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Volumn 72, Issue 3, 2011, Pages 153-160

Assessing the impact of non-differential genotyping errors on rare variant tests of association

Author keywords

Case control; Misclassification; Power; Sequencing data

Indexed keywords

ANALYTICAL ERROR; ARTICLE; CLASSIFICATION; GENE FREQUENCY; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; GENOTYPING ERROR; HETEROZYGOTE DETECTION; HOMOZYGOTE; HUMAN; PHENOTYPE; RISK FACTOR; SAMPLE SIZE; SEQUENCE ANALYSIS; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL;

EID: 82255175718     PISSN: 00015652     EISSN: 14230062     Source Type: Journal    
DOI: 10.1159/000332222     Document Type: Article
Times cited : (15)

References (37)
  • 1
    • 39649117755 scopus 로고    scopus 로고
    • The impact of next-generation sequencing technology on genetics
    • Mardis ER: The impact of next-generation sequencing technology on genetics. Trends Genet 2008; 24: 133-141.
    • (2008) Trends Genet , vol.24 , pp. 133-141
    • Mardis, E.R.1
  • 3
    • 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
  • 4
    • 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
    • Madsen, B.E.1    Browning, S.R.2
  • 5
    • 76649136928 scopus 로고    scopus 로고
    • An evaluation of statistical approaches to rare variant analysis in genetic association studies
    • Morris AP, Zeggini E: An evaluation of statistical approaches to rare variant analysis in genetic association studies. Genet Epidemiol 2010; 34: 188-193.
    • (2010) Genet Epidemiol , vol.34 , pp. 188-193
    • Morris, A.P.1    Zeggini, E.2
  • 6
    • 78249243049 scopus 로고    scopus 로고
    • Extending rarevariant testing strategies: Analysis of noncoding sequence imputed genotypes
    • Zawistowski M, Gopalakrishnan S, Ding J, Li Y, Grimm S, Zöllner S: Extending rarevariant testing strategies: analysis of noncoding sequence imputed genotypes. Am J Hum Genet 2010; 87: 604-617.
    • (2010) Am J Hum Genet , vol.87 , pp. 604-617
    • Zawistowski, M.1    Gopalakrishnan, S.2    Ding, J.3    Li, Y.4    Grimm, S.5    Zöllner, S.6
  • 7
    • 77949552913 scopus 로고    scopus 로고
    • Approaches for evaluating rare polymorphisms in genetic association studies
    • Li Q, Zhang H, Yu K: Approaches for evaluating rare polymorphisms in genetic association studies. Hum Hered 2010; 69: 219-228.
    • (2010) Hum Hered , vol.69 , pp. 219-228
    • Li, Q.1    Zhang, H.2    Yu, K.3
  • 8
    • 78249272314 scopus 로고    scopus 로고
    • To identify associations with rare variants, just WHaIT: Weighted haplotype and imputation-based tests
    • Li Y, Byrnes AE, Li M: To identify associations with rare variants, just WHaIT: weighted haplotype and imputation-based tests. Am J Hum Genet 2010; 87: 728-735.
    • (2010) Am J Hum Genet , vol.87 , pp. 728-735
    • Li, Y.1    Byrnes, A.E.2    Li, M.3
  • 11
    • 79958100783 scopus 로고    scopus 로고
    • Adaptive tests for association analysis of rare variants
    • Pan W, Shen X: Adaptive tests for association analysis of rare variants. Genet Epidemiol 2011; 35: 381-388.
    • (2011) Genet Epidemiol , vol.35 , pp. 381-388
    • Pan, W.1    Shen, X.2
  • 12
    • 79960136351 scopus 로고    scopus 로고
    • A new expectation-maximization statistical test for case-control association studies considering rare variants obtained by high-throughput sequencing
    • Gordon D, Finch SJ, De La Vega F: A new expectation-maximization statistical test for case-control association studies considering rare variants obtained by high-throughput sequencing. Hum Hered 2011; 71: 113-125.
    • (2011) Hum Hered , vol.71 , pp. 113-125
    • Gordon, D.1    Finch, S.J.2    De La Vega, F.3
  • 13
    • 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 M, Lin X: Rare-variant association testing for sequencing data with the sequence kernel association test. Am J Hum Genet 2011; 89: 82-93.
    • (2011) Am J Hum Genet , vol.89 , pp. 82-93
    • Wu, M.C.1    Lee, S.2    Cai, T.3    Li, Y.4    Boehnke, M.5    Lin, X.6
  • 15
    • 79551589417 scopus 로고    scopus 로고
    • HiTEC: Accurate error correction in high-throughput sequencing data
    • Ilie L, Fazayeli F, Ilie S: HiTEC: accurate error correction in high-throughput sequencing data. Bioinformatics 2011; 27: 295-302.
    • (2011) Bioinformatics , vol.27 , pp. 295-302
    • Ilie, L.1    Fazayeli, F.2    Ilie, S.3
  • 16
    • 79956314887 scopus 로고    scopus 로고
    • Genotype and SNP calling from next-generation sequencing data
    • Nielsen R, Paul JS, Albrechtsen A, Song YS: Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 2011; 12: 443-451.
    • (2011) Nat Rev Genet , vol.12 , pp. 443-451
    • Nielsen, R.1    Paul, J.S.2    Albrechtsen, A.3    Song, Y.S.4
  • 17
    • 80053194792 scopus 로고    scopus 로고
    • Base-calling for next-generation sequencing platforms
    • DOI: 10.1093/bib/bbq077
    • Ledergerber C, Dessimoz C: Base-calling for next-generation sequencing platforms. Brief Bioinform 2011; DOI: 10.1093/bib/bbq077.
    • (2011) Brief Bioinform
    • Ledergerber, C.1    Dessimoz, C.2
  • 18
    • 30344454257 scopus 로고    scopus 로고
    • Characteristics of replicated singlenucleotide polymorphism genotypes from COGA: Affymetrix and center for inherited disease research
    • Tintle NL, Ahn K, Mendell NR, Gordon D, Finch SJ: Characteristics of replicated singlenucleotide polymorphism genotypes from COGA: affymetrix and center for inherited disease research. BMC Genet 2005; 6(suppl 1):S154.
    • (2005) BMC Genet , vol.6 , Issue.SUPPL. 1
    • Tintle, N.L.1    Ahn, K.2    Mendell, N.R.3    Gordon, D.4    Finch, S.J.5
  • 19
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R: Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008; 18: 1851-1858.
    • (2008) Genome Res , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 20
    • 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
  • 21
    • 20444495264 scopus 로고    scopus 로고
    • Factors affecting statistical power in the detection of genetic association
    • DOI 10.1172/JCI24756
    • Gordon D, Finch SJ: Factors affecting statistical power in the detection of genetic association. J Clin Invest 2005; 115: 1408-1418. (Pubitemid 40814644)
    • (2005) Journal of Clinical Investigation , vol.115 , Issue.6 , pp. 1408-1418
    • Gordon, D.1    Finch, S.J.2
  • 22
    • 33744481021 scopus 로고    scopus 로고
    • Effects of differential genotyping error rate on the type I error probability of case-control studies
    • DOI 10.1159/000092553
    • Moskvina V, Craddock N, Holmans P, Owen MJ, O'Donovan MC: Effects of differential genotyping error rate on the type I error probability of case-control studies. Hum Hered 2006; 61: 55-64. (Pubitemid 43804599)
    • (2006) Human Heredity , vol.61 , Issue.1 , pp. 55-64
    • Moskvina, V.1    Craddock, N.2    Holmans, P.3    Owen, M.J.4    O'Donovan, M.C.5
  • 23
    • 67650964051 scopus 로고    scopus 로고
    • Increase of rejection rate in case-control studies with differential genotyping error rates
    • Ahn K, Gordon D, Finch SJ: Increase of rejection rate in case-control studies with differential genotyping error rates. Stat Appl Genet Mol Biol 2009; 8: 25.
    • (2009) Stat Appl Genet Mol Biol , vol.8 , pp. 25
    • Ahn, K.1    Gordon, D.2    Finch, S.J.3
  • 24
    • 0942276432 scopus 로고    scopus 로고
    • What SNP Genotyping Errors Are Most Costly for Genetic Association Studies?
    • DOI 10.1002/gepi.10301
    • Kang SJ, Gordon D, Finch SJ: What SNP genotyping errors are most costly for genetic association studies? Genet Epidemiol 2004; 26: 132-141. (Pubitemid 38140486)
    • (2004) Genetic Epidemiology , vol.26 , Issue.2 , pp. 132-141
    • Kang, S.J.1    Gordon, D.2    Finch, S.J.3
  • 25
    • 19944421744 scopus 로고    scopus 로고
    • Quantifying the percent increase in minimum sample size for SNP genotyping errors in genetic model-based association studies
    • DOI 10.1159/000083540
    • Kang SJ, Finch SJ, Haynes C, Gordon D: Quantifying the percent increase in minimum sample size necessary for SNP genotyping errors in genetic model-based association studies. Hum Hered 2004; 58,139-144. (Pubitemid 40754345)
    • (2004) Human Heredity , vol.58 , Issue.3-4 , pp. 139-144
    • Sun, J.K.1    Finch, S.J.2    Haynes, C.3    Gordon, D.4
  • 26
    • 34047274759 scopus 로고    scopus 로고
    • The effects of SNP genotyping errors on the power of the Cochran-Armitage linear trend test for case/control association studies
    • Ahn K, Haynes C, Kim W, St. Fleur R, Gordon D, Finch SJ: The effects of SNP genotyping errors on the power of the Cochran-Armitage linear trend test for case/control association studies. Ann Hum Genet 2007; 71: 249-262.
    • (2007) Ann Hum Genet , vol.71 , pp. 249-262
    • Ahn, K.1    Haynes, C.2    Kim, W.3    St. Fleur, R.4    Gordon, D.5    Finch, S.J.6
  • 27
    • 1842859051 scopus 로고    scopus 로고
    • Power and sample size calculations for case-control genetic association tests when errors are present: Application to single nucleotide polymorphisms
    • DOI 10.1159/000066696
    • Gordon D, Finch SJ, Nothnagel M, Ott J: Power and sample size calculations for casecontrol genetic association tests when errors are present: application to single nucleotide polymorphisms. Hum Hered 2002; 54: 22-33. (Pubitemid 35404246)
    • (2002) Human Heredity , vol.54 , Issue.1 , pp. 22-33
    • Gordon, D.1    Finch, S.J.2    Nothnagel, M.3    Ott, J.4
  • 29
    • 71849116348 scopus 로고    scopus 로고
    • The relationship between imputation error and statistical power in genetic association studies in diverse populations
    • Huang L, Wang C, Rosenberg NA: The relationship between imputation error and statistical power in genetic association studies in diverse populations. Am J Hum Genet 2009; 85: 692-698.
    • (2009) Am J Hum Genet , vol.85 , pp. 692-698
    • Huang, L.1    Wang, C.2    Rosenberg, N.A.3
  • 30
    • 77953951189 scopus 로고    scopus 로고
    • APOE is not associated with Alzheimer disease: A cautionary tale of genotype imputation
    • Beecham GW, Martin ER, Gilbert JR, Haines JL, Pericak-Vance MA: APOE is not associated with Alzheimer disease: a cautionary tale of genotype imputation. Ann Hum Genet 2010; 74: 189-194.
    • (2010) Ann Hum Genet , vol.74 , pp. 189-194
    • Beecham, G.W.1    Martin, E.R.2    Gilbert, J.R.3    Haines, J.L.4    Ma, P.5
  • 33
    • 79959544447 scopus 로고    scopus 로고
    • Confounded by sequencing depth in association studies of rare alleles
    • Garner C: Confounded by sequencing depth in association studies of rare alleles. Genet Epidemiol 2011; 35: 261-268.
    • (2011) Genet Epidemiol , vol.35 , pp. 261-268
    • Garner, C.1
  • 34
    • 84861460466 scopus 로고    scopus 로고
    • R: A language and environment for statistical computing
    • R Development Core Team v2.11.1.
    • R Development Core Team: R: A Language and Environment for Statistical Computing. The R-Project, v2.11.1. www.r-project.org.
    • The R-Project
  • 35
    • 78751490178 scopus 로고    scopus 로고
    • A comparison of approaches to account for uncertainty in analysis of imputed genotypes
    • Zheng J, Li Y, Abecasis GR, Scheet P: A comparison of approaches to account for uncertainty in analysis of imputed genotypes. Genet Epidemiol 2011; 35: 102-110.
    • (2011) Genet Epidemiol , vol.35 , pp. 102-110
    • Zheng, J.1    Li, Y.2    Abecasis, G.R.3    Scheet, P.4
  • 36
    • 33846897439 scopus 로고    scopus 로고
    • Using duplicate genotyped data in genetic analyses: Testing association and estimating error rates
    • Tintle NL, Gordon D, McMahon FJ, Finch SJ: Using duplicate genotyped data in genetic analyses: testing association and estimating error rates. Stat App Genet Mol Biol 2007; 6: 4.
    • (2007) Stat App Genet Mol Biol , vol.6 , pp. 4
    • Tintle, N.L.1    Gordon, D.2    McMahon, F.J.3    Finch, S.J.4
  • 37
    • 67650954439 scopus 로고    scopus 로고
    • Incorporating duplicate genotype data into linear trend tests of genetic association: Methods and cost-effectiveness
    • Borchers B, Brown M, McLellan B, Bekmetjev A, Tintle NL: Incorporating duplicate genotype data into linear trend tests of genetic association: methods and cost-effectiveness. Stat App Genet Mol Biol 2009; 8: 24.
    • (2009) Stat App Genet Mol Biol , vol.8 , pp. 24
    • Borchers, B.1    Brown, M.2    McLellan, B.3    Bekmetjev, A.4    Tintle, N.L.5


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