A DNA resequencing array for genes involved in Parkinson's disease

Parkinsonism and Related Disorders

Volumn 18, Issue 4, 2012, Pages 386-390

  Wilkins, E J ^a,b   Rubio, J P ^a   Kotschet, K E ^a,f   Cowie, T F ^b   Boon, W C ^a,b   O'Hely, M ^c   Burfoot, R ^a   Wang, W ^e   Sue, C M ^g,h   Speed, T P ^c   Stankovitch, J ^d   Horne, M K ^a,b,f  

^a FLOREY INSTITUTE OF NEUROSCIENCE AND MENTAL HEALTH   (Australia)

^b UNIVERSITY OF MELBOURNE   (Australia)

^c WALTER AND ELIZA HALL INSTITUTE OF MEDICAL RESEARCH   (Australia)

^d UNIVERSITY OF TASMANIA   (Australia)

^e STANFORD UNIVERSITY   (United States)

^f ST VINCENT S HOSPITAL   (Australia)

^g UNIVERSITY OF SYDNEY   (Australia)

^h ROYAL NORTH SHORE HOSPITAL   (Australia)

Author keywords

Affymetrix resequencing array; DNA resequencing; Parkinsons disease

Indexed keywords

ACCURACY; ADULT; ANALYTICAL EQUIPMENT; APOE GENE; APP GENE; ARTICLE; ATP13A2 GENE; COMT GENE; CONTROLLED STUDY; DNA MICROARRAY; DNA RESEQUENCING; DNA SEQUENCE; GBA GENE; GCH1 GENE; GENE; GENE FUNCTION; GENE TECHNOLOGY; GENETIC ASSOCIATION; GENETIC SCREENING; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; LRRK2 GENE; MAJOR CLINICAL STUDY; MAPT GENE; NEUROPATHOLOGY; NR4A2 GENE; PARK2 GENE; PARK7 GENE; PARKINSON DISEASE; PINK1 GENE; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PSEN1 GENE; PSEN2 GENE; REPEAT PROCEDURE; REPRODUCIBILITY; SIBLING; SNCA GENE; SNCAIP GENE; TH GENE; UCHL1 GENE;

ADULT; AGED; ALPHA-SYNUCLEIN; FEMALE; GENE EXPRESSION PROFILING; GENETIC PREDISPOSITION TO DISEASE; GENOTYPE; HUMANS; MALE; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PARKINSON DISEASE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEIN KINASES; PROTEIN-SERINE-THREONINE KINASES; REPRODUCIBILITY OF RESULTS; UBIQUITIN-PROTEIN LIGASES;

EID: 84862783253     PISSN: 13538020     EISSN: 18735126     Source Type: Journal    
DOI: 10.1016/j.parkreldis.2011.12.012     Document Type: Article

References (29)

1. Sveinbjornsdottir S., Hicks A.A., Jonsson T., Petursson H., Gugmundsson G., Frigge M.L., et al. Familial aggregation of Parkinson's disease in Iceland. N Engl J Med 2000 Dec 14, 343(24):1765-1770.
2. Polymeropoulos M.H., Lavedan C., Leroy E., Ide S.E., Dehejia A., Dutra A., et al. Mutation in the alpha-synuclein gene identified in families with Parkinson's disease. Science 1997 Jun 27, 276(5321):2045-2047.
3. Kitada T., Asakawa S., Hattori N., Matsumine H., Yamamura Y., Minoshima S., et al. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Nature 1998 Apr 9, 392(6676):605-608.
4. Bonifati V., Rizzu P., van Baren M.J., Schaap O., Breedveld G.J., Krieger E., et al. Mutations in the DJ-1 gene associated with autosomal recessive early-onset parkinsonism. Science 2003 Jan 10, 299(5604):256-259.
5. Valente E.M., Abou-Sleiman P.M., Caputo V., Muqit M.M., Harvey K., Gispert S., et al. Hereditary early-onset Parkinson's disease caused by mutations in PINK1. Science 2004 May 21, 304(5674):1158-1160.
6. Paisan-Ruiz C., Jain S., Evans E.W., Gilks W.P., Simon J., van der Brug M., et al. Cloning of the gene containing mutations that cause PARK8-linked Parkinson's disease. Neuron 2004 Nov 18, 44(4):595-600.
7. Mizuta I., Satake W., Nakabayashi Y., Ito C., Suzuki S., Momose Y., et al. Multiple candidate gene analysis identifies alpha-synuclein as a susceptibility gene for sporadic Parkinson's disease. Hum Mol Genet 2006 Apr 1, 15(7):1151-1158.
8. Pankratz N., Wilk J.B., Latourelle J.C., DeStefano A.L., Halter C., Pugh E.W., et al. Genomewide association study for susceptibility genes contributing to familial Parkinson disease. Hum Genet. 2009 Jan, 124(6):593-605.
9. 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. 2009 Dec, 41(12):1308-1312.
10. Fung H.C., Scholz S., Matarin M., Simon-Sanchez J., Hernandez D., Britton A., et al. Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol 2006 Nov, 5(11):911-916.
11. 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. 2009 Dec, 41(12):1303-1307.
12. Maraganore D.M., de Andrade M., Elbaz A., Farrer M.J., Ioannidis J.P., Kruger R., et al. Collaborative analysis of alpha-synuclein gene promoter variability and Parkinson disease. Jama 2006 Aug 9, 296(6):661-670.
13. Di Fonzo A., Wu-Chou Y.H., Lu C.S., van Doeselaar M., Simons E.J., Rohe C.F., et al. A common missense variant in the LRRK2 gene, Gly2385Arg, associated with Parkinson's disease risk in Taiwan. Neurogenetics 2006 Jul, 7(3):133-138.
14. Ross O.A., Soto-Ortolaza A.I., Heckman M.G., Aasly J.O., Abahuni N., Annesi G., et al. Association of LRRK2 exonic variants with susceptibility to Parkinson's disease: a case-control study. Lancet Neurol 2011 Oct, 10(10):898-908.
15. Lwin A., Orvisky E., Goker-Alpan O., LaMarca M.E., Sidransky E. Glucocerebrosidase mutations in subjects with parkinsonism. Mol Genet Metab 2004 Jan, 81(1):70-73.
16. Srinivasan B.S., Doostzadeh J., Absalan F., Mohandessi S., Jalili R., Bigdeli S., et al. Whole genome survey of coding SNPs reveals a reproducible pathway determinant of Parkinson disease. Hum Mutat 2009 Feb, 30(2):228-238.
17. Maraganore D.M., de Andrade M., Lesnick T.G., Strain K.J., Farrer M.J., Rocca W.A., et al. High-resolution whole-genome association study of Parkinson disease. Am J Hum Genet 2005 Nov, 77(5):685-693.
18. ® resequencing array base calling algorithm version 2.0: performance in homozygous and heterozygous SNP detection 2006.
19. Hughes AJ, Daniel SE, Kilford L, Lees AJ. Accuracy of clinical diagnosis of idiopathic Parkinson's disease: a clinico-pathological study of 100 cases. J Neurol Neurosurg Psychiatry [Research Support, Non-U.S. Gov't] 2002 Jun;12(6):996-1006.
20. Huang Y., Halliday G.M., Vandebona H., Mellick G.D., Mastaglia F., Stevens J., et al. Prevalence and clinical features of common LRRK2 mutations in Australians with Parkinson's disease. Mov Disord 2007 May 15, 22(7):982-989.
21. Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., et al. The human genome browser at UCSC. Genome Res 2002 Jun, 12(6):996-1006.
22. Smit A, Hubley R, Green P. RepeatMasker Open-3.0. 1996-2004.
23. Lahiri D.K., Nurnberger J.I. A rapid non-enzymatic method for the preparation of HMW DNA from blood for RFLP studies. Nucleic Acids Res 1991 Oct 11, 19(19):5444.
24. Rozen S., Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132:365-386.
25. Finckh U., Seeman P., von Widdern O.C., Rolfs A. Simple PCR amplification of the entire glucocerebrosidase gene (GBA) coding region for diagnostic sequence analysis. DNA Seq 1998, 8(6):349-356.
26. Purcell S., Neale B., Todd-Brown K., Thomas L., Ferreira M.A., Bender D., et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 2007 Sep, 81(3):559-575.
27. Purcell S. PLINK v1.07.
28. Kothiyal P., Cox S., Ebert J., Aronow B.J., Greinwald J.H., Rehm H.L. An overview of custom array sequencing. Curr Protoc Hum Genet 2009 Apr, Chapter 7:Unit 7 17.
29. 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing. Nature 2010 Oct 28, 467(7319):1061-1073.