Meta-analysis of Parkinson's Disease: Identification of a novel locus, RIT2

Nathan Pankratz, Gary W. Beecham, Anita L. Destefano, Ted M. Dawson, Kimberly F. Doheny, Stewart A. Factor, Taye H. Hamza, Albert Y. Hung, Bradley T. Hyman, Adrian J. Ivinson, Dmitri Krainc, Jeanne C. Latourelle, Lorraine N. Clark, Karen Marder, Eden R. Martin, Richard Mayeux, Owen A. Ross, Clemens R. Scherzer, David K. Simon, Caroline TannerJeffery M. Vance, Zbigniew K. Wszolek, Cyrus P. Zabetian, Richard H. Myers, Haydeh Payami, William K. Scott, Tatiana Foroud

Research output: Contribution to journalArticle

150 Citations (Scopus)

Abstract

Objective: Genome-wide association (GWAS) methods have identified genes contributing to Parkinson's disease (PD); we sought to identify additional genes associated with PD susceptibility. Methods: A 2-stage design was used. First, individual level genotypic data from 5 recent PD GWAS (Discovery Sample: 4,238 PD cases and 4,239 controls) were combined. Following imputation, a logistic regression model was employed in each dataset to test for association with PD susceptibility and results from each dataset were meta-analyzed. Second, 768 single-nucleotide polymorphisms (SNPs) were genotyped in an independent Replication Sample (3,738 cases and 2,111 controls). Results: Genome-wide significance was reached for SNPs in SNCA (rs356165; G: odds ratio [OR] = 1.37; p = 9.3 × 10 -21), MAPT (rs242559; C: OR = 0.78; p = 1.5 × 10 -10), GAK/DGKQ (rs11248051; T: OR = 1.35; p = 8.2 × 10 -9/rs11248060; T: OR = 1.35; p = 2.0 × 10 -9), and the human leukocyte antigen (HLA) region (rs3129882; A: OR = 0.83; p = 1.2 × 10 -8), which were previously reported. The Replication Sample confirmed the associations with SNCA, MAPT, and the HLA region and also with GBA (E326K; OR = 1.71; p = 5 × 10 -8 Combined Sample) (N370; OR = 3.08; p = 7 × 10 -5 Replication sample). A novel PD susceptibility locus, RIT2, on chromosome 18 (rs12456492; p = 5 × 10 -5 Discovery Sample; p = 1.52 × 10 -7 Replication sample; p = 2 × 10 -10 Combined Sample) was replicated. Conditional analyses within each of the replicated regions identified distinct SNP associations within GBA and SNCA, suggesting that there may be multiple risk alleles within these genes. Interpretation: We identified a novel PD susceptibility locus, RIT2, replicated several previously identified loci, and identified more than 1 risk allele within SNCA and GBA.

Original languageEnglish
Pages (from-to)370-384
Number of pages15
JournalAnnals of Neurology
Volume71
Issue number3
DOIs
StatePublished - Mar 2012

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Parkinson Disease
Meta-Analysis
Odds Ratio
Disease Susceptibility
Single Nucleotide Polymorphism
Genome
HLA Antigens
Logistic Models
Alleles
Genes
Chromosomes, Human, Pair 18
varespladib methyl

ASJC Scopus subject areas

  • Neurology
  • Clinical Neurology

Cite this

Pankratz, N., Beecham, G. W., Destefano, A. L., Dawson, T. M., Doheny, K. F., Factor, S. A., ... Foroud, T. (2012). Meta-analysis of Parkinson's Disease: Identification of a novel locus, RIT2. Annals of Neurology, 71(3), 370-384. https://doi.org/10.1002/ana.22687

Meta-analysis of Parkinson's Disease : Identification of a novel locus, RIT2. / Pankratz, Nathan; Beecham, Gary W.; Destefano, Anita L.; Dawson, Ted M.; Doheny, Kimberly F.; Factor, Stewart A.; Hamza, Taye H.; Hung, Albert Y.; Hyman, Bradley T.; Ivinson, Adrian J.; Krainc, Dmitri; Latourelle, Jeanne C.; Clark, Lorraine N.; Marder, Karen; Martin, Eden R.; Mayeux, Richard; Ross, Owen A.; Scherzer, Clemens R.; Simon, David K.; Tanner, Caroline; Vance, Jeffery M.; Wszolek, Zbigniew K.; Zabetian, Cyrus P.; Myers, Richard H.; Payami, Haydeh; Scott, William K.; Foroud, Tatiana.

In: Annals of Neurology, Vol. 71, No. 3, 03.2012, p. 370-384.

Research output: Contribution to journalArticle

Pankratz, N, Beecham, GW, Destefano, AL, Dawson, TM, Doheny, KF, Factor, SA, Hamza, TH, Hung, AY, Hyman, BT, Ivinson, AJ, Krainc, D, Latourelle, JC, Clark, LN, Marder, K, Martin, ER, Mayeux, R, Ross, OA, Scherzer, CR, Simon, DK, Tanner, C, Vance, JM, Wszolek, ZK, Zabetian, CP, Myers, RH, Payami, H, Scott, WK & Foroud, T 2012, 'Meta-analysis of Parkinson's Disease: Identification of a novel locus, RIT2', Annals of Neurology, vol. 71, no. 3, pp. 370-384. https://doi.org/10.1002/ana.22687
Pankratz N, Beecham GW, Destefano AL, Dawson TM, Doheny KF, Factor SA et al. Meta-analysis of Parkinson's Disease: Identification of a novel locus, RIT2. Annals of Neurology. 2012 Mar;71(3):370-384. https://doi.org/10.1002/ana.22687
Pankratz, Nathan ; Beecham, Gary W. ; Destefano, Anita L. ; Dawson, Ted M. ; Doheny, Kimberly F. ; Factor, Stewart A. ; Hamza, Taye H. ; Hung, Albert Y. ; Hyman, Bradley T. ; Ivinson, Adrian J. ; Krainc, Dmitri ; Latourelle, Jeanne C. ; Clark, Lorraine N. ; Marder, Karen ; Martin, Eden R. ; Mayeux, Richard ; Ross, Owen A. ; Scherzer, Clemens R. ; Simon, David K. ; Tanner, Caroline ; Vance, Jeffery M. ; Wszolek, Zbigniew K. ; Zabetian, Cyrus P. ; Myers, Richard H. ; Payami, Haydeh ; Scott, William K. ; Foroud, Tatiana. / Meta-analysis of Parkinson's Disease : Identification of a novel locus, RIT2. In: Annals of Neurology. 2012 ; Vol. 71, No. 3. pp. 370-384.
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abstract = "Objective: Genome-wide association (GWAS) methods have identified genes contributing to Parkinson's disease (PD); we sought to identify additional genes associated with PD susceptibility. Methods: A 2-stage design was used. First, individual level genotypic data from 5 recent PD GWAS (Discovery Sample: 4,238 PD cases and 4,239 controls) were combined. Following imputation, a logistic regression model was employed in each dataset to test for association with PD susceptibility and results from each dataset were meta-analyzed. Second, 768 single-nucleotide polymorphisms (SNPs) were genotyped in an independent Replication Sample (3,738 cases and 2,111 controls). Results: Genome-wide significance was reached for SNPs in SNCA (rs356165; G: odds ratio [OR] = 1.37; p = 9.3 × 10 -21), MAPT (rs242559; C: OR = 0.78; p = 1.5 × 10 -10), GAK/DGKQ (rs11248051; T: OR = 1.35; p = 8.2 × 10 -9/rs11248060; T: OR = 1.35; p = 2.0 × 10 -9), and the human leukocyte antigen (HLA) region (rs3129882; A: OR = 0.83; p = 1.2 × 10 -8), which were previously reported. The Replication Sample confirmed the associations with SNCA, MAPT, and the HLA region and also with GBA (E326K; OR = 1.71; p = 5 × 10 -8 Combined Sample) (N370; OR = 3.08; p = 7 × 10 -5 Replication sample). A novel PD susceptibility locus, RIT2, on chromosome 18 (rs12456492; p = 5 × 10 -5 Discovery Sample; p = 1.52 × 10 -7 Replication sample; p = 2 × 10 -10 Combined Sample) was replicated. Conditional analyses within each of the replicated regions identified distinct SNP associations within GBA and SNCA, suggesting that there may be multiple risk alleles within these genes. Interpretation: We identified a novel PD susceptibility locus, RIT2, replicated several previously identified loci, and identified more than 1 risk allele within SNCA and GBA.",
author = "Nathan Pankratz and Beecham, {Gary W.} and Destefano, {Anita L.} and Dawson, {Ted M.} and Doheny, {Kimberly F.} and Factor, {Stewart A.} and Hamza, {Taye H.} and Hung, {Albert Y.} and Hyman, {Bradley T.} and Ivinson, {Adrian J.} and Dmitri Krainc and Latourelle, {Jeanne C.} and Clark, {Lorraine N.} and Karen Marder and Martin, {Eden R.} and Richard Mayeux and Ross, {Owen A.} and Scherzer, {Clemens R.} and Simon, {David K.} and Caroline Tanner and Vance, {Jeffery M.} and Wszolek, {Zbigniew K.} and Zabetian, {Cyrus P.} and Myers, {Richard H.} and Haydeh Payami and Scott, {William K.} and Tatiana Foroud",
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TY - JOUR

T1 - Meta-analysis of Parkinson's Disease

T2 - Identification of a novel locus, RIT2

AU - Pankratz, Nathan

AU - Beecham, Gary W.

AU - Destefano, Anita L.

AU - Dawson, Ted M.

AU - Doheny, Kimberly F.

AU - Factor, Stewart A.

AU - Hamza, Taye H.

AU - Hung, Albert Y.

AU - Hyman, Bradley T.

AU - Ivinson, Adrian J.

AU - Krainc, Dmitri

AU - Latourelle, Jeanne C.

AU - Clark, Lorraine N.

AU - Marder, Karen

AU - Martin, Eden R.

AU - Mayeux, Richard

AU - Ross, Owen A.

AU - Scherzer, Clemens R.

AU - Simon, David K.

AU - Tanner, Caroline

AU - Vance, Jeffery M.

AU - Wszolek, Zbigniew K.

AU - Zabetian, Cyrus P.

AU - Myers, Richard H.

AU - Payami, Haydeh

AU - Scott, William K.

AU - Foroud, Tatiana

PY - 2012/3

Y1 - 2012/3

N2 - Objective: Genome-wide association (GWAS) methods have identified genes contributing to Parkinson's disease (PD); we sought to identify additional genes associated with PD susceptibility. Methods: A 2-stage design was used. First, individual level genotypic data from 5 recent PD GWAS (Discovery Sample: 4,238 PD cases and 4,239 controls) were combined. Following imputation, a logistic regression model was employed in each dataset to test for association with PD susceptibility and results from each dataset were meta-analyzed. Second, 768 single-nucleotide polymorphisms (SNPs) were genotyped in an independent Replication Sample (3,738 cases and 2,111 controls). Results: Genome-wide significance was reached for SNPs in SNCA (rs356165; G: odds ratio [OR] = 1.37; p = 9.3 × 10 -21), MAPT (rs242559; C: OR = 0.78; p = 1.5 × 10 -10), GAK/DGKQ (rs11248051; T: OR = 1.35; p = 8.2 × 10 -9/rs11248060; T: OR = 1.35; p = 2.0 × 10 -9), and the human leukocyte antigen (HLA) region (rs3129882; A: OR = 0.83; p = 1.2 × 10 -8), which were previously reported. The Replication Sample confirmed the associations with SNCA, MAPT, and the HLA region and also with GBA (E326K; OR = 1.71; p = 5 × 10 -8 Combined Sample) (N370; OR = 3.08; p = 7 × 10 -5 Replication sample). A novel PD susceptibility locus, RIT2, on chromosome 18 (rs12456492; p = 5 × 10 -5 Discovery Sample; p = 1.52 × 10 -7 Replication sample; p = 2 × 10 -10 Combined Sample) was replicated. Conditional analyses within each of the replicated regions identified distinct SNP associations within GBA and SNCA, suggesting that there may be multiple risk alleles within these genes. Interpretation: We identified a novel PD susceptibility locus, RIT2, replicated several previously identified loci, and identified more than 1 risk allele within SNCA and GBA.

AB - Objective: Genome-wide association (GWAS) methods have identified genes contributing to Parkinson's disease (PD); we sought to identify additional genes associated with PD susceptibility. Methods: A 2-stage design was used. First, individual level genotypic data from 5 recent PD GWAS (Discovery Sample: 4,238 PD cases and 4,239 controls) were combined. Following imputation, a logistic regression model was employed in each dataset to test for association with PD susceptibility and results from each dataset were meta-analyzed. Second, 768 single-nucleotide polymorphisms (SNPs) were genotyped in an independent Replication Sample (3,738 cases and 2,111 controls). Results: Genome-wide significance was reached for SNPs in SNCA (rs356165; G: odds ratio [OR] = 1.37; p = 9.3 × 10 -21), MAPT (rs242559; C: OR = 0.78; p = 1.5 × 10 -10), GAK/DGKQ (rs11248051; T: OR = 1.35; p = 8.2 × 10 -9/rs11248060; T: OR = 1.35; p = 2.0 × 10 -9), and the human leukocyte antigen (HLA) region (rs3129882; A: OR = 0.83; p = 1.2 × 10 -8), which were previously reported. The Replication Sample confirmed the associations with SNCA, MAPT, and the HLA region and also with GBA (E326K; OR = 1.71; p = 5 × 10 -8 Combined Sample) (N370; OR = 3.08; p = 7 × 10 -5 Replication sample). A novel PD susceptibility locus, RIT2, on chromosome 18 (rs12456492; p = 5 × 10 -5 Discovery Sample; p = 1.52 × 10 -7 Replication sample; p = 2 × 10 -10 Combined Sample) was replicated. Conditional analyses within each of the replicated regions identified distinct SNP associations within GBA and SNCA, suggesting that there may be multiple risk alleles within these genes. Interpretation: We identified a novel PD susceptibility locus, RIT2, replicated several previously identified loci, and identified more than 1 risk allele within SNCA and GBA.

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