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Trabzuni, D.* ; Ryten, M.* ; Emmett, W.* ; Ramasamy, A.* ; Lackner, K.J.* ; Zeller, T.* ; Walker, R.* ; Smith, C.* ; Lewis, P.A.* ; Mamais, A.* ; de Silva, R.* ; Vandrovcova, J.* ; International Parkinson's Disease Genomics Consortium (IPDGC) (Illig, T. ; Lichtner, P.) ; Hernandez, D.* ; Nalls, M.A.* ; Sharma, M.* ; Garnier, S.* ; Lesage, S.* ; Simon-Sanchez, J.* ; Gasser, T.* ; Heutink, P.* ; Brice, A.* ; Singleton, A.* ; Cai, H.* ; Schadt, E.* ; Wood, N.W.* ; Bandopadhyay, R.* ; Weale, M.E.* ; Hardy, J.* ; Plagnol, V.*

Fine-mapping, gene expression and splicing analysis of the disease associated LRRK2 locus.

PLoS ONE 8:e70724 (2013)
Publ. Version/Full Text Volltext DOI PMC
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Association studies have identified several signals at the LRRK2 locus for Parkinson's disease (PD), Crohn's disease (CD) and leprosy. However, little is known about the molecular mechanisms mediating these effects. To further characterize this locus, we fine-mapped the risk association in 5,802 PD and 5,556 controls using a dense genotyping array (ImmunoChip). Using samples from 134 post-mortem control adult human brains (UK Human Brain Expression Consortium), where up to ten brain regions were available per individual, we studied the regional variation, splicing and regulation of LRRK2. We found convincing evidence for a common variant PD association located outside of the LRRK2 protein coding region (rs117762348, A>G, P = 2.56×10(-8), case/control MAF 0.083/0.074, odds ratio 0.86 for the minor allele with 95% confidence interval [0.80-0.91]). We show that mRNA expression levels are highest in cortical regions and lowest in cerebellum. We find an exon quantitative trait locus (QTL) in brain samples that localizes to exons 32-33 and investigate the molecular basis of this eQTL using RNA-Seq data in n = 8 brain samples. The genotype underlying this eQTL is in strong linkage disequilibrium with the CD associated non-synonymous SNP rs3761863 (M2397T). We found two additional QTLs in liver and monocyte samples but none of these explained the common variant PD association at rs117762348. Our results characterize the LRRK2 locus, and highlight the importance and difficulties of fine-mapping and integration of multiple datasets to delineate pathogenic variants and thus develop an understanding of disease mechanisms.
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Publication type Article: Journal article
Document type Scientific Article
Language english
Publication Year 2013
HGF-reported in Year 2013
ISSN (print) / ISBN 1932-6203
Journal PLoS ONE
Quellenangaben Volume: 8, Issue: 8, Pages: , Article Number: e70724 Supplement: ,
Publisher Public Library of Science (PLoS)
Publishing Place Lawrence, Kan.
Reviewing status Peer reviewed
Institute(s) Institute of Human Genetics (IHG)
Research Unit Molecular Epidemiology (AME)
POF-Topic(s) 30501 - Systemic Analysis of Genetic and Environmental Factors that Impact Health
Research field(s) Genetics and Epidemiology
PSP Element(s) G-500700-001
G-504200-001
PubMed ID 23967090
DOI 10.1371/journal.pone.0070724
Erfassungsdatum 2013-11-13
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