Identification of a novel Parkinson's disease locus via stratified genome-wide association study

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Hill Burns, Erin M ^a   Wissemann, William T ^a   Hamza, Taye H ^a   Factor, Stewart A ^b   Zabetian, Cyrus P ^c   Payami, Haydeh ^a,d  

^a WADSWORTH CENTER   (United States)

^b EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

^d STATE UNIVERSITY OF NEW YORK   (United States)

Author keywords

Chromosome 1p; Genetic heterogeneity; GWAS; HLA; MAPT; Parkinson's disease; Secondary GWAS; SNCA; Stratified GWAS

Indexed keywords

ALPHA SYNUCLEIN; HLA ANTIGEN; SNCA PROTEIN, HUMAN;

CHROMOSOME 1; GENE LOCUS; GENETIC ASSOCIATION; GENETICS; HUMAN; HUMAN GENOME; PARKINSON DISEASE; PATHOLOGY; RISK; SINGLE NUCLEOTIDE POLYMORPHISM;

ALPHA-SYNUCLEIN; CHROMOSOMES, HUMAN, PAIR 1; GENETIC LOCI; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HLA ANTIGENS; HUMANS; ODDS RATIO; PARKINSON DISEASE; POLYMORPHISM, SINGLE NUCLEOTIDE;

EID: 84893652966     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-118     Document Type: Article

References (49)

1. Satake W, Nakabayashi Y, Mizuta I, Hirota Y, Ito C, Kubo M, Kawaguchi T, Tsunoda T, Watanabe M, Takeda A, et al. Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease. Nat Genet 2009, 41:1303-1307. 10.1038/ng.485, 19915576.
2. Simon-Sanchez J, Schulte C, Bras JM, Sharma M, Gibbs JR, Berg D, Paisan-Ruiz C, Lichtner P, Scholz SW, Hernandez DG, et al. Genome-wide association study reveals genetic risk underlying Parkinson's disease. Nat Genet 2009, 41:1308-1312. 10.1038/ng.487, 2787725, 19915575.
3. Hamza TH, Zabetian CP, Tenesa A, Laederach A, Montimurro J, Yearout D, Kay DM, Doheny KF, Paschall J, Pugh E, et al. Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease. Nat Genet 2010, 42:781-785. 10.1038/ng.642, 2930111, 20711177.
4. Do CB, Tung JY, Dorfman E, Kiefer AK, Drabant EM, Francke U, Mountain JL, Goldman SM, Tanner CM, Langston JW, et al. Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson's disease. PLoS Genet 2011, 7:e1002141. 10.1371/journal.pgen.1002141, 3121750, 21738487.
5. Pankratz N, Beecham GW, DeStefano AL, Dawson TM, Doheny KF, Factor SA, Hamza TH, Hung AY, Hyman BT, Ivinson AJ, et al. Meta-analysis of Parkinson's disease: identification of a novel locus, RIT2. Ann Neurol 2012, 71:370-384. 10.1002/ana.22687, 3354734, 22451204.
6. Hamza TH, Chen H, Hill-Burns EM, Rhodes SL, Montimurro J, Kay DM, Tenesa A, Kusel VI, Sheehan P, Eaaswarkhanth M, et al. Genome-wide gene-environment study identifies Glutamate receptor gene GRIN2A as a Parkinson's disease modifier gene via interaction with coffee. PLoS Genet 2011, 7:e1002237. 10.1371/journal.pgen.1002237, 3158052, 21876681.
7. Hill-Burns EM, Singh N, Ganguly P, Hamza TH, Montimurro J, Kay DM, Yearout D, Sheehan P, Frodey K, McLear JA, et al. A genetic basis for the variable effect of smoking/nicotine on Parkinson's disease. Pharmacogenomics J 2013, 13:530-537. 10.1038/tpj.2012.38, 23032990.
8. Polymeropoulos MH, Lavedan C, Leroy E, Ide SE, Dehejia A, Dutra A, Pike B, Root H, Rubenstein J, Boyer R, et al. Mutation in the alpha-synuclein gene identified in families with Parkinson's disease. Science 1997, 276:2045-2047. 10.1126/science.276.5321.2045, 9197268.
9. Singleton AB, Farrer M, Johnson J, Singleton A, Hague S, Kachergus J, Hulihan M, Peuralinna T, Dutra A, Nussbaum R, et al. alpha-Synuclein locus triplication causes Parkinson's disease. Science 2003, 302:841. 10.1126/science.1090278, 14593171.
10. Zimprich A, Biskup S, Leitner P, Lichtner P, Farrer M, Lincoln S, Kachergus J, Hulihan M, Uitti RJ, Calne DB, et al. Mutations in LRRK2 cause autosomal-dominant parkinsonism with pleomorphic pathology. Neuron 2004, 44:601-607. 10.1016/j.neuron.2004.11.005, 15541309.
11. Paisan-Ruiz C, Jain S, Evans EW, Gilks WP, Simon J, van der Brug M, de Munain AL, Aparicio S, Gil AM, Khan N, et al. Cloning of the gene containing mutations that cause PARK8-linked Parkinson's disease. Neuron 2004, 44:595-600. 10.1016/j.neuron.2004.10.023, 15541308.
12. 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 parkinsonism. Nature 1998, 392:605-608. 10.1038/33416, 9560156.
13. Valente EM, Abou-Sleiman PM, Caputo V, Muqit MM, Harvey K, Gispert S, Ali Z, Del Turco D, Bentivoglio AR, Healy DG, et al. Hereditary early-onset Parkinson's disease caused by mutations in PINK1. Science 2004, 304:1158-1160. 10.1126/science.1096284, 15087508.
14. Bonifati V, Rizzu P, van Baren MJ, Schaap O, Breedveld GJ, Krieger E, Dekker MC, Squitieri F, Ibanez P, Joosse M, et al. Mutations in the DJ-1 gene associated with autosomal recessive early-onset parkinsonism. Science 2003, 299:256-259. 10.1126/science.1077209, 12446870.
15. Ramirez A, Heimbach A, Grundemann J, Stiller B, Hampshire D, Cid LP, Goebel I, Mubaidin AF, Wriekat AL, Roeper J, et al. Hereditary parkinsonism with dementia is caused by mutations in ATP13A2, encoding a lysosomal type 5 P-type ATPase. Nat Genet 2006, 38:1184-1191. 10.1038/ng1884, 16964263.
16. Vilarino-Guell C, Wider C, Ross OA, Dachsel JC, Kachergus JM, Lincoln SJ, Soto-Ortolaza AI, Cobb SA, Wilhoite GJ, Bacon JA, et al. VPS35 mutations in Parkinson disease. Am J Hum Genet 2011, 89:162-167. 10.1016/j.ajhg.2011.06.001, 3135796, 21763482.
17. McCulloch CC, Kay DM, Factor SA, Samii A, Nutt JG, Higgins DS, Griffith A, Roberts JW, Leis BC, Montimurro JS, et al. Exploring gene-environment interactions in Parkinson's disease. Hum Genet 2008, 123:257-265. 10.1007/s00439-008-0466-z, 18210157.
18. Ritz BR, Manthripragada AD, Costello S, Lincoln SJ, Farrer MJ, Cockburn M, Bronstein J. Dopamine transporter genetic variants and pesticides in Parkinson's disease. Environ Health Perspect 2009, 117:964-969. 2702414, 19590691.
19. Healy DG, Falchi M, O'Sullivan SS, Bonifati V, Durr A, Bressman S, Brice A, Aasly J, Zabetian CP, Goldwurm S, et al. Phenotype, genotype, and worldwide genetic penetrance of LRRK2-associated Parkinson's disease: a case-control study. Lancet Neurol 2008, 7:583-590. 10.1016/S1474-4422(08)70117-0, 2832754, 18539534.
20. Lesage S, Anheim M, Condroyer C, Pollak P, Durif F, Dupuits C, Viallet F, Lohmann E, Corvol JC, Honore A, et al. Large-scale screening of the Gaucher's disease-related glucocerebrosidase gene in Europeans with Parkinson's disease. Hum Mol Genet 2011, 20:202-210. 10.1093/hmg/ddq454, 20947659.
21. Kay DM, Bird TD, Zabetian CP, Factor SA, Samii A, Higgins DS, Nutt J, Roberts JW, Griffith A, Leis BC, et al. Validity and utility of a LRRK2 G2019S mutation test for the diagnosis of Parkinson's disease. Genet Test 2006, 10:221-227. 10.1089/gte.2006.10.221, 17020475.
22. Hughes AJ, Daniel SE, Ben-Shlomo Y, Lees AJ. The accuracy of diagnosis of parkinsonian syndromes in a specialist movement disorder service. Brain 2002, 125:861-870. 10.1093/brain/awf080, 11912118.
23. Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 2009, 5:e1000529. 10.1371/journal.pgen.1000529, 2689936, 19543373.
24. Aulchenko YS, Ripke S, Isaacs A, van Duijn CM. GenABEL: an R library for genome-wide association analysis. Bioinformatics 2007, 23:1294-1296. 10.1093/bioinformatics/btm108, 17384015.
25. Neter J, Kunter M, Nachtsheim C, Wasserman W. Applied Linear Statistical Models 1996, New York, NY: McGraw-Hill/Irwin, 4.
26. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005, 21:263-265. 10.1093/bioinformatics/bth457, 15297300.
27. Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, Gliedt TP, Boehnke M, Abecasis GR, Willer CJ. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics 2010, 26:2336-2337. 10.1093/bioinformatics/btq419, 2935401, 20634204.
28. Myers AJ, Gibbs JR, Webster JA, Rohrer K, Zhao A, Marlowe L, Kaleem M, Leung D, Bryden L, Nath P, et al. A survey of genetic human cortical gene expression. Nat Genet 2007, 39:1494-1499. 10.1038/ng.2007.16, 17982457.
29. Heinzen EL, Ge D, Cronin KD, Maia JM, Shianna KV, Gabriel WN, Welsh-Bohmer KA, Hulette CM, Denny TN, Goldstein DB. Tissue-specific genetic control of splicing: implications for the study of complex traits. PLoS Biol 2008, 6:e1.
30. Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, Lai SL, Arepalli S, Dillman A, Rafferty IP, Troncoso J, et al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 2010, 6:e1000952. 10.1371/journal.pgen.1000952, 2869317, 20485568.
31. Colantuoni C, Lipska BK, Ye T, Hyde TM, Tao R, Leek JT, Colantuoni EA, Elkahloun AG, Herman MM, Weinberger DR, Kleinman JE. Temporal dynamics and genetic control of transcription in the human prefrontal cortex. Nature 2011, 478:519-523. 10.1038/nature10524, 3510670, 22031444.
32. Liu C, Cheng L, Badner JA, Zhang D, Craig DW, Redman M, Gershon ES. Whole-genome association mapping of gene expression in the human prefrontal cortex. Mol Psychiatry 2010, 15:779-784. 10.1038/mp.2009.128, 3057235, 20351726.
33. Kimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, Yamashita R, Yamamoto J, Sekine M, Tsuritani K, Wakaguri H, et al. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res 2006, 16:55-65. 1356129, 16344560.
34. The ENCODE Project Consortium A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 2011, 9:e1001046. 10.1371/journal.pbio.1001046, 3079585, 21526222, The ENCODE Project Consortium.
35. Sawcer S, Hellenthal G, Pirinen M, Spencer CC, Patsopoulos NA, Moutsianas L, Dilthey A, Su Z, Freeman C, Hunt SE, et al. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. Nature 2011, 476:214-219. 10.1038/nature10251, 3182531, 21833088.
36. Spiegel S, Milstien S. The outs and the ins of sphingosine-1-phosphate in immunity. Nat Rev Immunol 2011, 11:403-415. 10.1038/nri2974, 3368251, 21546914.
37. Hanson MA, Roth CB, Jo E, Griffith MT, Scott FL, Reinhart G, Desale H, Clemons B, Cahalan SM, Schuerer SC, et al. Crystal structure of a lipid G protein-coupled receptor. Science 2012, 335:851-855. 10.1126/science.1215904, 3338336, 22344443.
38. Kokovay E, Wang Y, Kusek G, Wurster R, Lederman P, Lowry N, Shen Q, Temple S. VCAM1 is essential to maintain the structure of the SVZ niche and acts as an environmental sensor to regulate SVZ lineage progression. Cell Stem Cell 2012, 11:220-230. 10.1016/j.stem.2012.06.016, 22862947.
39. Kirschke CP, Huang L. ZnT7, a novel mammalian zinc transporter, accumulates zinc in the Golgi apparatus. J Biol Chem 2003, 278:4096-4102. 10.1074/jbc.M207644200, 12446736.
40. Cuajungco MP, Lees GJ. Zinc metabolism in the brain: relevance to human neurodegenerative disorders. Neurobiol Dis 1997, 4:137-169. 10.1006/nbdi.1997.0163, 9361293.
41. Dexter DT, Jenner P, Schapira AH, Marsden CD. Alterations in levels of iron, ferritin, and other trace metals in neurodegenerative diseases affecting the basal ganglia. The Royal Kings and Queens Parkinson's Disease Research Group. Ann Neurol 1992, 32 Suppl:S94-100.
42. Tarohda T, Ishida Y, Kawai K, Yamamoto M, Amano R. Regional distributions of manganese, iron, copper, and zinc in the brains of 6-hydroxydopamine-induced parkinsonian rats. Anal Bioanal Chem 2005, 383:224-234. 10.1007/s00216-005-3423-x, 16132122.
43. Noh J, Chang SY, Wang SY, Chung JM. Dual function of Zn2+ on the intrinsic excitability of dopaminergic neurons in rat substantia nigra. Neuroscience 2011, 175:85-92.
44. Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ, Hanna J, Lodato MA, Frampton GM, Sharp PA, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA 2010, 107:21931-21936. 10.1073/pnas.1016071107, 3003124, 21106759.
45. Dimas AS, Deutsch S, Stranger BE, Montgomery SB, Borel C, Attar-Cohen H, Ingle C, Beazley C, Gutierrez Arcelus M, Sekowska M, et al. Common regulatory variation impacts gene expression in a cell type-dependent manner. Science 2009, 325:1246-1250. 10.1126/science.1174148, 2867218, 19644074.
46. Grundberg E, Small KS, Hedman AK, Nica AC, Buil A, Keildson S, Bell JT, Yang TP, Meduri E, Barrett A, et al. Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet 2012, 44:1084-1089. 10.1038/ng.2394, 3784328, 22941192.
47. Devine MJ, Gwinn K, Singleton A, Hardy J. Parkinson's disease and alpha-synuclein expression. Mov Disord 2011, 26:2160-2168. 10.1002/mds.23948, 21887711.
48. Mata IF, Shi M, Agarwal P, Chung KA, Edwards KL, Factor SA, Galasko DR, Ginghina C, Griffith A, Higgins DS, et al. SNCA variant associated with Parkinson disease and plasma alpha-synuclein level. Arch Neurol 2010, 67:1350-1356. 3010848, 21060011.
49. Wissemann WT, Hill-Burns EM, Zabetian CP, Factor SA, Patsopoulos N, Hoglund B, Holcomb C, Donahue RJ, Thomson G, Erlich H, et al. Association of Parkinson disease with structural and regulatory Variants in the HLA region. Am J Hum Genet 2013, 93:984-993. 10.1016/j.ajhg.2013.10.009, 24183452.