메뉴 건너뛰기




Volumn 12, Issue 10, 2004, Pages 805-812

Handling missing values in population data: Consequences for maximum likelihood estimation of haplotype frequencies

Author keywords

Bioinformatics; EM algorithm; Haplotype; HLA; Linkage disequilibrium; Missing values

Indexed keywords

HLA A ANTIGEN; HLA B ANTIGEN; HLA DR ANTIGEN;

EID: 6444239772     PISSN: 10184813     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.ejhg.5201233     Document Type: Article
Times cited : (26)

References (32)
  • 1
    • 0035010640 scopus 로고    scopus 로고
    • Automation in genotyping of single nucleotide polymorphisms
    • Gut IG: Automation in genotyping of single nucleotide polymorphisms. Hum Mutat 2001; 17: 475-492.
    • (2001) Hum. Mutat. , vol.17 , pp. 475-492
    • Gut, I.G.1
  • 3
    • 0002317292 scopus 로고
    • Haplotypes and linkage disequilibrium from three-locus phenotypes
    • Piazza A: Haplotypes and linkage disequilibrium from three-locus phenotypes. Histocompat Test Munksgaard 1975; 923-927.
    • (1975) Histocompat. Test Munksgaard , pp. 923-927
    • Piazza, A.1
  • 4
    • 0018079248 scopus 로고
    • Estimation of haplotype frequency and linkage disequilibrium parameter in the HLA system
    • Yasuda N: Estimation of haplotype frequency and linkage disequilibrium parameter in the HLA system. Tissue Antigens 1978; 12: 315-322.
    • (1978) Tissue Antigens , vol.12 , pp. 315-322
    • Yasuda, N.1
  • 5
    • 1542464843 scopus 로고    scopus 로고
    • Nomenclature for factors of the HLA system, update February 2003
    • Marsh SG: Nomenclature for factors of the HLA system, update February 2003. Hum Immunol 2003; 64: 656-657.
    • (2003) Hum. Immunol. , vol.64 , pp. 656-657
    • Marsh, S.G.1
  • 6
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data from incomplete
    • Dempster AP: Maximum likelihood from incomplete data from incomplete. J Roy Statist Soc 1977; 39: 921-927.
    • (1977) J. Roy. Statist. Soc. , vol.39 , pp. 921-927
    • Dempster, A.P.1
  • 7
    • 0029130796 scopus 로고
    • Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population
    • Excoffier L, Slatkin M: Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 1995; 12: 921-927.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 921-927
    • Excoffier, L.1    Slatkin, M.2
  • 9
    • 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: Accuracy of haplotype frequency estimation for biallelic loci, via the expectation-maximization algorithm for unphased diploid genotype data. Am J Hum Genet 2000; 67: 947-959.
    • (2000) Am. J. Hum. Genet. , vol.67 , pp. 947-959
    • Fallin, D.1    Schork, N.J.2
  • 10
    • 0036801154 scopus 로고    scopus 로고
    • The impact of genotyping error on haplotype reconstruction and frequency estimation
    • Kirk KM, Cardon LR: The impact of genotyping error on haplotype reconstruction and frequency estimation. Eur J Hum Genet Oct 2002; 10: 616-622.
    • (2002) Eur. J. Hum. Genet. Oct. , vol.10 , pp. 616-622
    • Kirk, K.M.1    Cardon, L.R.2
  • 11
    • 0036488012 scopus 로고    scopus 로고
    • Effectiveness of computational methods in haplotype prediction
    • Xu CF, Lewis K, Cantone KL et al: Effectiveness of computational methods in haplotype prediction. Hum Genet 2002; 110: 148-156.
    • (2002) Hum. Genet. , vol.110 , pp. 148-156
    • Xu, C.F.1    Lewis, K.2    Cantone, K.L.3
  • 12
    • 0036143316 scopus 로고    scopus 로고
    • Haplotype frequency estimation in patient populations: The effect of departures from Hardy-Weinberg proportions and collapsing over a locus in the HLA region
    • Single RM, Meyer D, Hollenbach JA et al: Haplotype frequency estimation in patient populations: the effect of departures from Hardy-Weinberg proportions and collapsing over a locus in the HLA region. Genet Epidemiol 2002; 22: 186-195.
    • (2002) Genet. Epidemiol. , vol.22 , pp. 186-195
    • Single, R.M.1    Meyer, D.2    Hollenbach, J.A.3
  • 13
    • 0001200144 scopus 로고
    • Testing linkage disequilibrium between a disease gene and marker loci
    • Xie X, Ott J: Testing linkage disequilibrium between a disease gene and marker loci. Am J Hum Genet 1993; 53 (Suppl): 1107.
    • (1993) Am. J. Hum. Genet. , vol.53 , Issue.SUPPL. , pp. 1107
    • Xie, X.1    Ott, J.2
  • 14
    • 6444244094 scopus 로고    scopus 로고
    • ARLEQUIN a program for population genetic analysis
    • [computer program]. Version
    • ARLEQUIN a program for population genetic analysis [computer program]. Version;, 1996-2002.
    • (1996)
  • 15
    • 0036844521 scopus 로고    scopus 로고
    • Partition-Ligation-Expectation-Maximization Algorithm for Haplotype Inference with Single-Nucleotide Polymorphisms
    • Qin ZS, Niu T, Liu JS: Partition-Ligation-Expectation-Maximization Algorithm for Haplotype Inference with Single-Nucleotide Polymorphisms. Am J Hum Genet 2002; 71: 1242-1267.
    • (2002) Am. J. Hum. Genet. , vol.71 , pp. 1242-1267
    • Qin, Z.S.1    Niu, T.2    Liu, J.S.3
  • 16
    • 0029372419 scopus 로고
    • HAPLO: A program using the EM algorithm to estimate the frequencies of multi-site haplotypes
    • Hawley ME, Kidd KK: HAPLO: a program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J Hered 1995; 86: 409-411.
    • (1995) J. Hered. , vol.86 , pp. 409-411
    • Hawley, M.E.1    Kidd, K.K.2
  • 17
    • 0028913523 scopus 로고
    • An E-M algorithm and testing strategy for multiple-locus haplotypes
    • Long JC, Williams RC, Urbanek M: An E-M algorithm and testing strategy for multiple-locus haplotypes. Am J Hum Genet 1995; 56 799-810.
    • (1995) Am. J. Hum. Genet. , vol.56 , pp. 799-810
    • Long, J.C.1    Williams, R.C.2    Urbanek, M.3
  • 18
    • 0001588586 scopus 로고    scopus 로고
    • Haplotype analysis in population based study
    • Mander AP: Haplotype analysis in population based study. Stata J 2001; 1: 58-75.
    • (2001) Stata. J. , vol.1 , pp. 58-75
    • Mander, A.P.1
  • 19
    • 0036338150 scopus 로고    scopus 로고
    • Merlin - Rapid analysis of dense genetic maps using sparse gene flow trees
    • Abecasis GR, Cherny SS, Cookson WO, Cardon LR: Merlin - rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 2002; 30: 97-101.
    • (2002) Nat. Genet. , vol.30 , pp. 97-101
    • Abecasis, G.R.1    Cherny, S.S.2    Cookson, W.O.3    Cardon, L.R.4
  • 20
    • 0033358595 scopus 로고    scopus 로고
    • Transmission/disequilibrium tests for extended marker haplotypes
    • Clayton D, Jones H: Transmission/disequilibrium tests for extended marker haplotypes. Am J Hum Genet 1999; 65: 1161-1169.
    • (1999) Am. J. Hum. Genet. , vol.65 , pp. 1161-1169
    • Clayton, D.1    Jones, H.2
  • 21
    • 0036127943 scopus 로고    scopus 로고
    • Faster haplotype frequency estimation using unrelated subjects
    • Zhao JH, Sham PC: Faster haplotype frequency estimation using unrelated subjects. Hum Hered 2002; 53: 36-41.
    • (2002) Hum. Hered. , vol.53 , pp. 36-41
    • Zhao, J.H.1    Sham, P.C.2
  • 23
    • 0029145920 scopus 로고
    • HLA-A, -B, -DR haplotype frequencies in France - Implications for recruitment of potential bone marrow donors
    • Lonjou C, Clayton J, Cambon-Thomsen A, Raffoux C: HLA-A, -B, -DR haplotype frequencies in France - implications for recruitment of potential bone marrow donors. Transplantation 1995; 60: 375-383.
    • (1995) Transplantation , vol.60 , pp. 375-383
    • Lonjou, C.1    Clayton, J.2    Cambon-Thomsen, A.3    Raffoux, C.4
  • 24
    • 6444241237 scopus 로고    scopus 로고
    • Arlequin Bugs; Available at
    • Excoffier L: Arlequin Bugs; Available at: http://lgb.unige.ch/arlequin/software/2.000/doc/buglist/buglist.html.
    • Excoffier, L.1
  • 25
    • 13344290899 scopus 로고
    • Counting methods in genetical statistics
    • Smith CAB: Counting methods in genetical statistics. Ann Hum Genet 1957; 21: 254-276.
    • (1957) Ann. Hum. Genet. , vol.21 , pp. 254-276
    • Smith, C.A.B.1
  • 26
    • 0002426291 scopus 로고
    • The estimation of gene frequencies in random mating population
    • Cepellini R: The estimation of gene frequencies in random mating population. Ann Hum Genet 1955; 20: 97-115.
    • (1955) Ann. Hum. Genet. , vol.20 , pp. 97-115
    • Cepellini, R.1
  • 27
    • 0025269067 scopus 로고
    • Inference of haplotypes from PCR-amplified samples of diploid populations
    • Clark AG: Inference of haplotypes from PCR-amplified samples of diploid populations. Mol Biol Evol 1990; 7: 111-122.
    • (1990) Mol. Biol. Evol. , vol.7 , pp. 111-122
    • Clark, A.G.1
  • 28
    • 0035071957 scopus 로고    scopus 로고
    • A new statistical method for haplotype reconstruction from population data
    • Stephens M, Smith NJ, Donnelly P: A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 2001; 68: 978-989.
    • (2001) Am. J. Hum. Genet. , vol.68 , pp. 978-989
    • Stephens, M.1    Smith, N.J.2    Donnelly, P.3
  • 29
    • 0036138183 scopus 로고    scopus 로고
    • Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms
    • Niu T, Qin ZS, Xu X, Liu JS: Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms. Am J Hum Genet 2002; 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
  • 30
    • 0029875565 scopus 로고    scopus 로고
    • Validation of large data sets, an essential prerequisite for data analysis: An analytical survey of the Bone Marrow Donors Worldwide
    • Schipper RF, Oudshoorn M, D'Amaro J et al: Validation of large data sets, an essential prerequisite for data analysis: an analytical survey of the Bone Marrow Donors Worldwide. Tissue Antigens 1996; 47: 169-178.
    • (1996) Tissue Antigens , vol.47 , pp. 169-178
    • Schipper, R.F.1    Oudshoorn, M.2    D'Amaro, J.3
  • 31
    • 6444229424 scopus 로고    scopus 로고
    • SNPHAP [computer program]. Clayton DG
    • SNPHAP [computer program]. Clayton DG, http://wwwgene.cimr.cam.ac.uk/clayton/software/.
  • 32
    • 0142179180 scopus 로고    scopus 로고
    • GCHap: Fast MLEs for haplotype frequencies by gene counting
    • Thomas A: GCHap: fast MLEs for haplotype frequencies by gene counting. Bioinformatics 2003; 19: 2002-2003.
    • (2003) Bioinformatics , vol.19 , pp. 2002-2003
    • Thomas, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.