Evaluation of Parkinson Disease Risk Variants as Expression-QTLs

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Latourelle, Jeanne C ^a   Dumitriu, Alexandra ^a,b   Hadzi, Tiffany C ^a   Beach, Thomas G ^c   Myers, Richard H ^a,b  

^a BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Boston University   (United States)

^c SUN HEALTH RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA SYNUCLEIN; TAU PROTEIN;

AGED; ARTICLE; CHROMOSOME 6; CLINICAL ARTICLE; CONTROLLED STUDY; DCAKD GENE; GENE; GENE DUPLICATION; GENE EXPRESSION; GENE PROBE; GENETIC ASSOCIATION; GENETIC CORRELATION; GENETIC RISK; GENETIC VARIABILITY; HLA SYSTEM; HUMAN; HUMAN TISSUE; LOC644246 GENE; LRRC37A GENE; LRRC37A2 GENE; MAPT GENE; MICROARRAY ANALYSIS; PARKINSON DISEASE; PREFRONTAL CORTEX; QUANTITATIVE TRAIT LOCUS; RIT2 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; SNCA GENE;

GENETIC PREDISPOSITION TO DISEASE; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PARKINSON DISEASE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI;

EID: 84867177517     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0046199     Document Type: Article

References (29)

1. Maraganore DM, de Andrade M, Lesnick TG, Strain KJ, Farrer MJ, et al. (2005) High-resolution whole-genome association study of Parkinson disease. Am J Hum Genet 77: 685-693.
2. Fung HC, Scholz S, Matarin M, Simon-Sanchez J, Hernandez D, et al. (2006) Genome-wide genotyping in Parkinson's disease and neurologically normal controls: first stage analysis and public release of data. Lancet Neurol 5: 911-916.
3. Pankratz N, Wilk JB, Latourelle JC, DeStefano AL, Halter C, et al. (2009) Genomewide association study for susceptibility genes contributing to familial Parkinson disease. Hum Genet 124: 593-605.
4. Simon-Sanchez J, Schulte C, Bras JM, Sharma M, Gibbs JR, et al. (2009) Genome-wide association study reveals genetic risk underlying Parkinson's disease. Nat Genet 41: 1308-1312.
5. Edwards TL, Scott WK, Almonte C, Burt A, Powell EH, et al. (2010) 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.
6. Hamza TH, Zabetian CP, Tenesa A, Laederach A, Montimurro J, et al. (2010) Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease. Nat Genet 42: 781-785.
7. Saad M, Lesage S, Saint-Pierre A, Corvol JC, Zelenika D, et al. (2011) 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.
8. Spencer CC, Plagnol V, Strange A, Gardner M, Paisan-Ruiz C, et al. (2011) 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.
9. International Parkinson Disease Genomics Consortium (2011) 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.
10. Pankratz N, Beecham GW, DeStefano AL, Dawson TM, Doheny KF, et al. (2012) Meta-analysis of Parkinson disease: Identification of a novel locus, RIT2. Annals of Neurology 71 (3) (): 370-384.
11. Stefansson H, Helgason A, Thorleifsson G, Steinthorsdottir V, Masson G, et al. (2005) A common inversion under selection in Europeans. Nat Genet 37: 129-137.
12. Zody MC, Jiang Z, Fung HC, Antonacci F, Hillier LW, et al. (2008) Evolutionary toggling of the MAPT 17q21.31 inversion region. Nat Genet 40: 1076-1083.
13. Dumitriu A, Latourelle JC, Hadzi TC, Pankratz N, Garza D, et al. (2012) Gene Expression Profiles in Parkinson Disease Prefrontal Cortex Implicate FOXO1 and Genes under Its Transcriptional Regulation. PLoS Genet 8: e1002794.
14. Ertekin-Taner N, (2011) Gene expression endophenotypes: a novel approach for gene discovery in Alzheimer's disease. Mol Neurodegener 6: 31.
15. Sankoh AJ, Huque MF, Dubey SD, (1997) Some comments on frequently used multiple endpoint adjustment methods in clinical trials. Stat Med 16: 2529-2542.
16. Gibbs JR, van der Brug MP, Hernandez DG, Traynor BJ, Nalls MA, et al. (2010) Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet 6: e1000952.
17. Kleinjan DA, van Heyningen V, (2005) Long-range control of gene expression: emerging mechanisms and disruption in disease. Am J Hum Genet 76: 8-32.
18. Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, et al. (2007) Population genomics of human gene expression. Nat Genet 39: 1217-1224.
19. Veyrieras JB, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, et al. (2008) High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet 4: e1000214.
20. Montgomery SB, Sammeth M, Gutierrez-Arcelus M, Lach RP, Ingle C, et al. (2010) Transcriptome genetics using second generation sequencing in a Caucasian population. Nature 464: 773-777.
21. Zeller T, Wild P, Szymczak S, Rotival M, Schillert A, et al. (2010) Genetics and beyond-the transcriptome of human monocytes and disease susceptibility. PLoS One 5: e10693.
22. Braak H, Del Tredici K, Rub U, de Vos RA, Jansen Steur EN, et al. (2003) Staging of brain pathology related to sporadic Parkinson's disease. Neurobiol Aging 24: 197-211.
23. Beach TG, Adler CH, Lue L, Sue LI, Bachalakuri J, et al. (2009) Unified staging system for Lewy body disorders: correlation with nigrostriatal degeneration, cognitive impairment and motor dysfunction. Acta neuropathologica 117: 613-634.
24. Wakabayashi K, Tanji K, Mori F, Takahashi H, (2007) The Lewy body in Parkinson's disease: molecules implicated in the formation and degradation of alpha-synuclein aggregates. Neuropathology 27: 494-506.
25. Ferrer I, Martinez A, Blanco R, Dalfo E, Carmona M, (2011) Neuropathology of sporadic Parkinson disease before the appearance of parkinsonism: preclinical Parkinson disease. J Neural Transm 118: 821-839.
26. Kauffmann A, Gentleman R, Huber W, (2009) arrayQualityMetrics-a bioconductor package for quality assessment of microarray data. Bioinformatics 25: 415-416.
27. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
28. Webster JA, Gibbs JR, Clarke J, Ray M, Zhang W, et al. (2009) Genetic control of human brain transcript expression in Alzheimer disease. Am J Hum Genet 84: 445-458.
29. Gao X, Starmer J, Martin ER, (2008) A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms. Genet Epidemiol 32: 361-369.