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Volumn 21, Issue 1, 2014, Pages

Identifying rare and common disease associated variants in genomic data using Parkinson's disease as a model

Author keywords

Genomic data; GWAS; HAS2; Kremen1; Next generation association study; Parkinson's disease; Rare variant association; Sequencing association study; SNCA; Wnt signalling pathway

Indexed keywords

ALPHA SYNUCLEIN; HYALURONAN SYNTHASE 2; SYNTHETASE; UNCLASSIFIED DRUG;

EID: 84908457848     PISSN: 10217770     EISSN: 14230127     Source Type: Journal    
DOI: 10.1186/s12929-014-0088-9     Document Type: Article
Times cited : (6)

References (55)
  • 1
    • 84867133601 scopus 로고    scopus 로고
    • Genetic and epigenetic contribution to complex traits
    • Kilpinen H, Dermitzakis ET: Genetic and epigenetic contribution to complex traits. Hum Mol Genet 2012, 21(R1):R24-R28.
    • (2012) Hum Mol Genet , vol.21 , Issue.R1 , pp. R24-R28
    • Kilpinen, H.1    Dermitzakis, E.T.2
  • 2
    • 84863994823 scopus 로고    scopus 로고
    • A novel variational Bayes multiple locus Z-statistic for genome-wide association studies with Bayesian model averaging
    • Logsdon BA, Carty CL, Reiner AP, Dai JY, Kooperberg C: A novel variational Bayes multiple locus Z-statistic for genome-wide association studies with Bayesian model averaging. Bioinformatics 2012, 28(13):1738-1744.
    • (2012) Bioinformatics , vol.28 , Issue.13 , pp. 1738-1744
    • Logsdon, B.A.1    Carty, C.L.2    Reiner, A.P.3    Dai, J.Y.4    Kooperberg, C.5
  • 4
    • 55549147191 scopus 로고    scopus 로고
    • Personal genomes: The case of the missing heritability
    • Maher B: Personal genomes: the case of the missing heritability. Nature 2008, 456:18-21.
    • (2008) Nature , vol.456 , pp. 18-21
    • Maher, B.1
  • 6
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • 1000 Genomes Project Consortium: An integrated map of genetic variation from 1,092 human genomes. Nature 2012, 491:56-65.
    • (2012) Nature , vol.491 , pp. 56-65
    • 1000 Genomes Project Consortium1
  • 8
    • 84872410521 scopus 로고    scopus 로고
    • Detecting rare variant effects using extreme phenotype sampling in sequencing association studies
    • Barnett IJ, Lee S, Lin X: Detecting rare variant effects using extreme phenotype sampling in sequencing association studies. Genet Epidemiol 2013, 37:142-151.
    • Genet Epidemiol , vol.2013 , Issue.37 , pp. 142-151
    • Barnett, I.J.1    Lee, S.2    Lin, X.3
  • 9
    • 84859171835 scopus 로고    scopus 로고
    • The Empirical Power of Rare Variant Association Methods: Results from Sanger Sequencing in 1,998 Individuals
    • Ladouceur M, Dastani Z, Aulchenko YS, Greenwood CMT, Richards JB: The Empirical Power of Rare Variant Association Methods: Results from Sanger Sequencing in 1,998 Individuals. PLoS Genet 2012, 8(2):e1002496.
    • (2012) PLoS Genet , vol.8 , Issue.2 , pp. e1002496
    • Ladouceur, M.1    Dastani, Z.2    Aulchenko, Y.S.3    Greenwood, C.M.T.4    Richards, J.B.5
  • 11
    • 77958102016 scopus 로고    scopus 로고
    • Statistical analysis strategies for association studies involving rare variants
    • Bansal V, Libiger O, Torkamani A, Schork NJ: Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet 2010, 11:773-785.
    • (2010) Nat Rev Genet , vol.11 , pp. 773-785
    • Bansal, V.1    Libiger, O.2    Torkamani, A.3    Schork, N.J.4
  • 12
    • 79952253512 scopus 로고    scopus 로고
    • A new testing strategy to identify rare variants with either risk or protective effect on disease
    • Ionita-Laza I, Buxbaum JD, Laird NM, Lange C: A new testing strategy to identify rare variants with either risk or protective effect on disease. PLoS Genet 2011, 7:e1001289.
    • (2011) PLoS Genet , vol.7 , pp. e1001289
    • Ionita-Laza, I.1    Buxbaum, J.D.2    Laird, N.M.3    Lange, C.4
  • 13
    • 80054728031 scopus 로고    scopus 로고
    • Comparison of statistical tests for disease association with rare variants
    • Basu S, Pan W: Comparison of statistical tests for disease association with rare variants. Genet Epidemiol 2011, 35:606-619.
    • (2011) Genet Epidemiol , vol.35 , pp. 606-619
    • Basu, S.1    Pan, W.2
  • 14
    • 50949095168 scopus 로고    scopus 로고
    • Methods for detecting associations with rare variants for common diseases: Application to analysis of sequence data
    • Li B, Leal SM: Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet 2008, 83:311-321.
    • (2008) Am J Hum Genet , vol.83 , pp. 311-321
    • Li, B.1    Leal, S.M.2
  • 15
    • 61449168010 scopus 로고    scopus 로고
    • A groupwise association test for rare mutations using a weighted sum statistic
    • Madsen BE, Browning SR: A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet 2009, 5:e1000384.
    • (2009) PLoS Genet , vol.5 , pp. e1000384
    • Madsen, B.E.1    Browning, S.R.2
  • 16
    • 84857169577 scopus 로고    scopus 로고
    • Reconsidering association testing methods using single-variant test statistics as alternatives to pooling tests for sequence data with rare variants
    • Kinnamon DD, Hershberger RE, Martin ER: Reconsidering association testing methods using single-variant test statistics as alternatives to pooling tests for sequence data with rare variants. PLoS ONE 2012, 7:e30238.
    • (2012) PLoS ONE , vol.7 , pp. e30238
    • Kinnamon, D.D.1    Hershberger, R.E.2    Martin, E.R.3
  • 17
    • 84874582196 scopus 로고    scopus 로고
    • Rare-variant genome-wide association studies: A new frontier in genetic analysis of complex traits
    • Wagner MJ: Rare-variant genome-wide association studies: a new frontier in genetic analysis of complex traits. Pharmacogenomics 2013, 14(4):413-424.
    • (2013) Pharmacogenomics , vol.14 , Issue.4 , pp. 413-424
    • Wagner, M.J.1
  • 18
    • 84867130076 scopus 로고    scopus 로고
    • Exome sequencing and complex disease: Practical aspects of rare variant association studies
    • Do R, Kathiresan S, Abecasis GR: Exome sequencing and complex disease: practical aspects of rare variant association studies. Hum Mol Genet 2012, 21:R1-R9.
    • (2012) Hum Mol Genet , vol.21 , pp. R1-R9
    • Do, R.1    Kathiresan, S.2    Abecasis, G.R.3
  • 19
    • 84872389630 scopus 로고    scopus 로고
    • Rare variant analysis for family-based design
    • De G, Yip W-K, Ionita-Laza I, Laird N: Rare variant analysis for family-based design. PLoS ONE 2013, 8(1):e48495.
    • (2013) PLoS ONE , vol.8 , Issue.1 , pp. e48495
    • De Yip W-K, G.1    Ionita-Laza, I.2    Laird, N.3
  • 20
    • 78149479773 scopus 로고    scopus 로고
    • Comprehensive Approach to Analyzing Rare Genetic Variants
    • Hoffmann TJ, Marini NJ, Witte JS: Comprehensive Approach to Analyzing Rare Genetic Variants. PLoS ONE 2010, 5(11):e13584.
    • (2010) PLoS ONE , vol.5 , Issue.11 , pp. e13584
    • Hoffmann, T.J.1    Marini, N.J.2    Witte, J.S.3
  • 22
    • 77951028197 scopus 로고    scopus 로고
    • A data-adaptive sum test for disease association with multiple common or rare variants
    • Han F, Pan W: A data-adaptive sum test for disease association with multiple common or rare variants. Hum Hered 2010, 70:42-54.
    • (2010) Hum Hered , vol.70 , pp. 42-54
    • Han, F.1    Pan, W.2
  • 24
    • 51749119425 scopus 로고    scopus 로고
    • Analysis of multiple SNPs in a candidate gene or region
    • Chapman J, Whittaker J: Analysis of multiple SNPs in a candidate gene or region. Genet Epidemiol 2008, 32:560-566.
    • (2008) Genet Epidemiol , vol.32 , pp. 560-566
    • Chapman, J.1    Whittaker, J.2
  • 25
    • 69949121284 scopus 로고    scopus 로고
    • Asymptotic tests of association with multiple SNPs in linkage disequilibrium
    • Pan W: Asymptotic tests of association with multiple SNPs in linkage disequilibrium. Genet Epidemiol 2009, 33:497-507.
    • (2009) Genet Epidemiol , vol.33 , pp. 497-507
    • Pan, W.1
  • 26
    • 0042881041 scopus 로고    scopus 로고
    • Mathematical multi-locus approaches to localizing complex human trait genes
    • Hoh J, Ott J: Mathematical multi-locus approaches to localizing complex human trait genes. Nat Rev Genet 2003, 4:701-709.
    • (2003) Nat Rev Genet , vol.4 , pp. 701-709
    • Hoh, J.1    Ott, J.2
  • 27
    • 80051499915 scopus 로고    scopus 로고
    • Rare-variant association testing for sequencing data with the sequence kernel association test
    • Wu MC, Lee S, Cai T, Li Y, Boehnke MC, Lin X: Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet 2011, 89(1):82-93.
    • (2011) Am J Hum Genet , vol.89 , Issue.1 , pp. 82-93
    • Wu, M.C.1    Lee, S.2    Cai, T.3    Li, Y.4    Boehnke, M.C.5    Lin, X.6
  • 28
    • 84862143024 scopus 로고    scopus 로고
    • Scan-Statistic Approach Identifies Clusters of Rare Disease Variants in LRP2, a Gene Linked and Associated with Autism Spectrum Disorders, in Three Datasets
    • Ionita-Laza I, Makarov V, Buxbaum JD, the ARRA Autism Sequencing Consortium: Scan-Statistic Approach Identifies Clusters of Rare Disease Variants in LRP2, a Gene Linked and Associated with Autism Spectrum Disorders, in Three Datasets. Am J Hum Genet 2012, 90(6):1002-1013.
    • (2012) Am J Hum Genet , vol.90 , Issue.6 , pp. 1002-1013
    • Ionita-Laza, I.1    Makarov, V.2    Buxbaum, J.D.3    ARRA Autism Sequencing Consortium4
  • 29
    • 84864942403 scopus 로고    scopus 로고
    • Optimal Unified Approach for Rare-Variant Association Testing with Application to Small-Sample Case-control Whole-Exome Sequencing Studies
    • Lee S, Emond MJ, Bamshad MJ, Barnes KC, Rieder MJ, Nickerson DA, Christiani DC, Wurfel MM, Lin X, NHLBI GO Exome Sequencing Project - ESP Lung Project Team: Optimal Unified Approach for Rare-Variant Association Testing with Application to Small-Sample Case-control Whole-Exome Sequencing Studies. Am J Hum Genet 2012, 91(2):224-237.
    • (2012) Am J Hum Genet , vol.91 , Issue.2 , pp. 224-237
    • Lee, S.1    Emond, M.J.2    Bamshad, M.J.3    Barnes, K.C.4    Rieder, M.J.5    Nickerson, D.A.6    Christiani, D.C.7    Wurfel, M.M.8    Lin, X.9
  • 30
    • 84878878253 scopus 로고    scopus 로고
    • Sequence kernel association tests for the combined effect of rare and common variants
    • Ionita-Laza I, Lee S, Makarov V, Buxbaum JD, Lin X: Sequence kernel association tests for the combined effect of rare and common variants. Am J Hum Genet 2013, 92(6):841-853.
    • (2013) Am J Hum Genet , vol.92 , Issue.6 , pp. 841-853
    • Ionita-Laza, I.1    Lee, S.2    Makarov, V.3    Buxbaum, J.D.4    Lin, X.5
  • 32
    • 0000586227 scopus 로고
    • Limit distributions of maximal segmental score among Markov-dependent partial sums
    • Karlin S, Dembo A: Limit distributions of maximal segmental score among Markov-dependent partial sums. Adv Appl Probab 1992, 24:113-140.
    • (1992) Adv Appl Probab , vol.24 , pp. 113-140
    • Karlin, S.1    Dembo, A.2
  • 33
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • Karlin S, Altschul SF: Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci U S A 1990, 87:2264-2268.
    • (1990) Proc Natl Acad Sci U S A , vol.87 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2
  • 36
    • 45749116906 scopus 로고    scopus 로고
    • Using the longest significance run to estimate region-specific p-values in genetic association mapping studies
    • Lian IB, Lin YH, Lin YC, Yang HC, Chang CJ, Fann CSJ: Using the longest significance run to estimate region-specific p-values in genetic association mapping studies. BMC Bioinformatics 2008, 9:246.
    • (2008) BMC Bioinformatics , vol.9 , pp. 246
    • Lian, I.B.1    Lin, Y.H.2    Lin, Y.C.3    Yang, H.C.4    Chang, C.J.5    Fann, C.S.J.6
  • 37
    • 77957737930 scopus 로고    scopus 로고
    • Robust tests for matched case-control genetic association studies
    • Zang Y, Fung WK: Robust tests for matched case-control genetic association studies. BMC Genet 2010, 11:91.
    • (2010) BMC Genet , vol.11 , pp. 91
    • Zang, Y.1    Fung, W.K.2
  • 39
    • 79961193174 scopus 로고    scopus 로고
    • HAPGEN2: Simulation of multiple disease SNPs
    • Su Z, Marchini J, Donnelly P: HAPGEN2: simulation of multiple disease SNPs. Bioinformatics 2011, 27(16):2304-2305.
    • (2011) Bioinformatics , vol.27 , Issue.16 , pp. 2304-2305
    • Su, Z.1    Marchini, J.2    Donnelly, P.3
  • 40
    • 84863724842 scopus 로고    scopus 로고
    • 1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data
    • Huang J, Ellinghaus D, Franke A, Howie B, Li Y: 1000 Genomes-based imputation identifies novel and refined associations for the Wellcome Trust Case Control Consortium phase 1 Data. Eur J Hum Genet 2014, 20(7):801-805.
    • (2014) Eur J Hum Genet , vol.20 , Issue.7 , pp. 801-805
    • Huang, J.1    Ellinghaus, D.2    Franke, A.3    Howie, B.4    Li, Y.5
  • 42
    • 84857149176 scopus 로고    scopus 로고
    • Human Genome and Sequence Variation
    • Edited by Speicher M, Antonarkis S, Motulsky A. New York: Springer
    • Antonarkis S: Human Genome and Sequence Variation. In Vogel and Motulsky's Human Genetics. 4th edition. Edited by Speicher M, Antonarkis S, Motulsky A. New York: Springer; 2010:31-53.
    • (2010) Vogel and Motulsky's Human Genetics. 4th Edition , pp. 31-53
    • Antonarkis, S.1
  • 50
    • 84884331630 scopus 로고    scopus 로고
    • Marginal association between SNP rs2046571 of the HAS2 gene and Parkinson's disease in the Chinese female population
    • Yuan Y, Tang BS, Yu RL, Li K, Lv ZY, Yan XX, Guo JF: Marginal association between SNP rs2046571 of the HAS2 gene and Parkinson's disease in the Chinese female population. Neurosci Lett 2013, 552:58-61.
    • (2013) Neurosci Lett , vol.552 , pp. 58-61
    • Yuan, Y.1    Tang, B.S.2    Yu, R.L.3    Li, K.4    Lv, Z.Y.5    Yan, X.X.6    Guo, J.F.7
  • 51
    • 84896846861 scopus 로고    scopus 로고
    • Wnt signaling in midbrain dopaminergic neuron development and regenerative medicine for Parkinson's disease
    • Arenas E: Wnt signaling in midbrain dopaminergic neuron development and regenerative medicine for Parkinson's disease. J Mol Cell Biol 2014, 6(1):42-53.
    • (2014) J Mol Cell Biol , vol.6 , Issue.1 , pp. 42-53
    • Arenas, E.1
  • 52
    • 84887108451 scopus 로고    scopus 로고
    • MicroRNA-431 regulates axon regeneration in mature sensory neurons by targeting the Wnt antagonist Kremen1
    • Wu D, Murashov AK: MicroRNA-431 regulates axon regeneration in mature sensory neurons by targeting the Wnt antagonist Kremen1. Fron Mol Neurosci 2013, 6:35.
    • Fron Mol Neurosci , vol.2013 , Issue.6 , pp. 35
    • Wu, D.1    Murashov, A.K.2
  • 54
    • 0035911649 scopus 로고    scopus 로고
    • Molecular cloning and characterization of Kremen, a novel kringle-containing transmembrane protein
    • Nakamura T, Aoki S, Kitajima K, Takahashi T, Matsumoto K, Nakamura T: Molecular cloning and characterization of Kremen, a novel kringle-containing transmembrane protein. Biochim Biophys Acta 2001, 1518(1-2):63-72.
    • (2001) Biochim Biophys Acta , vol.1518 , Issue.1-2 , pp. 63-72
    • Nakamura, T.1    Aoki, S.2    Kitajima, K.3    Takahashi, T.4    Matsumoto, K.5    Nakamura, T.6


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