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Genetics and genomics of Parkinson’s disease

Michelle K Lin, Matthew J Farrer

Genome Medicine · 2014 · Review

doi:10.1186/gm566

Abstract

Parkinson's disease (PD) is a progressively debilitating neurodegenerative syndrome. Although best described as a movement disorder, the condition has prominent autonomic, cognitive, psychiatric, sensory and sleep components. Striatal dopaminergic innervation and nigral neurons are progressively lost, with associated Lewy pathology readily apparent on autopsy. Nevertheless, knowledge of the molecular events leading to this pathophysiology is limited. Current therapies offer symptomatic benefit but they fail to slow progression and patients continue to deteriorate. Recent discoveries in sporadic, Mendelian and more complex forms of parkinsonism provide novel insight into disease etiology; 28 genes, including those encoding alpha-synuclein (SNCA), leucine-rich repeat kinase 2 (LRRK2) and microtubule-associated protein tau (MAPT), have been linked and/or associated with PD. A consensus regarding the affected biological pathways and molecular processes has also started to emerge. In early-onset and more a typical PD, deficits in mitophagy pathways and lysosomal function appear to be prominent. By contrast, in more typical late-onset PD, chronic, albeit subtle, dysfunction in synaptic transmission, early endosomal trafficking and receptor recycling, as well as chaperone-mediated autophagy, provide a unifying synthesis of the molecular pathways involved. Disease-modification (neuroprotection) is no longer such an elusive goal given the unparalleled opportunity for diagnosis, translational neuroscience and therapeutic development provided by genetic discovery.

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    Plowey ED Johnson JW Steer E Zhu W Eisenberg DA Valentino NM Liu YJ Chu CT Mutant LRRK2 enhances glutamatergic synapse activity and evokes excitotoxic dendrite degenerationBiochim Biophys Acta2014 doi: 10.1016/j.bbadis.2014.05.016

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  84. 84.

    Parisiadou L Yu J Sgobio C Xie C Liu G Sun L Gu XL Lin X Crowley NA Lovinger DM Cai H LRRK2 regulates synaptogenesis and dopamine receptor activation through modulation of PKA activityNat Neurosci2014 17367376

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    MacLeod D Dowman J Hammond R Leete T Inoue K Abeliovich A The familial Parkinsonism gene LRRK2 regulates neurite process morphologyNeuron2006 52587593

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  86. 86.

    Dachsel JC Behrouz B Yue M Beevers JE Melrose HL Farrer MJ A comparative study of Lrrk2 function in primary neuronal culturesParkinsonism Relat Disord2010 16650655

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  88. 88.

    Matta S Van Kolen K da Cunha R van den Bogaart G Mandemakers W Miskiewicz K De Bock PJ Morais VA Vilain S Haddad D Delbroek L Swerts J Chávez-Gutiérrez L Esposito G Daneels G Karran E Holt M Gevaert K Moechars DW De Strooper B Verstreken P LRRK2 controls an EndoA phosphorylation cycle in synaptic endocytosisNeuron2012 7510081021

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  89. 89.
  90. 90.

    Sakaguchi-Nakashima A Meir JY Jin Y Matsumoto K Hisamoto N LRK-1, a C. elegans PARK8-related kinase, regulates axonal-dendritic polarity of SV proteinsCurr Biol2007 17592598

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  91. 91.

    Tong Y Shen J alpha-synuclein and LRRK2: partners in crimeNeuron2009 64771773

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  92. 92.

    Dzamko N Halliday GM An emerging role for LRRK2 in the immune systemBiochem Soc Trans2012 4011341139

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  93. 93.

    Vilariño-Güell C Rajput A Milnerwood AJ Shah B Szu-Tu C Trinh J Yu I Encarnacion M Munsie LN Tapia L Gustavsson EK Chou P Tatarnikov I Evans DM Pishotta FT Volta M Beccano-Kelly D Thompson C Lin MK Sherman HE Han HJ Guenther BL Wasserman WW Bernard V Ross CJ Appel-Cresswell S Stoessl AJ Robinson CA Dickson DW Ross OA DNAJC13 mutations in Parkinson diseaseHum Mol Genet2014 2317941801

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  94. 94.

    Helfer E Harbour ME Henriot V Lakisic G Sousa-Blin C Volceanov L Seaman MN Gautreau A Endosomal recruitment of the WASH complex: active sequences and mutations impairing interaction with the retromerBiol Cell2013 105191207

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  95. 95.

    Seaman MN Gautreau A Billadeau DD Retromer-mediated endosomal protein sorting: all WASHed up!Trends Cell Biol2013 23522528

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  96. 96.

    MacLeod DA Rhinn H Kuwahara T Zolin A Di Paolo G McCabe BD Marder KS Honig LS Clark LN Small SA Abeliovich A RAB7L1 interacts with LRRK2 to modify intraneuronal protein sorting and Parkinson’s disease riskNeuron2013 77425439

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  97. 97.

    Settembre C Fraldi A Medina DL Ballabio A Signals from the lysosome: a control centre for cellular clearance and energy metabolismNat Rev Mol Cell Biol2013 14283296

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  98. 98.

    Sidransky E Nalls MA Aasly JO Aharon-Peretz J Annesi G Barbosa ER Bar-Shira A Berg D Bras J Brice A Chen CM Clark LN Condroyer C De Marco EV Dürr A Eblan MJ Fahn S Farrer MJ Fung HC Gan-Or Z Gasser T Gershoni-Baruch R Giladi N Griffith A Gurevich T Januario C Kropp P Lang AE Lee-Chen GJ Lesage S Multicenter analysis of glucocerebrosidase mutations in Parkinson’s diseaseN Engl J Med2009 36116511661

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  99. 99.

    Bras J Singleton A Cookson MR Hardy J Emerging pathways in genetic Parkinson’s disease: potential role of ceramide metabolism in Lewy body diseaseFEBS J2008 27557675773

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    Mazzulli JR Xu YH Sun Y Knight AL McLean PJ Caldwell GA Sidransky E Grabowski GA Krainc D Gaucher disease glucocerebrosidase and alpha-synuclein form a bidirectional pathogenic loop in synucleinopathiesCell2011 1463752

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  101. 101.

    Sardi SP Clarke J Viel C Chan M Tamsett TJ Treleaven CM Bu J Sweet L Passini MA Dodge JC Yu WH Sidman RL Cheng SH Shihabuddin LS Augmenting CNS glucocerebrosidase activity as a therapeutic strategy for parkinsonism and other Gaucher-related synucleinopathiesProc Natl Acad Sci U S A2013 11035373542

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    Ramirez A Heimbach A Grundemann J Stiller B Hampshire D Cid LP Goebel I Mubaidin AF Wriekat AL Roeper J Al-Din A Hillmer AM Karsak M Liss B Woods CG Behrens MI Kubisch C Hereditary parkinsonism with dementia is caused by mutations in ATP13A2, encoding a lysosomal type 5 P-type ATPaseNat Genet2006 3811841191

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    Schultheis PJ Fleming SM Clippinger AK Lewis J Tsunemi T Giasson B Dickson DW Mazzulli JR Bardgett ME Haik KL Ekhator O Chava AK Howard J Gannon M Hoffman E Chen Y Prasad V Linn SC Tamargo RJ Westbroek W Sidransky E Krainc D Shull GE Atp13a2-deficient mice exhibit neuronal ceroid lipofuscinosis, limited alpha-synuclein accumulation and age-dependent sensorimotor deficitsHum Mol Genet2013 2220672082

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    Gregory A Hayflick S Pagon RA, Adam MP, Bird TD, Dolan CR, Fong CT, Smith RJH, Stephens KNeurodegeneration with brain iron accumulation disorders overviewGeneReviews1993-2014 Seattle: University of Washington136

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    Langston JW Ballard P Tetrud JW Irwin I Chronic Parkinsonism in humans due to a product of meperidine-analog synthesisScience1983 219979980

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    Keeney PM Xie J Capaldi RA Bennett JP Jr Parkinson’s disease brain mitochondrial complex I has oxidatively damaged subunits and is functionally impaired and misassembledJ Neurosci2006 2652565264

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    Spinazzola A Invernizzi F Carrara F Lamantea E Donati A Dirocco M Giordano I Meznaric-Petrusa M Baruffini E Ferrero I Zeviani M Clinical and molecular features of mitochondrial DNA depletion syndromesJ Inherit Metab Dis2009 32143158

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    Dai Y Kiselak T Clark J Clore E Zheng K Cheng A Kujoth GC Prolla TA Maratos-Flier E Simon DK Behavioral and metabolic characterization of heterozygous and homozygous POLG mutator miceMitochondrion2013 13282291

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    Kitada T Asakawa S Hattori N Matsumine H Yamamura Y Minoshima S Yokochi M Mizuno Y Shimizu N Mutations in the parkin gene cause autosomal recessive juvenile parkinsonismNature1998 392605608

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    Ko HS von Coelln R Sriram SR Kim SW Chung KK Pletnikova O Troncoso J Johnson B Saffary R Goh EL Song H Park BJ Kim MJ Kim S Dawson VL Dawson TM Accumulation of the authentic parkin substrate aminoacyl-tRNA synthetase cofactor, p38/JTV-1, leads to catecholaminergic cell deathJ Neurosci2005 2579687978

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  111. 111.

    Fallon L Belanger CM Corera AT Kontogiannea M Regan-Klapisz E Moreau F Voortman J Haber M Rouleau G Thorarinsdottir T Brice A van Bergen En Henegouwen PM Fon EA A regulated interaction with the UIM protein Eps15 implicates parkin in EGF receptor trafficking and PI(3)K-Akt signallingNat Cell Biol2006 8834842

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  112. 112.

    Staropoli JF McDermott C Martinat C Schulman B Demireva E Abeliovich A Parkin is a component of an SCF-like ubiquitin ligase complex and protects postmitotic neurons from kainate excitotoxicityNeuron2003 37735749

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  113. 113.

    Burchell VS Nelson DE Sanchez-Martinez A Delgado-Camprubi M Ivatt RM Pogson JH Randle SJ Wray S Lewis PA Houlden H Abramov AY Hardy J Wood NW Whitworth AJ Laman H Plun-Favreau H The Parkinson’s disease-linked proteins Fbxo7 and Parkin interact to mediate mitophagyNat Neurosci2013 1612571265

    Not in our library10.1038/nn.3489

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    Park J Lee SB Lee S Kim Y Song S Kim S Bae E Kim J Shong M Kim JM Chung J Mitochondrial dysfunction in Drosophila PINK1 mutants is complemented by parkinNature2006 44111571161

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  115. 115.

    Clark IE Dodson MW Jiang C Cao JH Huh JR Seol JH Yoo SJ Hay BA Guo M Drosophila pink1 is required for mitochondrial function and interacts genetically with parkinNature2006 44111621166

    Not in our library10.1038/nature04779

  116. 116.

    Trempe JF Sauve V Grenier K Seirafi M Tang MY Menade M Al-Abdul-Wahid S Krett J Wong K Kozlov G Nagar B Fon EA Gehring K Structure of parkin reveals mechanisms for ubiquitin ligase activationScience2013 34014511455

    Not in our library10.1126/science.1237908

  117. 117.

    Koyano F Okatsu K Kosako H Tamura Y Go E Kimura M Kimura Y Tsuchiya H Yoshihara H Hirokawa T Endo T Fon EA Trempe JF Saeki Y Tanaka K Matsuda N Ubiquitin is phosphorylated by PINK1 to activate parkinNature2014 510162166

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  118. 118.

    Hasson SA Kane LA Yamano K Huang CH Sliter DA Buehler E Wang C Heman-Ackah SM Hessa T Guha R Martin SE Youle RJ High-content genome-wide RNAi screens identify regulators of parkin upstream of mitophagyNature2013 504291295

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  119. 119.

    McCoy MK Kaganovich A Rudenko IN Ding J Cookson MR Hexokinase activity is required for recruitment of parkin to depolarized mitochondriaHum Mol Genet2014 23145156

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  120. 120.

    Hajek P Chomyn A Attardi G Identification of a novel mitochondrial complex containing mitofusin 2 and stomatin-like protein 2J Biol Chem2007 28256705681

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    Rakovic A Grunewald A Voges L Hofmann S Orolicki S Lohmann K Klein C PINK1-interacting proteins: proteomic analysis of overexpressed PINK1Parkinsons Dis2011 2011153979

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  123. 123.

    Bonifati V Rizzu P van Baren MJ Schaap O Breedveld GJ Krieger E Dekker MC Squitieri F Ibanez P Joosse M van Dongen JW Vanacore N van Swieten JC Brice A Meco G van Duijn CM Oostra BA Heutink P Mutations in the DJ-1 gene associated with autosomal recessive early-onset parkinsonismScience2003 299256259

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  124. 124.

    Joselin AP Hewitt SJ Callaghan SM Kim RH Chung YH Mak TW Shen J Slack RS Park DS ROS-dependent regulation of Parkin and DJ-1 localization during oxidative stress in neuronsHum Mol Genet2012 2148884903

    Not in our library10.1093/hmg/dds325

  125. 125.
  126. 126.

    Goldberg MS Pisani A Haburcak M Vortherms TA Kitada T Costa C Tong Y Martella G Tscherter A Martins A Bernardi G Roth BL Pothos EN Calabresi P Shen J Nigrostriatal dopaminergic deficits and hypokinesia caused by inactivation of the familial Parkinsonism-linked gene DJ-1Neuron2005 45489496

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  127. 127.

    Goldberg MS Fleming SM Palacino JJ Cepeda C Lam HA Bhatnagar A Meloni EG Wu N Ackerson LC Klapstein GJ Gajendiran M Roth BL Chesselet MF Maidment NT Levine MS Shen J Parkin-deficient mice exhibit nigrostriatal deficits but not loss of dopaminergic neuronsJ Biol Chem2003 2784362843635

    Not in our library10.1074/jbc.m308947200

  128. 128.

    Shin JH Ko HS Kang H Lee Y Lee YI Pletinkova O Troconso JC Dawson VL Dawson TM PARIS (ZNF746) repression of PGC-1α contributes to neurodegeneration in Parkinson’s diseaseCell2011 144689702

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  129. 129.

    Martin LJ Pan Y Price AC Sterling W Copeland NG Jenkins NA Price DL Lee MK Parkinson’s disease alpha-synuclein transgenic mice develop neuronal mitochondrial degeneration and cell deathJ Neurosci2006 264150

    Not in our library10.1523/jneurosci.4308-05.2006

  130. 130.

    Cooper O Seo H Andrabi S Guardia-Laguarta C Graziotto J Sundberg M McLean JR Carrillo-Reid L Xie Z Osborn T Hargus G Deleidi M Lawson T Bogetofte H Perez-Torres E Clark L Moskowitz C Mazzulli J Chen L Volpicelli-Daley L Romero N Jiang H Uitti RJ Huang Z Opala G Scarffe LA Dawson VL Klein C Feng J Ross OA Pharmacological rescue of mitochondrial deficits in iPSC-derived neural cells from patients with familial Parkinson’s diseaseSci Transl Med2012 4141ra190

    Not in our library10.1126/scitranslmed.3003985

  131. 131.
  132. 132.

    Wang X Yan MH Fujioka H Liu J Wilson-Delfosse A Chen SG Perry G Casadesus G Zhu X LRRK2 regulates mitochondrial dynamics and function through direct interaction with DLP1Hum Mol Genet2012 2119311944

    Not in our library10.1093/hmg/dds003

  133. 133.

    Zhi D Chen R Statistical guidance for experimental design and data analysis of mutation detection in rare monogenic mendelian diseases by exome sequencingPLoS One2012 7e31358

    Not in our library10.1371/journal.pone.0031358

  134. 134.

    Choy RW Park M Temkin P Herring BE Marley A Nicoll RA von Zastrow M Retromer mediates a discrete route of local membrane delivery to dendritesNeuron2014 825562

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  135. 135.

    Stocchi F Olanow CW Obstacles to the development of a neuroprotective therapy for Parkinson’s diseaseMov Disord2013 2837

    Not in our library10.1002/mds.25337

  136. 136.

    Spillantini MG Schmidt ML Lee VM Trojanowski JQ Jakes R Goedert M Alpha-synuclein in Lewy bodiesNature1997 388839840

    Not in our library10.1038/42166

  137. 137.

    Abbas N Lücking CB Ricard S Dürr A Bonifati V De Michele G Bouley S Vaughan JR Gasser T Marconi R Broussolle E Brefel-Courbon C Harhangi BS Oostra BA Fabrizio E Böhme GA Pradier L Wood NW Filla A Meco G Denefle P Agid Y Brice A A wide variety of mutations in the parkin gene are responsible for autosomal recessive parkinsonism in Europe. French Parkinson’s Disease Genetics Study Group and the European Consortium on Genetic Susceptibility in Parkinson’s DiseaseHum Mol Genet1999 8567574

    Not in our library10.1093/hmg/8.4.567

  138. 138.

    van de Warrenburg BP Lammens M Lucking CB Denefle P Wesseling P Booij J Praamstra P Quinn N Brice A Horstink MW Clinical and pathologic abnormalities in a family with parkinsonism and parkin gene mutationsNeurology2001 56555557

    Not in our library10.1212/wnl.56.4.555

  139. 139.

    Farrer M Chan P Chen R Tan L Lincoln S Hernandez D Forno L Gwinn-Hardy K Petrucelli L Hussey J Singleton A Tanner C Hardy J Langston JW Lewy bodies and parkinsonism in families with parkin mutationsAnn Neurol2001 50293300

    Not in our library10.1002/ana.1132

  140. 140.

    Krüger R Vieira-Saecker AM Kuhn W Berg D Müller T Kühnl N Fuchs GA Storch A Hungs M Woitalla D Przuntek H Epplen JT Schöls L Riess O Increased susceptibility to sporadic Parkinson’s disease by a certain combined alpha-synuclein/apolipoprotein E genotypeAnn Neurol1999 45611617

    Not in our library10.1002/1531-8249(199905)45:5<611::aid-ana9>3.0.co;2-x

  141. 141.

    Maraganore DM Hernandez DG Singleton AB Farrer MJ McDonnell SK Hutton ML Hardy JA Rocca WA Case-control study of the extended tau gene haplotype in Parkinson’s diseaseAnn Neurol2001 50658661

    Not in our library10.1002/ana.1228

  142. 142.

    Höglinger GU Melhem NM Dickson DW Sleiman PM Wang LS Klei L Rademakers R de Silva R Litvan I Riley DE van Swieten JC Heutink P Wszolek ZK Uitti RJ Vandrovcova J Hurtig HI Gross RG Maetzler W Goldwurm S Tolosa E Borroni B Pastor P Cantwell LB Han MR Dillman A van der Brug MP Gibbs JR Cookson MR Hernandez DG PSP Genetics Study GroupIdentification of common variants influencing risk of the tauopathy progressive supranuclear palsyNat Genet2011 43699705

    Not in our library10.1038/ng.859

  143. 143.

    Farrer M Kachergus J Forno L Lincoln S Wang DS Hulihan M Maraganore D Gwinn-Hardy K Wszolek Z Dickson D Langston JW Comparison of kindreds with parkinsonism and alpha-synuclein genomic multiplicationsAnn Neurol2004 55174179

    Not in our library10.1002/ana.10846

  144. 144.

    Chartier-Harlin MC Kachergus J Roumier C Mouroux V Douay X Lincoln S Levecque C Larvor L Andrieux J Hulihan M Waucquier N Defebvre L Amouyel P Farrer M Destée A alpha-synuclein locus duplication as a cause of familial Parkinson’s diseaseLancet2004 36411671169

    Not in our library10.1016/s0140-6736(04)17103-1

  145. 145.

    Ibanez P Bonnet AM Debarges B Lohmann E Tison F Pollak P Agid Y Durr A Brice A Causal relation between alpha-synuclein gene duplication and familial Parkinson’s diseaseLancet2004 36411691171

    Not in our library10.1016/s0140-6736(04)17104-3

  146. 146.

    Nishioka K Ross OA Ishii K Kachergus JM Ishiwata K Kitagawa M Kono S Obi T Mizoguchi K Inoue Y Imai H Takanashi M Mizuno Y Farrer MJ Hattori N Expanding the clinical phenotype of SNCA duplication carriersMov Disord2009 2418111819

    Not in our library10.1002/mds.22682

  147. 147.

    Valente EM Abou-Sleiman PM Caputo V Muqit MM Harvey K Gispert S Ali Z Del Turco D Bentivoglio AR Healy DG Albanese A Nussbaum R González-Maldonado R Deller T Salvi S Cortelli P Gilks WP Latchman DS Harvey RJ Dallapiccola B Auburger G Wood NW Hereditary early-onset Parkinson’s disease caused by mutations in PINK1Science2004 30411581160

    Not in our library10.1126/science.1096284

  148. 148.

    Kachergus J Mata IF Hulihan M Taylor JP Lincoln S Aasly J Gibson JM Ross OA Lynch T Wiley J Payami H Nutt J Maraganore DM Czyzewski K Styczynska M Wszolek ZK Farrer MJ Toft M Identification of a novel LRRK2 mutation linked to autosomal dominant parkinsonism: evidence of a common founder across European populationsAm J Hum Genet2005 76672680

    Not in our library10.1086/429256

  149. 149.

    Chartier-Harlin MC Dachsel JC Vilariño-Güell C Lincoln SJ Leprêtre F Hulihan MM Kachergus J Milnerwood AJ Tapia L Song MS Le Rhun E Mutez E Larvor L Duflot A Vanbesien-Mailliot C Kreisler A Ross OA Nishioka K Soto-Ortolaza AI Cobb SA Melrose HL Behrouz B Keeling BH Bacon JA Hentati E Williams L Yanagiya A Sonenberg N Lockhart PJ Zubair AC Translation initiator EIF4G1 mutations in familial Parkinson diseaseAm J Hum Genet2011 89398406

    Not in our library10.1016/j.ajhg.2011.08.009

  150. 150.
  151. 151.

    Hatano Y Li Y Sato K Asakawa S Yamamura Y Tomiyama H Yoshino H Asahina M Kobayashi S Hassin-Baer S Lu CS Ng AR Rosales RL Shimizu N Toda T Mizuno Y Hattori N Novel PINK1 mutations in early-onset parkinsonismAnn Neurol2004 56424427

    Not in our library10.1002/ana.20251

  152. 152.

    Paisan-Ruiz C Bhatia KP Li A Hernandez D Davis M Wood NW Hardy J Houlden H Singleton A Schneider SA Characterization of PLA2G6 as a locus for dystonia-parkinsonismAnn Neurol2009 651923

    Not in our library10.1002/ana.21415

  153. 153.

    Lee HJ Suk JE Bae EJ Lee JH Paik SR Lee SJ Assembly-dependent endocytosis and clearance of extracellular alpha-synucleinInt J Biochem Cell Biol2008 4018351849

    Not in our library10.1016/j.biocel.2008.01.017

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