Fine mapping and resequencing of the PARK16 locus in Parkinson's disease

Journal of Human Genetics

Volumn 60, Issue 7, 2015, Pages 357-362

  Pihlstrøm, Lasse ^a,b   Rengmark, Aina ^a   Bjørnarå, Kari Anne ^c   Dizdar, Nil ^d   Fardell, Camilla ^e   Forsgren, Lars ^f   Holmberg, Björn ^e   Larsen, Jan Petter ^g   Linder, Jan ^f   Nissbrandt, Hans ^e   Tysnes, Ole Bjørn ^h   Dietrichs, Espen ^a,b   Toft, Mathias ^a  

^a OSLO UNIVERSITY HOSPITAL   (Norway)

^b UNIVERSITY OF OSLO   (Norway)

^c Drammen Hospital   (Norway)

^d LINKÖPING UNIVERSITY   (Sweden)

^e UNIVERSITY OF GOTHENBURG   (Sweden)

^f UMEÅ UNIVERSITY   (Sweden)

^g STAVANGER UNIVERSITY HOSPITAL   (Norway)

^h HAUKELAND UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

LEUCINE RICH REPEAT KINASE 2; LRRK2 PROTEIN, HUMAN; PROTEIN SERINE THREONINE KINASE; RAB PROTEIN; RAB29 PROTEIN, HUMAN;

ARTICLE; CHROMOSOME 1; CONTROLLED STUDY; EPISTASIS; GENE; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENE POOL; GENE SEQUENCE; GENETIC ASSOCIATION; GENETIC CODE; GENETIC HETEROGENEITY; GENOTYPE; HAPLOTYPE; HETEROZYGOTE; HOMOZYGOSITY; HUMAN; MAJOR CLINICAL STUDY; NORWAY; NUCKS1 GENE; PARK16 GENE; PARKINSON DISEASE; PM20D1 GENE; RAB7L1 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; SLC41A1 GENE; SLC45A3 GENE; SWEDEN; CASE CONTROL STUDY; CHROMOSOME MAP; DNA SEQUENCE; GENE FREQUENCY; GENETIC PREDISPOSITION; GENETICS;

CASE-CONTROL STUDIES; CHROMOSOME MAPPING; EPISTASIS, GENETIC; GENE FREQUENCY; GENETIC ASSOCIATION STUDIES; GENETIC PREDISPOSITION TO DISEASE; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; PARKINSON DISEASE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN-SERINE-THREONINE KINASES; RAB1 GTP-BINDING PROTEINS; SEQUENCE ANALYSIS, DNA;

EID: 84938070504     PISSN: 14345161     EISSN: 1435232X     Source Type: Journal    
DOI: 10.1038/jhg.2015.34     Document Type: Article

References (30)

1. Satake, W., Nakabayashi, Y., Mizuta, I., Hirota, Y., Ito, C. & Kubo, M. et al. Genome-wide association study identifies common variants at four loci as genetic risk factors for Parkinson's disease. Nat. Genet. 41, 1303-1307 (2009
2. Simon-Sanchez, J., Schulte, C., Bras, J. M., Sharma, M., Gibbs, J. R. & Berg, D. et al. Genome-wide association study reveals genetic risk underlying Parkinson's disease. Nat. Genet. 41, 1308-1312 (2009
3. Hamza, T. H., Zabetian, C. P., Tenesa, A., Laederach, A., Montimurro, J. & Yearout, D. et al. Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease. Nat. Genet. 42, 781-785 (2010
4. Edwards, T. L., Scott, W. K., Almonte, C., Burt, A., Powell, E. H. & Beecham, G. W. et al. Genome-wide association study confirms SNPs in SNCA and the MAPT region as common risk factors for Parkinson disease. Ann. Hum. Genet. 74, 97-109 (2010
5. Spencer, C. C., Plagnol, V., Strange, A., Gardner, M., Paisan-Ruiz, C. & Band, G. et al. Dissection of the genetics of Parkinson's disease identifies an additional association 5? of SNCA and multiple associated haplotypes at 17q21. Hum. Mol. Genet. 20, 345-353 (2011
6. Saad, M., Lesage, S., Saint-Pierre, A., Corvol, J. C., Zelenika, D. & Lambert, J. C. et al. Genome-wide association study confirms BST1 and suggests a locus on 12q24 as the risk loci for Parkinson's disease in the European population. Hum. Mol. Genet. 20, 615-627 (2011
7. Do, C. B., Tung, J. Y., Dorfman, E., Kiefer, A. K., Drabant, E. M. & Francke, U. et al. Web-based genome-wide association study identifies two novel loci and a substantial genetic component for Parkinson's disease. PLoS Genet. 7, e1002141 (2011
8. Nalls, M. A., Plagnol, V., Hernandez, D. G., Sharma, M., Sheerin, U. M. & Saad, M. et al. Imputation of sequence variants for identification of genetic risks for Parkinson's disease: a meta-analysis of genome-wide association studies. Lancet 377, 641-649 (2011
9. International Parkinson's Disease Genomics Consortium (IPDGC), Wellcome Truste Case Control Consortium 2 (WTCCC2). A two-stage meta-analysis identifies several new loci for Parkinson's disease. PLoS Genet. 7, e1002142 (2011
10. Pankratz, N., Beecham, G. W., DeStefano, A. L., Dawson, T. M., Doheny, K. F. & Factor, S. A. et al. Meta-analysis of Parkinson's disease: identification of a novel locus, RIT2. Ann. Neurol. 71, 370-384 (2012
11. Lill, C. M., Roehr, J. T., McQueen, M. B., Kavvoura, F. K., Bagade, S. & Schjeide, B. M. et al. Comprehensive research synopsis and systematic meta-analyses in Parkinson's disease genetics: the PDGene database. PLoS Genet. 8, e1002548 (2012
12. Nalls, M. A., Pankratz, N., Lill, C. M., Do, C. B., Hernandez, D. G. & Saad, M. et al. Large-scale meta-analysis of genome-wide association data identifies six new risk loci for Parkinson's disease. Nat. Genet. 46, 989-993 (2014
13. Mata, I. F., Yearout, D., Alvarez, V., Coto, E., De Mena, L. & Ribacoba, R. et al. Replication of MAPT and SNCA, but not PARK16-18, as susceptibility genes for Parkinson's disease. Mov. Disord. 26, 819-823 (2011
14. Tucci, A., Nalls, M. A., Houlden, H., Revesz, T., Singleton, A. B. & Wood, N. W. et al. Genetic variability at the PARK16 locus. Eur. J. Hum. Genet. 18, 1356-1359 (2010
15. Yan, Y., Tian, J., Mo, X., Zhao, G., Yin, X. & Pu, J. et al. Genetic variants in the RAB7L1 and SLC41A1 genes of the PARK16 locus in Chinese Parkinson's disease patients. Int. J. Neurosci. 121, 632-636 (2011
16. Kolisek, M., Sponder, G., Mastrototaro, L., Smorodchenko, A., Launay, P. & Vormann, J. et al. Substitution p.A350V in Na(+)/Mg(2)(+) exchanger SLC41A1, potentially associated with Parkinson's disease, is a gain-of-function mutation. PLoS One 8, e71096 (2013
17. MacLeod, D. A., Rhinn, H., Kuwahara, T., Zolin, A., Di Paolo, G. & McCabe, B. D. et al. RAB7L1 interacts with LRRK2 to modify intraneuronal protein sorting and Parkinson's disease risk. Neuron 77, 425-439 (2013
18. Pihlstrom, L., Axelsson, G., Bjornara, K. A., Dizdar, N., Fardell, C. & Forsgren, L. et al. Supportive evidence for 11 loci from genome-wide association studies in Parkinson's disease. Neurobiol. Aging 34, 1708e1707-1713 (2013
19. Pihlstrom, L., Rengmark, A., Bjornara, K. A. & Toft, M. Effective variant detection by targeted deep sequencing of DNA pools: an example from Parkinson's disease. Ann. Hum. Genet. 78, 243-252 (2014
20. Tan, E. K., Kwok, H. H., Tan, L. C., Zhao, W. T., Prakash, K. M. & Au, W. L. et al. Analysis of GWAS-linked loci in Parkinson disease reaffirms PARK16 as a susceptibility locus. Neurology 75, 508-512 (2010
21. Vilarino-Guell, C., Ross, O. A., Aasly, J. O., White, L. R., Rajput, A. & Rajput, A. H. et al. An independent replication of PARK16 in Asian samples. Neurology 75, 2248-2249 (2010
22. Ramirez, A., Ziegler, A., Winkler, S., Kottwitz, J., Giesen, R. & Diaz-Grez, F. et al. Association of Parkinson disease to PARK16 in a Chilean sample. Parkinsonism Relat. Disord. 17, 70-71 (2011
23. Chang, X. L., Mao, X. Y., Li, H. H., Zhang, J. H., Li, N. N. & Burgunder, J. M. et al. Association of GWAS loci with PD in China. Am. J. Med. Genet. B Neuropsychiatr. Genet. 156B, 334-339 (2011
24. Yan, Y. P., Mo, X. Y., Tian, J., Zhao, G. H., Yin, X. Z. & Jin, F. Y. et al. An association between the PARK16 locus and Parkinson's disease in a cohort from eastern China. Parkinsonism Relat. Disord. 17, 737-739 (2011
25. Wang, C., Cai, Y., Zheng, Z., Tang, B. S., Xu, Y. & Wang, T. et al. Penetrance of LRRK2 G2385R and R1628P is modified by common PD-associated genetic variants. Parkinsonism Relat. Disord. 18, 958-963 (2012
26. Zhou, L. L., Zhang, X., Bao, Q. Q., Liu, R. P., Gong, M. Y. & Mao, G. Y. et al. Association analysis of PARK16-18 variants and Parkinson's disease in a Chinese population. J. Clin. Neurosci. 21, 1029-1032 (2014
27. Soto-Ortolaza, A. I., Heckman, M. G., Labbe, C., Serie, D. J., Puschmann, A. & Rayaprolu, S. et al. GWAS risk factors in Parkinson's disease: LRRK2 coding variation and genetic interaction with PARK16. Am. J. Neurodegener. Dis. 2, 287-299 (2013
28. Gan-Or, Z., Bar-Shira, A., Dahary, D., Mirelman, A., Kedmi, M. & Gurevich, T. et al. Association of sequence alterations in the putative promoter of RAB7L1 with a reduced parkinson disease risk. Arch. Neurol. 69, 105-110 (2012
29. Raj, T., Rothamel, K., Mostafavi, S., Ye, C., Lee, M. N. & Replogle, J. M. et al. Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes. Science 344, 519-523 (2014
30. Ramasamy, A., Trabzuni, D., Guelfi, S., Varghese, V., Smith, C. & Walker, R. et al. Genetic variability in the regulation of gene expression in ten regions of the human brain. Nat. Neurosci. 17, 1418-1428 (2014