메뉴 건너뛰기




Volumn 186, Issue 1, 2010, Pages 321-338

A principled approach to deriving approximate conditional sampling distributions in population genetics models with recombination

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; FINITE ELEMENT ANALYSIS; GENE LOCUS; GENE NUMBER; GENETIC MODEL; HUMAN; MATHEMATICAL ANALYSIS; POPULATION GENETICS; PRIORITY JOURNAL; SIMULATION;

EID: 78751665863     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.110.117986     Document Type: Article
Times cited : (25)

References (38)
  • 1
    • 61449135985 scopus 로고    scopus 로고
    • Fast and flexible simulation of DNA sequence data
    • CHEN, G. K., P. MARJORAM and J. D. WALL, 2009 Fast and flexible simulation of DNA sequence data. Genome Res. 19: 136-142.
    • (2009) Genome Res. , vol.19 , pp. 136-142
    • Chen, G.K.1    Marjoram, P.2    Wall, J.D.3
  • 2
    • 3042700117 scopus 로고    scopus 로고
    • Evidence for substantial fine-scale variation in recombination rates across the human genome
    • CRAWFORD, D. C., T. BHANGALE, N. LI, G. HELLENTHAL, M. J. RIEDER et al., 2004 Evidence for substantial fine-scale variation in recombination rates across the human genome. Nat. Genet. 36: 700-706.
    • (2004) Nat. Genet. , vol.36 , pp. 700-706
    • Crawford, D.C.1    Bhangale, T.2    Li, N.3    Hellenthal, G.4    Rieder, M.J.5
  • 3
    • 65849353922 scopus 로고    scopus 로고
    • An approximate likelihood for genetic data under a model with recombination and population splitting
    • DAVISON, D., J. K. PRITCHARD and G. COOP, 2009 An approximate likelihood for genetic data under a model with recombination and population splitting. Theor. Popul. Biol. 75(4): 331-345.
    • (2009) Theor. Popul. Biol. , vol.75 , Issue.4 , pp. 331-345
    • Davison, D.1    Pritchard, J.K.2    Coop, G.3
  • 4
    • 3142712394 scopus 로고    scopus 로고
    • Importance sampling on coalescent histories I
    • DE IORIO, M., and R. C. GRIFFITHS, 2004a Importance sampling on coalescent histories I. Adv. Appl. Probab. 36: 417-433.
    • (2004) Adv. Appl. Probab. , vol.36 , pp. 417-433
    • De Iorio, M.1    Griffiths, R.C.2
  • 5
    • 3142769862 scopus 로고    scopus 로고
    • Importance sampling on coalescent histories II
    • DE IORIO, M., and R. C. GRIFFITHS, 2004b Importance sampling on coalescent histories II. Adv. Appl. Probab. 36: 434-454.
    • (2004) Adv. Appl. Probab. , vol.36 , pp. 434-454
    • De Iorio, M.1    Griffiths, R.C.2
  • 6
    • 0035675042 scopus 로고    scopus 로고
    • Estimating recombination rates from population genetic data
    • FEARNHEAD, P., and P. DONNELLY, 2001 Estimating recombination rates from population genetic data. Genetics 159: 1299-1318. (Pubitemid 34033469)
    • (2001) Genetics , vol.159 , Issue.3 , pp. 1299-1318
    • Fearnhead, P.1    Donnelly, P.2
  • 7
    • 0036433716 scopus 로고    scopus 로고
    • Approximate likelihood methods for estimating local recombination rates
    • FEARNHEAD, P., and P. DONNELLY, 2002 Approximate likelihood methods for estimating local recombination rates. J. R. Stat. Soc. B 64: 657-680.
    • (2002) J. R. Stat. Soc. B , vol.64 , pp. 657-680
    • Fearnhead, P.1    Donnelly, P.2
  • 8
    • 27244445943 scopus 로고    scopus 로고
    • A novel method with improved power to detect recombination hotspots from polymorphism data reveals multiple hotspots in human genes
    • FEARNHEAD, P., and N. G. C. SMITH, 2005 A novel method with improved power to detect recombination hotspots from polymorphism data reveals multiple hotspots in human genes. Am. J. Hum. Genet. 77: 781-794.
    • (2005) Am. J. Hum. Genet. , vol.77 , pp. 781-794
    • Fearnhead, P.1    Smith, N.G.C.2
  • 9
    • 35549000476 scopus 로고    scopus 로고
    • Estimating meiotic gene conversion rates from population genetic data
    • GAY, J. C., S. MYERS and G. MCVEAN, 2007 Estimating meiotic gene conversion rates from population genetic data. Genetics 177: 881-894.
    • (2007) Genetics , vol.177 , pp. 881-894
    • Gay, J.C.1    Myers, S.2    Mcvean, G.3
  • 10
    • 0000579476 scopus 로고
    • Neutral two-locus multiple allele models with recombination
    • GRIFFITHS, R. C., 1981 Neutral two-locus multiple allele models with recombination. Theor. Popul. Biol. 19: 169-186.
    • (1981) Theor. Popul. Biol. , vol.19 , pp. 169-186
    • Griffiths, R.C.1
  • 11
    • 0030498194 scopus 로고    scopus 로고
    • Ancestral inference from samples of DNA sequences with recombination
    • GRIFFITHS, R. C., and P. MARJORAM, 1996 Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol. 3(4): 479-502.
    • (1996) J. Comput. Biol. , vol.3 , Issue.4 , pp. 479-502
    • Griffiths, R.C.1    Marjoram, P.2
  • 12
    • 49349097737 scopus 로고    scopus 로고
    • Importance sampling and the two-locus model with subdivided population structure
    • GRIFFITHS, R. C., P. A. JENKINS and Y. S. SONG, 2008 Importance sampling and the two-locus model with subdivided population structure. Adv. Appl. Probab. 40(2): 473-500.
    • (2008) Adv. Appl. Probab. , vol.40 , Issue.2 , pp. 473-500
    • Griffiths, R.C.1    Jenkins, P.A.2    Song, Y.S.3
  • 13
    • 44949241466 scopus 로고    scopus 로고
    • Inferring human colonization history using a copying model
    • HELLENTHAL, G., A. AUTON and D. FALUSH, 2008 Inferring human colonization history using a copying model. PLoS Genet. 4: e1000078.
    • (2008) PLoS Genet. , vol.4
    • Hellenthal, G.1    Auton, A.2    Falush, D.3
  • 14
    • 67651222400 scopus 로고    scopus 로고
    • A flexible and accurate genotype imputation method for the next generation of genome-wide association studies
    • HOWIE, B. N., P. DONNELLY and J. MARCHINI, 2009 A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 5(6): e1000529.
    • (2009) PLoS Genet. , vol.5 , Issue.6
    • Howie, B.N.1    Donnelly, P.2    Marchini, J.3
  • 15
    • 0020744702 scopus 로고
    • Properties of a neutral allele model with intragenic recombination
    • HUDSON, R. R., 1983 Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23: 183-201.
    • (1983) Theor. Popul. Biol. , vol.23 , pp. 183-201
    • Hudson, R.R.1
  • 16
    • 0035692320 scopus 로고    scopus 로고
    • Two-locus sampling distributions and their application
    • HUDSON, R. R., 2001 Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
    • (2001) Genetics , vol.159 , pp. 1805-1817
    • Hudson, R.R.1
  • 17
    • 72449134764 scopus 로고    scopus 로고
    • Closed-form two-locus sampling distributions: Accuracy and universality
    • JENKINS, P. A., and Y. S. SONG, 2009 Closed-form two-locus sampling distributions: accuracy and universality. Genetics 183: 1087-1103.
    • (2009) Genetics , vol.183 , pp. 1087-1103
    • Jenkins, P.A.1    Song, Y.S.2
  • 18
    • 77953815370 scopus 로고    scopus 로고
    • An asymptotic sampling formula for the coalescent with recombination
    • JENKINS, P. A., and Y. S. SONG, 2010 An asymptotic sampling formula for the coalescent with recombination. Ann. Appl. Probab. 20: 1005-1028.
    • (2010) Ann. Appl. Probab. , vol.20 , pp. 1005-1028
    • Jenkins, P.A.1    Song, Y.S.2
  • 19
    • 73449098993 scopus 로고    scopus 로고
    • Inference of microbial recombination rates from metagenomic data
    • JOHNSON, P., and M. SLATKIN, 2009 Inference of microbial recombination rates from metagenomic data. PLoS Genet. 5(10): e1000674.
    • (2009) PLoS Genet. , vol.5 , Issue.10
    • Johnson, P.1    Slatkin, M.2
  • 21
    • 0002556819 scopus 로고
    • On the genealogy of large populations
    • KINGMAN, J. F. C., 1982b On the genealogy of large populations. J. Appl. Probab. 19A: 27-43.
    • (1982) J. Appl. Probab. , vol.19 A , pp. 27-43
    • Kingman, J.F.C.1
  • 22
    • 0033756316 scopus 로고    scopus 로고
    • Maximum likelihood estimation of recombination rates from population data
    • KUHNER, M. K., J. YAMATO and J. FELSENSTEIN, 2000 Maximum likelihood estimation of recombination rates from population data. Genetics 156: 1393-1401.
    • (2000) Genetics , vol.156 , pp. 1393-1401
    • Kuhner, M.K.1    Yamato, J.2    Felsenstein, J.3
  • 23
    • 0347361674 scopus 로고    scopus 로고
    • Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data
    • LI, N., and M. STEPHENS, 2003 Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165: 2213-2233.
    • (2003) Genetics , vol.165 , pp. 2213-2233
    • Li, N.1    Stephens, M.2
  • 24
    • 37549064336 scopus 로고    scopus 로고
    • Mach 1.0: Rapid haplotype reconstruction and missing genotype inference
    • LI, Y., and G. R. ABECASIS, 2006 Mach 1.0: rapid haplotype reconstruction and missing genotype inference. Am. J. Hum. Genet. S79: 2290.
    • (2006) Am. J. Hum. Genet. , vol.S79 , pp. 2290
    • Li, Y.1    Abecasis, G.R.2
  • 25
    • 34347344976 scopus 로고    scopus 로고
    • A new multipoint method for genome-wide association studies by imputation of genotypes
    • MARCHINI, J., B. HOWIE, S. R. MYERS, G. MCVEAN and P. DONNELLY, 2007 A new multipoint method for genome-wide association studies by imputation of genotypes. Nat. Genet. 39(7): 906-913.
    • (2007) Nat. Genet. , vol.39 , Issue.7 , pp. 906-913
    • Marchini, J.1    Howie, B.2    Myers, S.R.3    Mcvean, G.4    Donnelly, P.5
  • 26
    • 33748799967 scopus 로고    scopus 로고
    • Modern computational approaches for analysing molecular genetic variation data
    • MARJORAM, P., and S. TAVARÉ, 2006 Modern computational approaches for analysing molecular genetic variation data. Nat. Rev. Genet. 7: 759-770.
    • (2006) Nat. Rev. Genet. , vol.7 , pp. 759-770
    • Marjoram, P.1    Tavaré, S.2
  • 27
    • 33646348730 scopus 로고    scopus 로고
    • Fast "coalescent" simulation
    • MARJORAM, P., and J. D. WALL, 2006 Fast "coalescent" simulation. BMC Genet. 7: 16.
    • (2006) BMC Genet. , vol.7 , pp. 16
    • Marjoram, P.1    Wall, J.D.2
  • 29
    • 0036199914 scopus 로고    scopus 로고
    • A coalescent-based method for detecting and estimating recombination from gene sequences
    • MCVEAN, G., P. AWADALLA and P. FEARNHEAD, 2002 A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
    • (2002) Genetics , vol.160 , pp. 1231-1241
    • Mcvean, G.1    Awadalla, P.2    Fearnhead, P.3
  • 30
    • 2142773942 scopus 로고    scopus 로고
    • The fine-scale structure of recombination rate variation in the human genome
    • MCVEAN, G. A. T., S. R. MYERS, S. HUNT, P. DELOUKAS, D. R. BENTLEY et al., 2004 The fine-scale structure of recombination rate variation in the human genome. Science 304: 581-584.
    • (2004) Science , vol.304 , pp. 581-584
    • Mcvean, G.A.T.1    Myers, S.R.2    Hunt, S.3    Deloukas, P.4    Bentley, D.R.5
  • 31
    • 0033965571 scopus 로고    scopus 로고
    • Estimation of population parameters and recombination rates from single nucleotide polymorphisms
    • NIELSEN, R., 2000 Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154: 931-942.
    • (2000) Genetics , vol.154 , pp. 931-942
    • Nielsen, R.1
  • 32
    • 67651225410 scopus 로고    scopus 로고
    • Sensitive detection of chromosomal segments of distinct ancestry in admixed populations
    • PRICE, A. L., A. TANDON, N. PATTERSON, K. C. BARNES, N. RAFAELS et al., 2009 Sensitive detection of chromosomal segments of distinct ancestry in admixed populations. PLoS Genet. 5(6): e1000519.
    • (2009) PLoS Genet. , vol.5 , Issue.6
    • Price, A.L.1    Tandon, A.2    Patterson, N.3    Barnes, K.C.4    Rafaels, N.5
  • 33
    • 33644974019 scopus 로고    scopus 로고
    • A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase
    • SCHEET, P., and M. STEPHENS, 2006 A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am. J. Hum. Genet. 78: 629-644.
    • (2006) Am. J. Hum. Genet. , vol.78 , pp. 629-644
    • Scheet, P.1    Stephens, M.2
  • 34
    • 0034354581 scopus 로고    scopus 로고
    • Inference in molecular population genetics
    • STEPHENS, M., and P. DONNELLY, 2000 Inference in molecular population genetics. J. R. Stat. Soc. B 62: 605-655.
    • (2000) J. R. Stat. Soc. B , vol.62 , pp. 605-655
    • Stephens, M.1    Donnelly, P.2
  • 35
    • 13844270527 scopus 로고    scopus 로고
    • Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation
    • STEPHENS, M., and P. SCHEET, 2005 Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am. J. Hum. Genet. 76(3): 449-462.
    • (2005) Am. J. Hum. Genet. , vol.76 , Issue.3 , pp. 449-462
    • Stephens, M.1    Scheet, P.2
  • 36
    • 57149092597 scopus 로고    scopus 로고
    • Bayesian inference of fine-scale recombination rates using population genomic data
    • WANG, Y., and B. RANNALA, 2008 Bayesian inference of fine-scale recombination rates using population genomic data. Philos. Trans. R. Soc. B 363(1512): 3921-3930.
    • (2008) Philos. Trans. R. Soc. B , vol.363 , Issue.1512 , pp. 3921-3930
    • Wang, Y.1    Rannala, B.2
  • 37
    • 0033150745 scopus 로고    scopus 로고
    • Recombination as a point process along sequences
    • WIUF, C., and J. HEIN, 1999 Recombination as a point process along sequences. Theor. Popul. Biol. 55(3): 248-259.
    • (1999) Theor. Popul. Biol. , vol.55 , Issue.3 , pp. 248-259
    • Wiuf, C.1    Hein, J.2
  • 38
    • 66349109784 scopus 로고    scopus 로고
    • Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data
    • YIN, J., M. I. JORDAN and Y. S. SONG, 2009 Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data. Bioinformatics 25(12): i231-i239.
    • (2009) Bioinformatics , vol.25 , Issue.12
    • Yin, J.1    Jordan, M.I.2    Song, Y.S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.