Curr Genomics 2014; 14:486-501. [PMID: 24532982 PMCID: PMC3924245 DOI: 10.2174/1389202914666131210195808] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 09/09/2013] [Accepted: 10/22/2013] [Indexed: 12/23/2022] Open
Abstract
Intensive research over the last 15 years has led to the identification of several autosomal recessive and dominant
genes that cause familial Parkinson’s disease (PD). Importantly, the functional characterization of these genes has
shed considerable insights into the molecular mechanisms underlying the etiology and pathogenesis of PD. Collectively;
these studies implicate aberrant protein and mitochondrial homeostasis as key contributors to the development of PD, with
oxidative stress likely acting as an important nexus between the two pathogenic events. Interestingly, recent genome-wide
association studies (GWAS) have revealed variations in at least two of the identified familial PD genes (i.e. α-synuclein
and LRRK2) as significant risk factors for the development of sporadic PD. At the same time, the studies also uncovered
variability in novel alleles that is associated with increased risk for the disease. Additionally, in-silico meta-analyses of
GWAS data have allowed major steps into the investigation of the roles of gene-gene and gene-environment interactions
in sporadic PD. The emergent picture from the progress made thus far is that the etiology of sporadic PD is multi-factorial
and presumably involves a complex interplay between a multitude of gene networks and the environment. Nonetheless,
the biochemical pathways underlying familial and sporadic forms of PD are likely to be shared.
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Affiliation(s)
- Chou Chai
- Duke-NUS Graduate Medical School, Singapore
| | - Kah-Leong Lim
- Duke-NUS Graduate Medical School, Singapore ; Department of Physiology, National University of Singapore, Singapore ; Neurodegeneration Research Laboratory, National Neuroscience Institute, Singapore
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18
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Ma Y, Wang Y. Nonparametric modeling and analysis of association between Huntington's disease onset and CAG repeats. Stat Med 2013; 33:1369-82. [PMID: 24027120 DOI: 10.1002/sim.5971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 08/21/2013] [Indexed: 11/09/2022]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder with a dominant genetic mode of inheritance caused by an expansion of CAG repeats on chromosome 4. Typically, a longer sequence of CAG repeat length is associated with increased risk of experiencing earlier onset of HD. Previous studies of the association between HD onset age and CAG length have favored a logistic model, where the CAG repeat length enters the mean and variance components of the logistic model in a complex exponential-linear form. To relax the parametric assumption of the exponential-linear association to the true HD onset distribution, we propose to leave both mean and variance functions of the CAG repeat length unspecified and perform semiparametric estimation in this context through a local kernel and backfitting procedure. Motivated by including family history of HD information available in the family members of participants in the Cooperative Huntington's Observational Research Trial (COHORT), we develop the methodology in the context of mixture data, where some subjects have a positive probability of being risk free. We also allow censoring on the age at onset of disease and accommodate covariates other than the CAG length. We study the theoretical properties of the proposed estimator and derive its asymptotic distribution. Finally, we apply the proposed methods to the COHORT data to estimate the HD onset distribution using a group of study participants and the disease family history information available on their family members.
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Affiliation(s)
- Yanyuan Ma
- Department of Statistics, Texas A&M University, College Station, TX, U.S.A
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19
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Ma Y, Wang Y. Estimating disease onset distribution functions in mutation carriers with censored mixture data. J R Stat Soc Ser C Appl Stat 2013. [DOI: 10.1111/rssc.12025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Yanyuan Ma
- Texas A&M University; College Station USA
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Structure of the human Parkin ligase domain in an autoinhibited state. EMBO J 2013; 32:2099-112. [PMID: 23727886 PMCID: PMC3730226 DOI: 10.1038/emboj.2013.125] [Citation(s) in RCA: 244] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/07/2013] [Indexed: 12/04/2022] Open
Abstract
Mutations in the protein Parkin are associated with Parkinson's disease (PD), the second most common neurodegenerative disease in men. Parkin is an E3 ubiquitin (Ub) ligase of the structurally uncharacterized RING-in-between-RING(IBR)-RING (RBR) family, which, in an HECT-like fashion, forms a catalytic thioester intermediate with Ub. We here report the crystal structure of human Parkin spanning the Unique Parkin domain (UPD, also annotated as RING0) and RBR domains, revealing a tightly packed structure with unanticipated domain interfaces. The UPD adopts a novel elongated Zn-binding fold, while RING2 resembles an IBR domain. Two key interactions keep Parkin in an autoinhibited conformation. A linker that connects the IBR with the RING2 over a 50-Å distance blocks the conserved E2∼Ub binding site of RING1. RING2 forms a hydrophobic interface with the UPD, burying the catalytic Cys431, which is part of a conserved catalytic triad. Opening of intra-domain interfaces activates Parkin, and enables Ub-based suicide probes to modify Cys431. The structure further reveals a putative phospho-peptide docking site in the UPD, and explains many PD-causing mutations. The complete structural view of a RING-IBR-RING (RBR) ubiquitin ligase domain reveals an unexpected catalytic triad and explains the effects of various Parkin mutations underlying Parkinson's disease.
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Wang Y, Garcia TP, Ma Y. Nonparametric estimation for censored mixture data with application to the Cooperative Huntington's Observational Research Trial. J Am Stat Assoc 2012; 107:1324-1338. [PMID: 24489419 DOI: 10.1080/01621459.2012.699353] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
This work presents methods for estimating genotype-specific distributions from genetic epidemiology studies where the event times are subject to right censoring, the genotypes are not directly observed, and the data arise from a mixture of scientifically meaningful subpopulations. Examples of such studies include kin-cohort studies and quantitative trait locus (QTL) studies. Current methods for analyzing censored mixture data include two types of nonparametric maximum likelihood estimators (NPMLEs) which do not make parametric assumptions on the genotype-specific density functions. Although both NPMLEs are commonly used, we show that one is inefficient and the other inconsistent. To overcome these deficiencies, we propose three classes of consistent nonparametric estimators which do not assume parametric density models and are easy to implement. They are based on the inverse probability weighting (IPW), augmented IPW (AIPW), and nonparametric imputation (IMP). The AIPW achieves the efficiency bound without additional modeling assumptions. Extensive simulation experiments demonstrate satisfactory performance of these estimators even when the data are heavily censored. We apply these estimators to the Cooperative Huntington's Observational Research Trial (COHORT), and provide age-specific estimates of the effect of mutation in the Huntington gene on mortality using a sample of family members. The close approximation of the estimated non-carrier survival rates to that of the U.S. population indicates small ascertainment bias in the COHORT family sample. Our analyses underscore an elevated risk of death in Huntington gene mutation carriers compared to non-carriers for a wide age range, and suggest that the mutation equally affects survival rates in both genders. The estimated survival rates are useful in genetic counseling for providing guidelines on interpreting the risk of death associated with a positive genetic testing, and in facilitating future subjects at risk to make informed decisions on whether to undergo genetic mutation testings.
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Affiliation(s)
- Yuanjia Wang
- Department of Biostatistics, Columbia University, New York, NY 10032
| | - Tanya P Garcia
- Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843-3143
| | - Yanyuan Ma
- Department of Statistics, Texas A&M University, 3143 TAMU, College Station, TX 77843-3143
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Predicting Disease Onset from Mutation Status Using Proband and Relative Data with Applications to Huntington's Disease. JOURNAL OF PROBABILITY AND STATISTICS 2012; 2012. [PMID: 23476655 DOI: 10.1155/2012/375935] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Huntington's disease (HD) is a progressive neurodegenerative disorder caused by an expansion of CAG repeats in the IT15 gene. The age-at-onset (AAO) of HD is inversely related to the CAG repeat length and the minimum length thought to cause HD is 36. Accurate estimation of the AAO distribution based on CAG repeat length is important for genetic counseling and the design of clinical trials. In the Cooperative Huntington's Observational Research Trial (COHORT) study, the CAG repeat length is known for the proband participants. However, whether a family member shares the huntingtin gene status (CAG expanded or not) with the proband is unknown. In this work, we use the expectation-maximization (EM) algorithm to handle the missing huntingtin gene information in first-degree family members in COHORT, assuming that a family member has the same CAG length as the proband if the family member carries a huntingtin gene mutation. We perform simulation studies to examine performance of the proposed method and apply the methods to analyze COHORT proband and family combined data. Our analyses reveal that the estimated cumulative risk of HD symptom onset obtained from the combined data is slightly lower than the risk estimated from the proband data alone.
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Ma Y, Wang Y. Efficient distribution estimation for data with unobserved sub-population identifiers. Electron J Stat 2012; 6:710-737. [PMID: 23795232 DOI: 10.1214/12-ejs690] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We study efficient nonparametric estimation of distribution functions of several scientifically meaningful sub-populations from data consisting of mixed samples where the sub-population identifiers are missing. Only probabilities of each observation belonging to a sub-population are available. The problem arises from several biomedical studies such as quantitative trait locus (QTL) analysis and genetic studies with ungenotyped relatives where the scientific interest lies in estimating the cumulative distribution function of a trait given a specific genotype. However, in these studies subjects' genotypes may not be directly observed. The distribution of the trait outcome is therefore a mixture of several genotype-specific distributions. We characterize the complete class of consistent estimators which includes members such as one type of nonparametric maximum likelihood estimator (NPMLE) and least squares or weighted least squares estimators. We identify the efficient estimator in the class that reaches the semiparametric efficiency bound, and we implement it using a simple procedure that remains consistent even if several components of the estimator are mis-specified. In addition, our close inspections on two commonly used NPMLEs in these problems show the surprising results that the NPMLE in one form is highly inefficient, while in the other form is inconsistent. We provide simulation procedures to illustrate the theoretical results and demonstrate the proposed methods through two real data examples.
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Affiliation(s)
- Yanyuan Ma
- Department of Statistics, Texas A&M University, College Station, TX 77845
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24
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Srivastava A, Tang MX, Mejia-Santana H, Rosado L, Louis ED, Caccappolo E, Comella C, Colcher A, Siderowf A, Jennings D, Nance M, Bressman S, Scott WK, Tanner C, Mickel S, Andrews H, Waters C, Fahn S, Cote L, Frucht S, Ford B, Alcalay RN, Ross B, Rezak M, Novak K, Friedman JH, Pfeiffer R, Marsh L, Hiner B, Merle D, Ottman R, Clark LN, Marder K. The relation between depression and parkin genotype: the CORE-PD study. Parkinsonism Relat Disord 2011; 17:740-4. [PMID: 21856206 PMCID: PMC3221786 DOI: 10.1016/j.parkreldis.2011.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Revised: 06/30/2011] [Accepted: 07/12/2011] [Indexed: 10/17/2022]
Abstract
BACKGROUND Mutations in parkin are a known genetic risk factor for early onset Parkinson's disease (EOPD) but their role in non-motor manifestations is not well established. Genetic factors for depression are similarly not well characterized. We investigate the role of parkin mutations in depression among those with EOPD and their relatives. METHODS We collected psychiatric information using the Patient Health Questionnaire and Beck Depression Inventory II on 328 genotyped individuals including 88 probands with early onset PD (41 with parkin mutations, 47 without) and 240 first and second-degree relatives without PD. RESULTS Genotype was not associated with depression risk among probands. Among unaffected relatives of EOPD cases, only compound heterozygotes (n = 4), and not heterozygotes, had significantly increased risk of depressed mood (OR = 14.1; 95% CI 1.2-163.4), moderate to severe depression (OR = 17.8; 95% CI 1.0-332.0), depression (score ≥ 15) on the Beck Depression Inventory II (BDI-II) (OR = 51.9; 95% CI 4.1-657.4), and BDI-II total depression score (β = 8.4; 95% CI 2.4-11.3) compared to those without parkin mutations. CONCLUSIONS Relatives of EOPD cases with compound heterozygous mutations and without diagnosed PD may have a higher risk of depression compared to relatives without parkin mutations. These findings support evidence of a genetic contribution to depression and may extend the phenotypic spectrum of parkin mutations to include non-motor manifestations that precede the development of PD.
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Affiliation(s)
- A Srivastava
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - M-X Tang
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - H Mejia-Santana
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - L Rosado
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - ED Louis
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - E Caccappolo
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - C Comella
- Department of Neurology/Movement Disorder Section, Chicago, IL, USA
| | - A Colcher
- Parkinson’s Disease and Movement Disorders Center, Pennsylvania Hospital, Philadelphia, Pennsylvania, USA
| | - A Siderowf
- Parkinson’s Disease and Movement Disorders Center, Pennsylvania Hospital, Philadelphia, Pennsylvania, USA
| | - D Jennings
- The Institute for Neurodegenerative Disorders, New Haven, Connecticut 06510-2716, USA
| | - M Nance
- Struthers Parkinson’s Center, Park Nicollet Clinic, Golden Valley, MN, USA
| | - S Bressman
- The Alan and Barbara Mirken Department of Neurology, Beth Israel Medical Center, New York, New York, USA
- Department of Neurology, Albert Einstein College of Medicine
| | - WK Scott
- Dr. John T Macdonald Foundation Department of Human Genetics, John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - C Tanner
- Parkinson’s Institute, Sunnyvale, California, USA
| | - S Mickel
- Marshfield Clinic, Department of Neurology, Marshfield, WI 54449, USA
| | - H Andrews
- New York State Psychiatric Institute, Data Coordinating Center, New York, NY, USA
| | - C Waters
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - S Fahn
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - L Cote
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - S Frucht
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - B Ford
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - RN Alcalay
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - B Ross
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - M Rezak
- Department of Neurology, at NorthShore University Health System, Evanston, Illinois, USA
- Department of Neurology, at Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - K Novak
- Department of Neurology, at NorthShore University Health System, Evanston, Illinois, USA
- Department of Neurology, at Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - JH Friedman
- Parkinson’s Disease and Movement Disorders Center of NeuroHealth, Warwick, Rhode Island
- Department of Clinical Neurosciences, The Warren Alpert School of Medicine of Brown University, Providence, Rhode Island. USA
| | - R Pfeiffer
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - L Marsh
- Morris K. Udall Parkinson’s Disease Research Center of Excellence, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Psychiatry and Behavioral Sciences Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Neurology and Neurological Sciences Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - B Hiner
- Medical College of Wisconsin, Milwaukee, Wisconsin USA
| | - D Merle
- New York State Psychiatric Institute, Data Coordinating Center, New York, NY, USA
| | - R Ottman
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
- Epidemiology Division, New York State Psychiatric Institute, New York, NY, USA
| | - LN Clark
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Center for Human Genetics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - K Marder
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
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Semenova EV, Shadrina MI, Slominsky PA, Ivanova-Smolenskaya IA, Bagyeva G, Illarioshkin SN, Limborska SA. Analysis of PARK2 gene exon rearrangements in Russian patients with sporadic Parkinson's disease. Mov Disord 2011; 27:139-42. [DOI: 10.1002/mds.23901] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 06/03/2011] [Accepted: 06/16/2011] [Indexed: 01/29/2023] Open
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Scheuerle A, Wilson K. PARK2 copy number aberrations in two children presenting with autism spectrum disorder: further support of an association and possible evidence for a new microdeletion/microduplication syndrome. Am J Med Genet B Neuropsychiatr Genet 2011; 156B:413-20. [PMID: 21360662 DOI: 10.1002/ajmg.b.31176] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Accepted: 01/24/2011] [Indexed: 01/31/2023]
Abstract
Microdeletions of PARK2 have been reported previously in seven patients with autism spectrum disorder. There are no reports of PARK2 microduplications in this population. Presented are two patients, one with deletion and the other with duplication, both with autism spectrum disorder, though their syndromic phenotypes vary. The deletion patient is cognitively normal and ectomorphic: the duplication patient is cognitively impaired, underweight and short. Further, the microduplication patient has demonstrated adverse medication reactions to psychotropic medications active in the dopamine metabolic pathway: cyclopentolate, lisdexamfetamine, methylphenidate. These patients support an association between PARK2 mutations and autism spectrum disorder and suggest that duplications may be equally causative. It is hypothesized that the disparate patient phenotypes may represent a deletion/duplication syndrome and that the adverse medication reactions may be a pharmacogenetic phenomenon.
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Schapira AHV, Gegg M. Mitochondrial contribution to Parkinson's disease pathogenesis. PARKINSONS DISEASE 2011; 2011:159160. [PMID: 21687805 PMCID: PMC3109314 DOI: 10.4061/2011/159160] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 02/17/2011] [Accepted: 02/23/2011] [Indexed: 12/21/2022]
Abstract
The identification of the etiologies and pathogenesis of Parkinson's disease (PD) should play an important role in enabling the development of novel treatment strategies to prevent or slow the progression of the disease. The last few years have seen enormous progress in this respect. Abnormalities of mitochondrial function and increased free radical mediated damage were described in post mortem PD brain before the first gene mutations causing familial PD were published. Several genetic causes are now known to induce loss of dopaminergic cells and parkinsonism, and study of the mechanisms by which these mutations produce this effect has provided important insights into the pathogenesis of PD and confirmed mitochondrial dysfunction and oxidative stress pathways as central to PD pathogenesis. Abnormalities of protein metabolism including protein mis-folding and aggregation are also crucial to the pathology of PD. Genetic causes of PD have specifically highlighted the importance of mitochondrial dysfunction to PD: PINK1, parkin, DJ-1 and most recently alpha-synuclein proteins have been shown to localise to mitochondria and influence function. The turnover of mitochondria by autophagy (mitophagy) has also become a focus of attention. This review summarises recent discoveries in the contribution of mitochondrial abnormalities to PD etiology and pathogenesis.
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Affiliation(s)
- Anthony H V Schapira
- Department of Clinical Neurosciences, UCL Institute of Neurology, Rowland Hill Street, London NW3 2PF, UK
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Hassin-Baer S, Hattori N, Cohen OS, Massarwa M, Israeli-Korn SD, Inzelberg R. Phenotype of the 202 adenine deletion in the parkin gene: 40 years of follow-up. Mov Disord 2011; 26:719-22. [PMID: 21506149 DOI: 10.1002/mds.23456] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2010] [Revised: 08/31/2010] [Accepted: 09/03/2010] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND We describe the four decades follow-up of 14 parkin patients belonging to two large eight-generation-long in-bred Muslim-Arab kindreds. RESULTS All patients had a single base-pair of adenine deletion at nucleotide 202 of exon 2 (202A) of the parkin gene (all homozygous, one heterozygous). Parkinson's disease onset age was 17-68 years. Special features were intractable axial symptoms (low back pain, scoliosis, camptocormia, antecollis), postural tremor, and preserved cognition. CONCLUSIONS The 202A deletion of the parkin gene causes early-onset Parkinson's disease with marked levodopa/STN-DBS-resistant axial features. Postural tremor and preserved cognition, even after 40 years of disease, were also evident.
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Affiliation(s)
- Sharon Hassin-Baer
- The Sagol Neuroscience Center, Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel
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Neuropsychological Profile of Parkin Mutation Carriers with and without Parkinson Disease: The CORE-PD Study. J Int Neuropsychol Soc 2011; 17:91-100. [PMID: 21092386 PMCID: PMC3366462 DOI: 10.1017/s1355617710001190] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The cognitive profile of early onset Parkinson's disease (EOPD) has not been clearly defined. Mutations in the parkin gene are the most common genetic risk factor for EOPD and may offer information about the neuropsychological pattern of performance in both symptomatic and asymptomatic mutation carriers. EOPD probands and their first-degree relatives who did not have Parkinson's disease (PD) were genotyped for mutations in the parkin gene and administered a comprehensive neuropsychological battery. Performance was compared between EOPD probands with (N = 43) and without (N = 52) parkin mutations. The same neuropsychological battery was administered to 217 first-degree relatives to assess neuropsychological function in individuals who carry parkin mutations but do not have PD. No significant differences in neuropsychological test performance were found between parkin carrier and noncarrier probands. Performance also did not differ between EOPD noncarriers and carrier subgroups (i.e., heterozygotes, compound heterozygotes/homozygotes). Similarly, no differences were found among unaffected family members across genotypes. Mean neuropsychological test performance was within normal range in all probands and relatives. Carriers of parkin mutations, whether or not they have PD, do not perform differently on neuropsychological measures as compared to noncarriers. The cognitive functioning of parkin carriers over time warrants further study.
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Schaid DJ, McDonnell SK, Riska SM, Carlson EE, Thibodeau SN. Estimation of genotype relative risks from pedigree data by retrospective likelihoods. Genet Epidemiol 2010; 34:287-98. [PMID: 20039378 DOI: 10.1002/gepi.20460] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Pedigrees collected for linkage studies are a valuable resource that could be used to estimate genetic relative risks (RRs) for genetic variants recently discovered in case-control genome wide association studies. To estimate RRs from highly ascertained pedigrees, a pedigree "retrospective likelihood" can be used, which adjusts for ascertainment by conditioning on the phenotypes of pedigree members. We explore a variety of approaches to compute the retrospective likelihood, and illustrate a Newton-Raphson method that is computationally efficient particularly for single nucleotide polymorphisms (SNPs) modeled as log-additive effect of alleles on the RR. We also illustrate, by simulations, that a naïve "composite likelihood" method that can lead to biased RR estimates, mainly by not conditioning on the ascertainment process-or as we propose-the disease status of all pedigree members. Applications of the retrospective likelihood to pedigrees collected for a prostate cancer linkage study and recently reported risk-SNPs illustrate the utility of our methods, with results showing that the RRs estimated from the highly ascertained pedigrees are consistent with odds ratios estimated in case-control studies. We also evaluate the potential impact of residual correlations of disease risk among family members due to shared unmeasured risk factors (genetic or environmental) by allowing for a random baseline risk parameter. When modeling only the affected family members in our data, there was little evidence for heterogeneity in baseline risks across families.
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Affiliation(s)
- Daniel J Schaid
- Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
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Marder KS, Tang MX, Mejia-Santana H, Rosado L, Louis ED, Comella CL, Colcher A, Siderowf AD, Jennings D, Nance MA, Bressman S, Scott WK, Tanner CM, Mickel SF, Andrews HF, Waters C, Fahn S, Ross BM, Cote LJ, Frucht S, Ford B, Alcalay RN, Rezak M, Novak K, Friedman JH, Pfeiffer RF, Marsh L, Hiner B, Neils GD, Verbitsky M, Kisselev S, Caccappolo E, Ottman R, Clark LN. Predictors of parkin mutations in early-onset Parkinson disease: the consortium on risk for early-onset Parkinson disease study. ACTA ACUST UNITED AC 2010; 67:731-8. [PMID: 20558392 DOI: 10.1001/archneurol.2010.95] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
BACKGROUND Mutations in the parkin gene are the most common genetic cause of early-onset Parkinson disease (PD). Results from a multicenter study of patients with PD systematically sampled by age at onset have not been reported to date. OBJECTIVE To determine risk factors associated with carrying parkin mutations. DESIGN Cross-sectional observational study. SETTING Thirteen movement disorders centers. PARTICIPANTS A total of 956 patients with early-onset PD, defined as age at onset younger than 51 years. MAIN OUTCOME MEASURES Presence of heterozygous, homozygous, or compound heterozygous parkin mutations. RESULTS Using a previously validated interview, 14.7% of patients reported a family history of PD in a first-degree relative. Sixty-four patients (6.7%) had parkin mutations (3.9% heterozygous, 0.6% homozygous, and 2.2% compound heterozygous). Copy number variation was present in 52.3% of mutation carriers (31.6% of heterozygous, 83.3% of homozygous, and 81.0% of compound heterozygous). Deletions in exons 3 and 4 and 255delA were common among Hispanics (specifically Puerto Ricans). Younger age at onset (<40 years) (odds ratio [OR], 5.0; 95% confidence interval [CI], 2.8-8.8; P = .001), Hispanic race/ethnicity (OR compared with white non-Hispanic race/ethnicity, 2.7; 95% CI, 1.3-5.7; P = .009), and family history of PD in a first-degree relative (OR compared with noncarriers, 2.8; 95% CI, 1.5-5.3; P = .002) were associated with carrying any parkin mutation (heterozygous, homozygous, or compound heterozygous). Hispanic race/ethnicity was associated with carrying a heterozygous mutation (OR compared with white non-Hispanic race/ethnicity, 2.8; 95% CI, 1.1-7.2; P = .03) after adjustment for covariates. CONCLUSIONS Age at onset, Hispanic race/ethnicity, and family history of PD are associated with carrying any parkin mutation (heterozygous, homozygous, or compound heterozygous) and heterozygous mutations alone. The increased odds of carrying a parkin mutation among Hispanics warrants further study.
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Affiliation(s)
- Karen S Marder
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, 630 W 168th St, Unit 16, New York, NY 10032, USA.
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Nuytemans K, Theuns J, Cruts M, Van Broeckhoven C. Genetic etiology of Parkinson disease associated with mutations in the SNCA, PARK2, PINK1, PARK7, and LRRK2 genes: a mutation update. Hum Mutat 2010; 31:763-80. [PMID: 20506312 PMCID: PMC3056147 DOI: 10.1002/humu.21277] [Citation(s) in RCA: 353] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 04/21/2010] [Accepted: 04/21/2010] [Indexed: 12/13/2022]
Abstract
To date, molecular genetic analyses have identified over 500 distinct DNA variants in five disease genes associated with familial Parkinson disease; alpha-synuclein (SNCA), parkin (PARK2), PTEN-induced putative kinase 1 (PINK1), DJ-1 (PARK7), and Leucine-rich repeat kinase 2 (LRRK2). These genetic variants include approximately 82% simple mutations and approximately 18% copy number variations. Some mutation subtypes are likely underestimated because only few studies reported extensive mutation analyses of all five genes, by both exonic sequencing and dosage analyses. Here we present an update of all mutations published to date in the literature, systematically organized in a novel mutation database (http://www.molgen.ua.ac.be/PDmutDB). In addition, we address the biological relevance of putative pathogenic mutations. This review emphasizes the need for comprehensive genetic screening of Parkinson patients followed by an insightful study of the functional relevance of observed genetic variants. Moreover, while capturing existing data from the literature it became apparent that several of the five Parkinson genes were also contributing to the genetic etiology of other Lewy Body Diseases and Parkinson-plus syndromes, indicating that mutation screening is recommendable in these patient groups.
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Affiliation(s)
- Karen Nuytemans
- Neurodegenerative Brain Diseases Group, Department of Molecular GeneticsVIB, Antwerpen, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of AntwerpAntwerpen, Belgium
| | - Jessie Theuns
- Neurodegenerative Brain Diseases Group, Department of Molecular GeneticsVIB, Antwerpen, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of AntwerpAntwerpen, Belgium
| | - Marc Cruts
- Neurodegenerative Brain Diseases Group, Department of Molecular GeneticsVIB, Antwerpen, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of AntwerpAntwerpen, Belgium
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, Department of Molecular GeneticsVIB, Antwerpen, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of AntwerpAntwerpen, Belgium
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Brüggemann N, Mitterer M, Lanthaler AJ, Djarmati A, Hagenah J, Wiegers K, Winkler S, Pawlack H, Lohnau T, Pramstaller PP, Klein C, Lohmann K. Frequency of heterozygous Parkin mutations in healthy subjects: need for careful prospective follow-up examination of mutation carriers. Parkinsonism Relat Disord 2009; 15:425-9. [PMID: 19162522 DOI: 10.1016/j.parkreldis.2008.11.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 11/25/2008] [Accepted: 11/28/2008] [Indexed: 11/26/2022]
Abstract
The role of single heterozygous mutations in the putatively recessive Parkin gene in Parkinson disease (PD) is a vividly debated issue, partly caused by the largely unknown frequency of these mutations in healthy individuals. We investigated mutations in all 12 Parkin exons in 356 controls from two European populations including individuals from South Tyrol and Germany. None of the controls carried a homozygous or compound heterozygous mutation. Seventeen carriers of rare heterozygous alterations were detected, of which 13 (13/356; 3.7%) are considered to alter protein structure including four different gene dosage alterations, four missense mutations, and two frameshift mutations. Two of the mutations occurred recurrently in the South Tyrolean population. There was no obvious difference in the mutation frequency between the two populations. One of the presumably healthy mutation carrier was available for re-examination at the age of 67 years. He presented with mild signs of parkinsonism but not fulfilling diagnostic criteria for definite PD. To elucidate the role of heterozygosity is important for genetic testing and counseling of mutation carriers. A detailed clinical prospective and follow-up examination of mutation carriers is required for a better understanding of the role of heterozygous Parkin mutations.
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Affiliation(s)
- Norbert Brüggemann
- Schilling Department of Clinical and Molecular Neurogenetics and Department of Neurology, University of Lübeck, Ratzeburger Allee 160, Schleswig-Holstein, 23538 Lübeck, Germany
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