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Volumn 3, Issue 3, 2008, Pages

Haplotype reconstruction error as a classical misclassification problem: Introducing sensitivity and specificity as error measures

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL ERROR; ARTICLE; CORRELATION ANALYSIS; GENE FREQUENCY; GENE LOCUS; GENETIC ANALYSIS; GERMANY; HAPLOTYPE; MATHEMATICAL COMPUTING; POPULATION GENETICS; SENSITIVITY AND SPECIFICITY; SIMULATION; SINGLE NUCLEOTIDE POLYMORPHISM; GENOTYPE; HUMAN;

EID: 46649087971     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0001853     Document Type: Article
Times cited : (8)

References (35)
  • 3
    • 0035058585 scopus 로고    scopus 로고
    • Haplotypes vs single marker linkage disequilibrium tests: What do we gain?
    • Akey J, Jin L, Xiong M (2001) Haplotypes vs single marker linkage disequilibrium tests: what do we gain? Eur J Hum Genet 9: 291-300.
    • (2001) Eur J Hum Genet , vol.9 , pp. 291-300
    • Akey, J.1    Jin, L.2    Xiong, M.3
  • 4
    • 10044254265 scopus 로고    scopus 로고
    • The role of haplotypes in candidate gene studies
    • Clark AG (2004) The role of haplotypes in candidate gene studies. Genet Epidemiol 27: 321-333.
    • (2004) Genet Epidemiol , vol.27 , pp. 321-333
    • Clark, A.G.1
  • 5
    • 0033863391 scopus 로고    scopus 로고
    • SNPing away at complex diseases: Analysis of single-nucleotide polymorphisms around APOE in Alzheimer disease
    • Martin ER, Lai EH, Gilbert JR, Rogala AR, Afshari AJ, et al. (2000) SNPing away at complex diseases: analysis of single-nucleotide polymorphisms around APOE in Alzheimer disease. Am J Hum Genet 67: 383-394.
    • (2000) Am J Hum Genet , vol.67 , pp. 383-394
    • Martin, E.R.1    Lai, E.H.2    Gilbert, J.R.3    Rogala, A.R.4    Afshari, A.J.5
  • 6
    • 0036792816 scopus 로고    scopus 로고
    • On the advantage of haplotype analysis in the presence of multiple disease susceptibility alleles
    • Morris RW, Kaplan NL (2002) On the advantage of haplotype analysis in the presence of multiple disease susceptibility alleles. Genet Epidemiol 23: 221-233.
    • (2002) Genet Epidemiol , vol.23 , pp. 221-233
    • Morris, R.W.1    Kaplan, N.L.2
  • 7
    • 0029130796 scopus 로고
    • Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population
    • Excoffier L, Slatkin M (1995) Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12: 921-927.
    • (1995) Mol Biol Evol , vol.12 , pp. 921-927
    • Excoffier, L.1    Slatkin, M.2
  • 8
    • 0035071957 scopus 로고    scopus 로고
    • A new statistical method for haplotype reconstruction from population data
    • Stephens M, Smith NJ, Donnelly P (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978-989.
    • (2001) Am J Hum Genet , vol.68 , pp. 978-989
    • Stephens, M.1    Smith, N.J.2    Donnelly, P.3
  • 9
    • 0242691208 scopus 로고    scopus 로고
    • A comparison of bayesian methods for haplotype reconstruction from population genotype data
    • Stephens M, Donnelly P (2003) A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73: 1162-1169.
    • (2003) Am J Hum Genet , vol.73 , pp. 1162-1169
    • Stephens, M.1    Donnelly, P.2
  • 10
    • 0036138183 scopus 로고    scopus 로고
    • Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms
    • Niu T, Qin ZS, Xu X, Liu JS (2002) Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet 70: 157-169.
    • (2002) Am J Hum Genet , vol.70 , pp. 157-169
    • Niu, T.1    Qin, Z.S.2    Xu, X.3    Liu, J.S.4
  • 11
    • 25444442089 scopus 로고    scopus 로고
    • Comparison of the accuracy of methods of computational haplotype inference using a large empirical dataset
    • Adkins RM (2004) Comparison of the accuracy of methods of computational haplotype inference using a large empirical dataset. BMC Genet 5: 22.
    • (2004) BMC Genet , vol.5 , pp. 22
    • Adkins, R.M.1
  • 12
    • 18444418259 scopus 로고    scopus 로고
    • Comparison of haplotype inference methods using genotypic data from unrelated individuals
    • Xu H, Wu X, Spitz MR, Shete S (2004) Comparison of haplotype inference methods using genotypic data from unrelated individuals. Hum Hered 58: 63-68.
    • (2004) Hum Hered , vol.58 , pp. 63-68
    • Xu, H.1    Wu, X.2    Spitz, M.R.3    Shete, S.4
  • 13
    • 0033794938 scopus 로고    scopus 로고
    • Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data
    • Fallin D, Schork NJ (2000) Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. Am J Hum Genet 67: 947-959.
    • (2000) Am J Hum Genet , vol.67 , pp. 947-959
    • Fallin, D.1    Schork, N.J.2
  • 15
    • 0027197252 scopus 로고
    • Exposure measurement error: Influence on exposure-disease relationships and methods of correction
    • Thomas D, Stram D, Dwyer J (1993) Exposure measurement error: Influence on exposure-disease relationships and methods of correction. Annu Rev Public Health 14: 69-93.
    • (1993) Annu Rev Public Health , vol.14 , pp. 69-93
    • Thomas, D.1    Stram, D.2    Dwyer, J.3
  • 16
    • 0036284203 scopus 로고    scopus 로고
    • Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals
    • Zaykin DV, Westfall PH, Young SS, Karnoub MA, Wagner MJ, et al. (2002) Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum Hered 53: 79-91.
    • (2002) Hum Hered , vol.53 , pp. 79-91
    • Zaykin, D.V.1    Westfall, P.H.2    Young, S.S.3    Karnoub, M.A.4    Wagner, M.J.5
  • 17
    • 0344410771 scopus 로고    scopus 로고
    • Inference on haplotype effects in case-control studies using unphased genotype data
    • Epstein MP, Satten GA (2003) Inference on haplotype effects in case-control studies using unphased genotype data. Am J Hum Genet 73: 1316-1329.
    • (2003) Am J Hum Genet , vol.73 , pp. 1316-1329
    • Epstein, M.P.1    Satten, G.A.2
  • 18
    • 23944527309 scopus 로고    scopus 로고
    • Analysis of case-control studies of genetic and environmental factors with missing genetic information and haplotype-phase ambiguity
    • Spinka C, Carroll RJ, Chatterjee N (2005) Analysis of case-control studies of genetic and environmental factors with missing genetic information and haplotype-phase ambiguity. Genet Epidemiol 29: 108-127.
    • (2005) Genet Epidemiol , vol.29 , pp. 108-127
    • Spinka, C.1    Carroll, R.J.2    Chatterjee, N.3
  • 19
    • 0036155283 scopus 로고    scopus 로고
    • Score tests for association between traits and haplotypes when linkage phase is ambiguous
    • Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland CA (2002) Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 70: 425-434.
    • (2002) Am J Hum Genet , vol.70 , pp. 425-434
    • Schaid, D.J.1    Rowland, C.M.2    Tines, D.E.3    Jacobson, R.M.4    Poland, C.A.5
  • 20
    • 0041672374 scopus 로고    scopus 로고
    • Estimation and tests of haplotype-environment interaction when linkage phase is ambiguous
    • Lake SL, Lyon H, Tantisira K, Silverman EK, Weiss ST, et al. (2003) Estimation and tests of haplotype-environment interaction when linkage phase is ambiguous. Hum Hered 55: 56-65.
    • (2003) Hum Hered , vol.55 , pp. 56-65
    • Lake, S.L.1    Lyon, H.2    Tantisira, K.3    Silverman, E.K.4    Weiss, S.T.5
  • 21
    • 33645517140 scopus 로고    scopus 로고
    • Likelihood-based inference on haplotype effects in genetic association studies
    • Lin DY, Zeng D (2006) Likelihood-based inference on haplotype effects in genetic association studies. J Am Stat Assoc 101: 89-104.
    • (2006) J Am Stat Assoc , vol.101 , pp. 89-104
    • Lin, D.Y.1    Zeng, D.2
  • 23
    • 33645058874 scopus 로고    scopus 로고
    • A General Method for Dealing with Misclassification in Regression: The Misclassification SIMEX
    • Kuchenhoff H, Mwalili SM, Lesaffire E (2006) A General Method for Dealing with Misclassification in Regression: The Misclassification SIMEX. Biometrics 62: 85-96.
    • (2006) Biometrics , vol.62 , pp. 85-96
    • Kuchenhoff, H.1    Mwalili, S.M.2    Lesaffire, E.3
  • 24
    • 1842539516 scopus 로고    scopus 로고
    • A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequelibrium with each other
    • Nyholt DR (2004) A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequelibrium with each other. Am J Hum Genet 74: 765-769.
    • (2004) Am J Hum Genet , vol.74 , pp. 765-769
    • Nyholt, D.R.1
  • 25
    • 0142156650 scopus 로고    scopus 로고
    • Modeling and E-M estimation of haplotype-specific relative risks from genotype data for a case-control study of unrelated individuals
    • Scram DO, Leigh PC, Bretsky P, Freedman M, Hirschhorn JN, et al. (2003) Modeling and E-M estimation of haplotype-specific relative risks from genotype data for a case-control study of unrelated individuals. Hum Hered 55: 179-190.
    • (2003) Hum Hered , vol.55 , pp. 179-190
    • Scram, D.O.1    Leigh, P.C.2    Bretsky, P.3    Freedman, M.4    Hirschhorn, J.N.5
  • 26
    • 23844472247 scopus 로고    scopus 로고
    • KORA-gen resource for population genetics, controls and a broad spectrum of disease phenotypes
    • Wichmann HE, Gieger C, Illig T (2005) KORA-gen resource for population genetics, controls and a broad spectrum of disease phenotypes. Gesundheitswesen 67 Suppl 1: S26-S30.
    • (2005) Gesundheitswesen , vol.67 , Issue.SUPPL. 1
    • Wichmann, H.E.1    Gieger, C.2    Illig, T.3
  • 27
    • 10744226206 scopus 로고    scopus 로고
    • The endotoxin receptor TLR4 polymorphism is not associated with diabetes or components of the metabolic syndrome
    • Illig T, Bongardt F, Schopfer A, Holle R, Muller S, et al. (2003) The endotoxin receptor TLR4 polymorphism is not associated with diabetes or components of the metabolic syndrome. Diabetes 52: 2861-2864.
    • (2003) Diabetes , vol.52 , pp. 2861-2864
    • Illig, T.1    Bongardt, F.2    Schopfer, A.3    Holle, R.4    Muller, S.5
  • 28
    • 6344261708 scopus 로고    scopus 로고
    • Significant association of the interleukin-6 gene polymorphisms C-174G and A-598G with type 2 diabetes
    • Illig T, Bongardt F, Schopfer A, Muller-Scholze S, Rathmann W, et al. (2004) Significant association of the interleukin-6 gene polymorphisms C-174G and A-598G with type 2 diabetes. J Clin Endocrinol Metab 89: 5053-5058.
    • (2004) J Clin Endocrinol Metab , vol.89 , pp. 5053-5058
    • Illig, T.1    Bongardt, F.2    Schopfer, A.3    Muller-Scholze, S.4    Rathmann, W.5
  • 29
    • 0029150074 scopus 로고
    • A comparison of linkage disequilibrium measures for fine-scale mapping
    • Devlin B, Risch N (1995) A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29: 311-322.
    • (1995) Genomics , vol.29 , pp. 311-322
    • Devlin, B.1    Risch, N.2
  • 30
    • 0033045222 scopus 로고    scopus 로고
    • Matrix methods for estimating odds ratios with misclassified exposure data: Extensions and comparisons
    • Morrissey MJ, Spiegelman D (1999) Matrix methods for estimating odds ratios with misclassified exposure data: extensions and comparisons. Biometrics 55: 338-344.
    • (1999) Biometrics , vol.55 , pp. 338-344
    • Morrissey, M.J.1    Spiegelman, D.2
  • 31
    • 33748087480 scopus 로고    scopus 로고
    • Are molecular haplotypes worth the time and expense? A cost-effective method for applying molecular haplotypes
    • Levenstien MA, Ott J, Gordon D (2006) Are molecular haplotypes worth the time and expense? A cost-effective method for applying molecular haplotypes. PLoS Genet 2: e127.
    • (2006) PLoS Genet , vol.2
    • Levenstien, M.A.1    Ott, J.2    Gordon, D.3
  • 32
    • 0038406155 scopus 로고    scopus 로고
    • A method for the assessment of disease associations with single-nudeotide polymorphism haplotypes and environmental variables in case-control studies
    • Zhao LP, U SS, Khalid N (2003) A method for the assessment of disease associations with single-nudeotide polymorphism haplotypes and environmental variables in case-control studies. Am J Hum Genet 72: 1231-1250.
    • (2003) Am J Hum Genet , vol.72 , pp. 1231-1250
    • Zhao1    LP, U.S.2    Khalid, N.3
  • 33
    • 33644751829 scopus 로고    scopus 로고
    • Genetic architecture of the APMI gene and its influence on adiponectin plasma levels and parameters ofthe metabolic syndrome in 1,727 healthy caucasians
    • Heid IM, Wagner SA, Gohlke H, Iglseder B, Mueller JC, et al. (2006) Genetic architecture of the APMI gene and its influence on adiponectin plasma levels and parameters ofthe metabolic syndrome in 1,727 healthy caucasians. Diabetes 55: 375-384.
    • (2006) Diabetes , vol.55 , pp. 375-384
    • Heid, I.M.1    Wagner, S.A.2    Gohlke, H.3    Iglseder, B.4    Mueller, J.C.5
  • 34
    • 15544366469 scopus 로고    scopus 로고
    • Accounting for haplotype uncertainty in matched association studies: A comparison of simple and flexible techniques
    • Kraft P, Cox DG, Paynter RA, Hunter D, De Vivo I (2005) Accounting for haplotype uncertainty in matched association studies: a comparison of simple and flexible techniques. Genet Epidemiol 28: 261-272.
    • (2005) Genet Epidemiol , vol.28 , pp. 261-272
    • Kraft, P.1    Cox, D.G.2    Paynter, R.A.3    Hunter, D.4    De Vivo, I.5
  • 35
    • 10044294770 scopus 로고    scopus 로고
    • Evaluating associations of haplotypes with traits
    • Schaid DJ (2004) Evaluating associations of haplotypes with traits. Genet Epidemiol 27: 348-364.
    • (2004) Genet Epidemiol , vol.27 , pp. 348-364
    • Schaid, D.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.