메뉴 건너뛰기




Volumn 10, Issue 4, 2010, Pages 355-363

An interactive effect of batch size and composition contributes to discordant results in GWAS with the CHIAMO genotyping algorithm

Author keywords

association studies; CHIAMO calling algorithm; genome wide; genotype calling error; repeatability

Indexed keywords

ARTICLE; CASE CONTROL STUDY; CLASSIFIER; CORONARY ARTERY DISEASE; GENETIC ALGORITHM; GENETIC ASSOCIATION; GENOTYPE; MICROARRAY ANALYSIS; PRIORITY JOURNAL; QUALITY CONTROL; REPRODUCIBILITY; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL ANALYSIS; ALGORITHM; DNA MICROARRAY; GENETICS; HUMAN; REINFORCEMENT; STATISTICS AND NUMERICAL DATA;

EID: 77955168118     PISSN: 1470269X     EISSN: 14731150     Source Type: Journal    
DOI: 10.1038/tpj.2010.47     Document Type: Article
Times cited : (11)

References (26)
  • 1
    • 33847176604 scopus 로고    scopus 로고
    • A genome-wide association study identifies novel risk loci for type 2 diabetes
    • Sladek R, Rocheleau G, Rung J, Dina C, Shen L, Serre D et al. A genome-wide association study identifies novel risk loci for type 2 diabetes. Nature 2007; 445: 881-885.
    • (2007) Nature , vol.445 , pp. 881-885
    • Sladek, R.1    Rocheleau, G.2    Rung, J.3    Dina, C.4    Shen, L.5    Serre, D.6
  • 2
    • 84969213492 scopus 로고    scopus 로고
    • Genome-wide association study of 14000 cases of seven common diseases and 3000 shared controls
    • The Wellcome Trust Case Control Consortium.
    • The Wellcome Trust Case Control Consortium. Genome-wide association study of 14000 cases of seven common diseases and 3000 shared controls. Nature 2007; 447: 661-678.
    • (2007) Nature , vol.447 , pp. 661-678
  • 6
    • 34249895023 scopus 로고    scopus 로고
    • Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes
    • Zeggini E, Weedon MN, Lindgren CM, Frayling TM, Elliott KS, Lango H et al. Replication of genome-wide association signals in UK samples reveals risk loci for type 2 diabetes. Science 2007; 316: 1336-1341.
    • (2007) Science , vol.316 , pp. 1336-1341
    • Zeggini, E.1    Weedon, M.N.2    Lindgren, C.M.3    Frayling, T.M.4    Elliott, K.S.5    Lango, H.6
  • 7
    • 34249885875 scopus 로고    scopus 로고
    • A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants
    • Scott LJ, Mohlke KL, Bonnycastle LL, Willer CJ, Li Y, Duren WL et al. A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants. Science 2007; 316: 1341-1345.
    • (2007) Science , vol.316 , pp. 1341-1345
    • Scott, L.J.1    Mohlke, K.L.2    Bonnycastle, L.L.3    Willer, C.J.4    Li, Y.5    Duren, W.L.6
  • 8
    • 34250006413 scopus 로고    scopus 로고
    • Genome-wide association study identifies novel breast cancer susceptibility loci
    • Easton DF, Pooley KA, Dunning AM, Pharoah PDP, Thompson D, Ballinger DG et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 2007; 447: 1087-1093.
    • (2007) Nature , vol.447 , pp. 1087-1093
    • Easton, D.F.1    Pooley, K.A.2    Dunning, A.M.3    Pdp, P.4    Thompson, D.5    Ballinger, D.G.6
  • 9
    • 34447129720 scopus 로고    scopus 로고
    • Non-replication and inconsistency in the genome-wide association setting
    • Ioannidis JPA. Non-replication and inconsistency in the genome-wide association setting. Hum Hered 2007; 64: 203-213.
    • (2007) Hum Hered , vol.64 , pp. 203-213
    • Ioannidis, J.P.A.1
  • 10
    • 41049087605 scopus 로고    scopus 로고
    • Heterogeneity in meta-analyses of genome-wide association investigations
    • Ioannidis JPA, Patsopoulos NA, Evangelou E. Heterogeneity in meta-analyses of genome-wide association investigations. PLoS One 2007; 2: e841.
    • (2007) PLoS One , vol.2
    • Jpa, I.1    Patsopoulos, N.A.2    Evangelou, E.3
  • 11
    • 53749093122 scopus 로고    scopus 로고
    • Evaluation of the potential excess of statistically significant findings in published genetic association studies: Application to Alzheimer's disease
    • Kavvoura FK, McQueen MB, Khoury MJ, Tanzi RE, Bertram L, Ioannidis JPA. Evaluation of the potential excess of statistically significant findings in published genetic association studies: application to Alzheimer's disease. Am J Epidemiol 2008; 168: 855-865.
    • (2008) Am J Epidemiol , vol.168 , pp. 855-865
    • Kavvoura, F.K.1    McQueen, M.B.2    Khoury, M.J.3    Tanzi, R.E.4    Bertram, L.5    Ioannidis, J.P.A.6
  • 12
    • 65249183403 scopus 로고    scopus 로고
    • Meta-analysis in genome-wide association studies
    • Zeggini E, Ioannidis JPA. Meta-analysis in genome-wide association studies. Pharmacogenomics 2009; 10: 191-201.
    • (2009) Pharmacogenomics , vol.10 , pp. 191-201
    • Zeggini, E.1    Ioannidis, J.P.A.2
  • 14
    • 33749013001 scopus 로고    scopus 로고
    • Implications of small effect sizes of individual genetic variants on the design and interpretation of genetic association studies of complex diseases
    • Ioannidis JPA, Trikalinos TA, Khoury MJ. Implications of small effect sizes of individual genetic variants on the design and interpretation of genetic association studies of complex diseases. Am J Epidemiol 2006; 164: 609-614.
    • (2006) Am J Epidemiol , vol.164 , pp. 609-614
    • Jpa, I.1    Trikalinos, T.A.2    Khoury, M.J.3
  • 15
    • 77955144299 scopus 로고    scopus 로고
    • Replication in genome-wide association studies
    • Kraft P, Zeggini E, Ioannidis JPA. Replication in genome-wide association studies. Stat Sci 2009; 24: 561-573.
    • (2009) Stat Sci , vol.24 , pp. 561-573
    • Kraft, P.1    Zeggini, E.2    Ioannidis, J.P.A.3
  • 16
    • 57649136554 scopus 로고    scopus 로고
    • Progress and challenges in genome-wide association studies in humans
    • Donnelly P. Progress and challenges in genome-wide association studies in humans. Nature 2008; 456: 728-731.
    • (2008) Nature , vol.456 , pp. 728-731
    • Donnelly, P.1
  • 17
    • 34249888775 scopus 로고    scopus 로고
    • Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels
    • Saxena R, Voight BF, Lyssenko V, Burtt NP, de Bakker P, Chen H et al. Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels. Science 2007; 316: 1331-1336.
    • (2007) Science , vol.316 , pp. 1331-1336
    • Saxena, R.1    Voight, B.F.2    Lyssenko, V.3    Burtt, N.P.4    De Bakker, P.5    Chen, H.6
  • 20
    • 33845879059 scopus 로고    scopus 로고
    • SNiPer-HD: Improved genotype calling accuracy by an expectation- maximization algorithm for high-density SNP arrays
    • Hua J, Craig DW, Brun M, Webster J, Zismann V, Tembe W et al. SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays. Bioinformatics 2007; 23: 57-63.
    • (2007) Bioinformatics , vol.23 , pp. 57-63
    • Hua, J.1    Craig, D.W.2    Brun, M.3    Webster, J.4    Zismann, V.5    Tembe, W.6
  • 21
    • 34147136617 scopus 로고    scopus 로고
    • Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data
    • Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics 2007; 8: 485-499.
    • (2007) Biostatistics , vol.8 , pp. 485-499
    • Carvalho, B.1    Bengtsson, H.2    Speed, T.P.3    Irizarry, R.A.4
  • 22
    • 49649088465 scopus 로고    scopus 로고
    • Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500K array set using 270 HapMap samples
    • Hong H, Su Z, Ge W, Shi L, Perkins R, Fang H et al. Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500K array set using 270 HapMap samples. BMC Bioinf 2008; 9: S17.
    • (2008) BMC Bioinf , vol.9
    • Hong, H.1    Su, Z.2    Ge, W.3    Shi, L.4    Perkins, R.5    Fang, H.6
  • 23
    • 34548292504 scopus 로고    scopus 로고
    • PLINK: A toolset for whole-genome association and population-based linkage analysis
    • Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D et al. PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 2007; 81: 559-575.
    • (2007) Am J Hum Genet , vol.81 , pp. 559-575
    • Purcell, S.1    Neale, B.2    Todd-Brown, K.3    Thomas, L.4    Ma, F.5    Bender, D.6
  • 24
    • 0000937686 scopus 로고
    • Tests for linear trends in proportions and frequencies
    • Armitage P. Tests for linear trends in proportions and frequencies. Biometrics 1971; 11: 375-386.
    • (1971) Biometrics , vol.11 , pp. 375-386
    • Armitage, P.1
  • 25
    • 47149098635 scopus 로고    scopus 로고
    • Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays
    • Lin S, Carvalho B, Cutler DJ, Arking DE, Chakravarti A, Irizarry RA. Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays. Genome Biol 2008; 9: R63.
    • (2008) Genome Biol , vol.9
    • Lin, S.1    Carvalho, B.2    Cutler, D.J.3    De, A.4    Chakravarti, A.5    Irizarry, R.A.6
  • 26
    • 33748491517 scopus 로고    scopus 로고
    • The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements
    • MAQC Consortium. The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006; 24: 1151-1161.
    • (2006) Nat Biotechnol , vol.24 , pp. 1151-1161
    • Maqc, Consortium.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.