메뉴 건너뛰기




Volumn 17, Issue 1, 2007, Pages 96-107

Intra- and interpopulation genotype reconstruction from tagging SNPs

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; FEASIBILITY STUDY; GENE MAPPING; GENE TRANSFER; GENETIC ALGORITHM; GENETIC DATABASE; GENETIC VARIABILITY; GENOME; GENOTYPE; HAPLOTYPE; HUMAN; PRIORITY JOURNAL; PROMOTER REGION; QUANTITATIVE ANALYSIS; RACE DIFFERENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 33845995419     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.5741407     Document Type: Article
Times cited : (35)

References (59)
  • 1
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • Alter, O., Brown, P.O., and Botstein, D. 2000. Singular value decomposition for genome-wide expression data processing and modeling. Proc. Natl. Acad. Sci. 97: 10101-10106.
    • (2000) Proc. Natl. Acad. Sci , vol.97 , pp. 10101-10106
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 2
    • 13444269543 scopus 로고    scopus 로고
    • Haploview: Analysis and visualization of LD and haplotype maps
    • Barrett, J.C., Fry, B., Maller, J., and Daly, M.J. 2005. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics 21: 263-265.
    • (2005) Bioinformatics , vol.21 , pp. 263-265
    • Barrett, J.C.1    Fry, B.2    Maller, J.3    Daly, M.J.4
  • 3
    • 0346373654 scopus 로고    scopus 로고
    • Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium
    • Carlson, C.S., Eberle, M.A., Rieder, M.J., Yi, Q., Kruglyak, L., and Nickerson, D.A. 2004. Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am. J. Hum. Genet. 74: 106-120.
    • (2004) Am. J. Hum. Genet , vol.74 , pp. 106-120
    • Carlson, C.S.1    Eberle, M.A.2    Rieder, M.J.3    Yi, Q.4    Kruglyak, L.5    Nickerson, D.A.6
  • 4
    • 84984932946 scopus 로고    scopus 로고
    • Population genetics-Making sense out of sequence
    • Chakravarti, A. 1999. Population genetics-Making sense out of sequence. Nat. Genet. 21: 56-60.
    • (1999) Nat. Genet , vol.21 , pp. 56-60
    • Chakravarti, A.1
  • 5
    • 0344033602 scopus 로고    scopus 로고
    • Detecting disease associations due to linkage disequilibrium using haplotype tags: A class of tests and the determinants of statistical power
    • Chapman, J.M., Cooper, J.D., Todd, J.A., and Clayton, D.G. 2003. Detecting disease associations due to linkage disequilibrium using haplotype tags: A class of tests and the determinants of statistical power. Hum. Hered. 56: 18-31.
    • (2003) Hum. Hered , vol.56 , pp. 18-31
    • Chapman, J.M.1    Cooper, J.D.2    Todd, J.A.3    Clayton, D.G.4
  • 6
    • 0025269067 scopus 로고
    • Inference of haplotypes from PCR-amplified samples of diploid populations
    • Clark, A.G. 1990. Inference of haplotypes from PCR-amplified samples of diploid populations. Mol. Biol. Evol. 7: 111-122.
    • (1990) Mol. Biol. Evol , vol.7 , pp. 111-122
    • Clark, A.G.1
  • 9
    • 39049193219 scopus 로고    scopus 로고
    • Transferability of tag SNPs to capture common genetic variation in DNA repair genes across multiple populations
    • De Bakker, P.I., Graham, R.R., Altshuler, D., Henderson, B.E., and Haiman, C.A. 2006. Transferability of tag SNPs to capture common genetic variation in DNA repair genes across multiple populations. Pac. Symp. Biocomput. 478-486.
    • (2006) Pac. Symp. Biocomput , pp. 478-486
    • De Bakker, P.I.1    Graham, R.R.2    Altshuler, D.3    Henderson, B.E.4    Haiman, C.A.5
  • 10
    • 10344253282 scopus 로고    scopus 로고
    • The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection
    • Ding, K., Zhou, K., Zhang, J., Knight, J., Zhang, X., and Shen, Y. 2005. The effect of haplotype-block definitions on inference of haplotype-block structure and htSNPs selection. Mol. Biol. Evol. 22: 148-159.
    • (2005) Mol. Biol. Evol , vol.22 , pp. 148-159
    • Ding, K.1    Zhou, K.2    Zhang, J.3    Knight, J.4    Zhang, X.5    Shen, Y.6
  • 11
    • 29244453931 scopus 로고    scopus 로고
    • On the Nyström method for approximating a Gram matrix for improved kernel-based learning
    • Drineas, P. and Mahoney, M.W. 2005. On the Nyström method for approximating a Gram matrix for improved kernel-based learning. J. Mach. Learn. Res. 6: 2153-2175.
    • (2005) J. Mach. Learn. Res , vol.6 , pp. 2153-2175
    • Drineas, P.1    Mahoney, M.W.2
  • 12
    • 33751113879 scopus 로고    scopus 로고
    • A randomized algorithm for a tensor-based generalization of the SVD
    • Elsevier
    • Drineas, P. and Mahoney, M. 2007. A randomized algorithm for a tensor-based generalization of the SVD. In Linear algebra and its applications. 420: 553-571. Elsevier.
    • (2007) Linear algebra and its applications , vol.420 , pp. 553-571
    • Drineas, P.1    Mahoney, M.2
  • 13
    • 33751115359 scopus 로고    scopus 로고
    • Fast Monte Carlo algorithms for matrices I: Approximating matrix multiplication
    • Drineas, P., Kannan, R., and Mahoney, M.W. 2006a. Fast Monte Carlo algorithms for matrices I: Approximating matrix multiplication. SIAM J. Comput. 36: 132-157.
    • (2006) SIAM J. Comput , vol.36 , pp. 132-157
    • Drineas, P.1    Kannan, R.2    Mahoney, M.W.3
  • 14
    • 33751075906 scopus 로고    scopus 로고
    • Fast Monte Carlo algorithms for matrices II: Computing a low-rank approximation to a matrix
    • Drineas, P., Kannan, R., and Mahoney, M.W. 2006b. Fast Monte Carlo algorithms for matrices II: Computing a low-rank approximation to a matrix. SIAM J. Comput. 36: 158-183.
    • (2006) SIAM J. Comput , vol.36 , pp. 158-183
    • Drineas, P.1    Kannan, R.2    Mahoney, M.W.3
  • 15
    • 33751097630 scopus 로고    scopus 로고
    • Fast Monte Carlo algorithms for matrices III: Computing a compressed approximate matrix decomposition
    • Drineas, P., Kannan, R., and Mahoney, M.W. 2006c. Fast Monte Carlo algorithms for matrices III: Computing a compressed approximate matrix decomposition. SIAM J. Comput. 36: 184-206.
    • (2006) SIAM J. Comput , vol.36 , pp. 184-206
    • Drineas, P.1    Kannan, R.2    Mahoney, M.W.3
  • 16
    • 10044221854 scopus 로고    scopus 로고
    • Genotype prediction using a dense map of SNPs
    • Evans, D.M., Cardon, L.R., and Morris, A.P. 2004. Genotype prediction using a dense map of SNPs. Genet. Epidemiol. 27: 375-384.
    • (2004) Genet. Epidemiol , vol.27 , pp. 375-384
    • Evans, D.M.1    Cardon, L.R.2    Morris, A.P.3
  • 17
    • 0029130796 scopus 로고
    • Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population
    • Excoffier, L. and 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
  • 18
    • 20444476106 scopus 로고    scopus 로고
    • Fast Monte-Carlo algorithms for finding low-rank approximations
    • Frieze, A., Kannan, R., and Vempala, S. 2004. Fast Monte-Carlo algorithms for finding low-rank approximations. J. ACM 51: 1025-1041.
    • (2004) J. ACM , vol.51 , pp. 1025-1041
    • Frieze, A.1    Kannan, R.2    Vempala, S.3
  • 20
    • 0035943090 scopus 로고    scopus 로고
    • Population genomics: Linkage disequilibrium holds the key
    • Goldstein, D.B. and Weale, M.E. 2001. Population genomics: Linkage disequilibrium holds the key. Curr. Biol. 11: R576-R579.
    • (2001) Curr. Biol , vol.11
    • Goldstein, D.B.1    Weale, M.E.2
  • 24
    • 19944420428 scopus 로고    scopus 로고
    • Optimal selection of SNP markers for disease association studies
    • Halldorsson, B.V., Istrail, S., and DeLaVega, F.M. 2004b. Optimal selection of SNP markers for disease association studies. Hum. Hered. 58: 190-202.
    • (2004) Hum. Hered , vol.58 , pp. 190-202
    • Halldorsson, B.V.1    Istrail, S.2    DeLaVega, F.M.3
  • 25
    • 0029372419 scopus 로고
    • HAPLO: A program using the EM algorithm to estimate the frequencies of multi-site haplotypes
    • Hawley, M.E. and Kidd, K.K. 1995. HAPLO: A program using the EM algorithm to estimate the frequencies of multi-site haplotypes. J. Hered. 86: 409-411.
    • (1995) J. Hered , vol.86 , pp. 409-411
    • Hawley, M.E.1    Kidd, K.K.2
  • 27
    • 0347362608 scopus 로고    scopus 로고
    • Principal component analysis for selection of optimal SNP-sets that capture intragenic genetic variation
    • Horne, B.D. and Camp, N.J. 2004. Principal component analysis for selection of optimal SNP-sets that capture intragenic genetic variation. Genet. Epidemiol. 26: 11-21.
    • (2004) Genet. Epidemiol , vol.26 , pp. 11-21
    • Horne, B.D.1    Camp, N.J.2
  • 28
    • 79959503826 scopus 로고    scopus 로고
    • The International HapMap Project
    • The International HapMap Consortium
    • The International HapMap Consortium. 2003. The International HapMap Project. Nature 426: 789-796.
    • (2003) Nature , vol.426 , pp. 789-796
  • 29
    • 79959524146 scopus 로고    scopus 로고
    • A haplotype map of the human genome
    • The International HapMap Consortium
    • The International HapMap Consortium. 2005. A haplotype map of the human genome. Nature 437: 1299-1320.
    • (2005) Nature , vol.437 , pp. 1299-1320
  • 30
    • 0034795550 scopus 로고    scopus 로고
    • Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex
    • Jeffreys, A.J., Kauppi, L., and Neumann, R. 2001. Intensely punctate meiotic recombination in the class II region of the major histocompatibility complex. Nat. Genet. 29: 217-222.
    • (2001) Nat. Genet , vol.29 , pp. 217-222
    • Jeffreys, A.J.1    Kauppi, L.2    Neumann, R.3
  • 32
    • 0037311771 scopus 로고    scopus 로고
    • Efficient selective screening of haplotype tag SNPs
    • Ke, X. and Cardon, L.R. 2003. Efficient selective screening of haplotype tag SNPs. Bioinformatics 19: 287-288.
    • (2003) Bioinformatics , vol.19 , pp. 287-288
    • Ke, X.1    Cardon, L.R.2
  • 34
    • 0029805706 scopus 로고    scopus 로고
    • The new genomics: Global views of biology
    • Lander, E.S. 1996. The new genomics: Global views of biology. Science 274: 536-539.
    • (1996) Science , vol.274 , pp. 536-539
    • Lander, E.S.1
  • 35
    • 6344233909 scopus 로고    scopus 로고
    • Finding haplotype tagging SNPs by use of principal components analysis
    • Lin, Z. and Altman, R.B. 2004. Finding haplotype tagging SNPs by use of principal components analysis. Am. J. Hum. Genet. 75: 850-861.
    • (2004) Am. J. Hum. Genet , vol.75 , pp. 850-861
    • Lin, Z.1    Altman, R.B.2
  • 36
    • 39049183755 scopus 로고    scopus 로고
    • The whole genome tagSNP selection and transferability among HapMap populations
    • Magi, R., Kaplinski, L., and Remm, M. 2006. The whole genome tagSNP selection and transferability among HapMap populations. Pac. Symp. Biocomput. 535-543.
    • (2006) Pac. Symp. Biocomput , pp. 535-543
    • Magi, R.1    Kaplinski, L.2    Remm, M.3
  • 37
    • 0038728035 scopus 로고    scopus 로고
    • Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes
    • Meng, Z., Zaykin, D.V., Xu, C.F., Wagner, M., and Ehm, M.G. 2003. Selection of genetic markers for association analyses, using linkage disequilibrium and haplotypes. Am. J. Hum. Genet. 73: 115-130.
    • (2003) Am. J. Hum. Genet , vol.73 , pp. 115-130
    • Meng, Z.1    Zaykin, D.V.2    Xu, C.F.3    Wagner, M.4    Ehm, M.G.5
  • 40
    • 0036138183 scopus 로고    scopus 로고
    • Bayesian haplotype inference for multiple linked single-nucleotide polymorphisms
    • Niu, T., Qin, Z.S., Xu, X., and Liu, J.S. 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
  • 42
    • 0036799545 scopus 로고    scopus 로고
    • The allelic architecture of human disease genes: Common disease-common variant or not?
    • Pritchard, J.K. and Cox, N.J. 2002. The allelic architecture of human disease genes: Common disease-common variant or not? Hum. Mol. Genet. 11: 2417-2423.
    • (2002) Hum. Mol. Genet , vol.11 , pp. 2417-2423
    • Pritchard, J.K.1    Cox, N.J.2
  • 47
    • 0035071957 scopus 로고    scopus 로고
    • A new statistical method for haplotype reconstruction from population data
    • Stephens, M., Smith, N.J., and 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
  • 48
    • 0043175289 scopus 로고    scopus 로고
    • Choosing haplotype-tagging SNPs based on unphased genotype data using a preliminary sample of unrelated subjects with an example from the multiethnic cohort study
    • Stram, D.O., Haiman, C.A., Hirschhorn, J.N., Altshuler, D., Henderson, I.N., Kolonel, B.E., and Pike, M.C. 2003. Choosing haplotype-tagging SNPs based on unphased genotype data using a preliminary sample of unrelated subjects with an example from the multiethnic cohort study. Hum. Hered. 55: 27-36.
    • (2003) Hum. Hered , vol.55 , pp. 27-36
    • Stram, D.O.1    Haiman, C.A.2    Hirschhorn, J.N.3    Altshuler, D.4    Henderson, I.N.5    Kolonel, B.E.6    Pike, M.C.7
  • 49
    • 0036574859 scopus 로고    scopus 로고
    • Haplotype diversity and the block structure of linkage disequilibrium
    • Stumpf, M.P. 2002. Haplotype diversity and the block structure of linkage disequilibrium. Trends Genet. 18: 226-228.
    • (2002) Trends Genet , vol.18 , pp. 226-228
    • Stumpf, M.P.1
  • 50
    • 33645775067 scopus 로고    scopus 로고
    • An utter refutation of the "Fundamental Theorem of the HapMap
    • Terwilliger, J.D. and Hiekkalinna, T. 2006. An utter refutation of the "Fundamental Theorem of the HapMap". Eur. J. Hum. Genet. 14: 426-437.
    • (2006) Eur. J. Hum. Genet , vol.14 , pp. 426-437
    • Terwilliger, J.D.1    Hiekkalinna, T.2
  • 51
    • 0042387813 scopus 로고    scopus 로고
    • Assessing the performance of the haplotype block model of linkage disequilibrium
    • Wall, J.D. and Pritchard, J.K. 2003a. Assessing the performance of the haplotype block model of linkage disequilibrium. Am. J. Hum. Genet. 73: 502-515.
    • (2003) Am. J. Hum. Genet , vol.73 , pp. 502-515
    • Wall, J.D.1    Pritchard, J.K.2
  • 52
    • 0043267974 scopus 로고    scopus 로고
    • Haplotype blocks and linkage disequilibrium in the human genome
    • Wall, J.D. and Pritchard, J.K. 2003b. Haplotype blocks and linkage disequilibrium in the human genome. Nat. Rev. Genet. 4: 587-597.
    • (2003) Nat. Rev. Genet , vol.4 , pp. 587-597
    • Wall, J.D.1    Pritchard, J.K.2
  • 53
    • 0036844238 scopus 로고    scopus 로고
    • Distribution of recombination crossovers and the origin of haplotype blocks: The interplay of population history, recombination, and mutation
    • Wang, N., Akey, J.M., Zhang, K., Chakraborty, R., and Jin, L. 2002. Distribution of recombination crossovers and the origin of haplotype blocks: The interplay of population history, recombination, and mutation. Am. J. Hum. Genet. 71: 1227-1234.
    • (2002) Am. J. Hum. Genet , vol.71 , pp. 1227-1234
    • Wang, N.1    Akey, J.M.2    Zhang, K.3    Chakraborty, R.4    Jin, L.5
  • 54
    • 0042387804 scopus 로고    scopus 로고
    • Selection and evaluation of tagging SNPs in the neuronal-sodium-channel gene SCN1A: Implications for linkage-disequilibrium gene mapping
    • Weale, M.E., Depondt, C., Macdonald, S.J., Smith, A., Lai, P.S., Shorvon, S.D., Wood, N.W., and Goldstein, D.B. 2003. Selection and evaluation of tagging SNPs in the neuronal-sodium-channel gene SCN1A: Implications for linkage-disequilibrium gene mapping. Am. J. Hum. Genet. 73: 551-565.
    • (2003) Am. J. Hum. Genet , vol.73 , pp. 551-565
    • Weale, M.E.1    Depondt, C.2    Macdonald, S.J.3    Smith, A.4    Lai, P.S.5    Shorvon, S.D.6    Wood, N.W.7    Goldstein, D.B.8
  • 56
    • 25444492613 scopus 로고    scopus 로고
    • Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition
    • Zeggini, E., Barton, A., Eyre, S., Ward, D., Ollier, W., Worthington, J., and John, S. 2005. Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition. BMC Genet. 6: 21.
    • (2005) BMC Genet , vol.6 , pp. 21
    • Zeggini, E.1    Barton, A.2    Eyre, S.3    Ward, D.4    Ollier, W.5    Worthington, J.6    John, S.7
  • 57
    • 0037188541 scopus 로고    scopus 로고
    • A dynamic programming algorithm for haplotype block partitioning
    • Zhang, K., Deng, M., Chen, T., Waterman, M.S., and Sun, F. 2002. A dynamic programming algorithm for haplotype block partitioning. Proc. Natl. Acad. Sci. 99: 7335-7339.
    • (2002) Proc. Natl. Acad. Sci , vol.99 , pp. 7335-7339
    • Zhang, K.1    Deng, M.2    Chen, T.3    Waterman, M.S.4    Sun, F.5
  • 58
    • 2442658957 scopus 로고    scopus 로고
    • Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies
    • Zhang, K., Qin, Z.S., Liu, J.S., Chen, T., Waterman, M.S., and Sun, F. 2004. Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res. 14: 908-916.
    • (2004) Genome Res , vol.14 , pp. 908-916
    • Zhang, K.1    Qin, Z.S.2    Liu, J.S.3    Chen, T.4    Waterman, M.S.5    Sun, F.6
  • 59
    • 12744253764 scopus 로고    scopus 로고
    • HapBlock: Haplo-type block partitioning and tag SNP selection software using a set of dynamic programming algorithms
    • Zhang, K., Qin, Z., Chen, T., Liu, J.S., Waterman, M.S., and Sun, F. 2005. HapBlock: Haplo-type block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics 21: 131-134.
    • (2005) Bioinformatics , vol.21 , pp. 131-134
    • Zhang, K.1    Qin, Z.2    Chen, T.3    Liu, J.S.4    Waterman, M.S.5    Sun, F.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.