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Volumn 26, Issue 12, 2010, Pages

Estimating genome-wide IBD sharing from SNP data via an efficient hidden Markov model of LD with application to gene mapping

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CHROMOSOME MAP; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENOME; GENOMICS; METHODOLOGY; PROBABILITY; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 77954189460     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq204     Document Type: Article
Times cited : (19)

References (42)
  • 1
    • 27244437783 scopus 로고    scopus 로고
    • Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers
    • Abecasis, G. and Wigginton, J. (2005) Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am. J. Hum. Genet., 77, 754-767.
    • (2005) Am. J. Hum. Genet. , vol.77 , pp. 754-767
    • Abecasis, G.1    Wigginton, J.2
  • 2
    • 0036338150 scopus 로고    scopus 로고
    • Merlin-rapid analysis of dense genetic maps using sparse gene flow trees
    • Abecasis, G.R. et al. (2002) Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat. Genet., 30, 97-101.
    • (2002) Nat. Genet. , vol.30 , pp. 97-101
    • Abecasis, G.R.1
  • 3
    • 27544473473 scopus 로고    scopus 로고
    • Quantitative traits loci analysis using the false discovery rate
    • Benjamini, Y. and Yekutieli, D. (2005) Quantitative traits loci analysis using the false discovery rate. Genetics, 171, 783-789.
    • (2005) Genetics , vol.171 , pp. 783-789
    • Benjamini, Y.1    Yekutieli, D.2
  • 4
    • 70349196360 scopus 로고    scopus 로고
    • Inferring ancestries efficiently in admixed populations with linkage disequilibrium
    • Bercovici, S. and Geiger, D. (2009) Inferring ancestries efficiently in admixed populations with linkage disequilibrium. J. Comput. Biol., 16, 1141-1150.
    • (2009) J. Comput. Biol. , vol.16 , pp. 1141-1150
    • Bercovici, S.1    Geiger, D.2
  • 5
    • 0036689597 scopus 로고    scopus 로고
    • On reducing the statespace of hidden markov models for the identity by descent process
    • Browning, S. and Browning, B. (2002) On reducing the statespace of hidden markov models for the identity by descent process. Theor. Popul. Biol., 62, 1-8.
    • (2002) Theor. Popul. Biol. , vol.62 , pp. 1-8
    • Browning, S.1    Browning, B.2
  • 6
    • 0037370629 scopus 로고    scopus 로고
    • Using haplotype blocks to map human complex trait loci
    • Cardon, L. andAbecasis, G. (2003). Using haplotype blocks to map human complex trait loci. Trends Genet., 19, 135-140.
    • (2003) Trends Genet , vol.19 , pp. 135-140
    • Cardon, L.1    Abecasis, G.2
  • 7
    • 2642583283 scopus 로고    scopus 로고
    • Mapping complex disease loci in whole-genome association studies
    • Carlson, C. et al. (2004) Mapping complex disease loci in whole-genome association studies. Nature, 429, 446-452.
    • (2004) Nature , vol.429 , pp. 446-452
    • Carlson, C.1
  • 8
    • 0027366195 scopus 로고
    • Faster sequential genetic linkage computations
    • Cottingham, R.W. et al. (1993) Faster sequential genetic linkage computations. Am. J. Hum. Genet., 53, 252-263.
    • (1993) Am. J. Hum. Genet. , vol.53 , pp. 252-263
    • Cottingham, R.W.1
  • 10
    • 0015183542 scopus 로고
    • Ageneral model for the analysis of pedigree data
    • Elston, R. and Stewart, J. (1971) Ageneral model for the analysis of pedigree data. Hum. Hered., 21, 523-542.
    • (1971) Hum. Hered. , vol.21 , pp. 523-542
    • Elston, R.1    Stewart, J.2
  • 11
    • 41649101685 scopus 로고    scopus 로고
    • Increasing power in association studies by using linkage disequilibrium structure and molecular function as prior information
    • Eskin, E. (2008) Increasing power in association studies by using linkage disequilibrium structure and molecular function as prior information. Genome Res., 18, 653-660.
    • (2008) Genome Res , vol.18 , pp. 653-660
    • Eskin, E.1
  • 12
    • 0038558013 scopus 로고    scopus 로고
    • Exact genetic linkage computations for general pedigrees
    • Fishelson, M. and Geiger, D. (2002) Exact genetic linkage computations for general pedigrees. Bioinformatics, 18(Suppl. 1), S189-S198.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Fishelson, M.1    Geiger, D.2
  • 13
    • 35348983887 scopus 로고    scopus 로고
    • A second generation human haplotype map of over 3.1 million snps
    • Frazer, K. et al. (2007) A second generation human haplotype map of over 3.1 million snps. Nature, 449, 851-861.
    • (2007) Nature , vol.449 , pp. 851-861
    • Frazer, K.1
  • 14
    • 66349117419 scopus 로고    scopus 로고
    • Speeding up HMM algorithms for genetic linkage analysis via chain reductions of the state space
    • Geiger, D. et al. (2008) Speeding up HMM algorithms for genetic linkage analysis via chain reductions of the state space. Bioinformatics, 25, i196-i203.
    • (2008) Bioinformatics , vol.25
    • Geiger, D.1
  • 15
    • 0031268341 scopus 로고    scopus 로고
    • Factorial hidden Markov models
    • Ghahramani, Z. and Jordan, M. (1997) Factorial hidden Markov models. Mach. Learn., 29, 245-273.
    • (1997) Mach. Learn. , vol.29 , pp. 245-273
    • Ghahramani, Z.1    Jordan, M.2
  • 16
    • 13844302126 scopus 로고    scopus 로고
    • High density linkage disequilibrium mapping using models of haplotype block variation
    • Greenspan, G. and Geiger, D. (2004) High density linkage disequilibrium mapping using models of haplotype block variation. Bioinformatics, 20(Suppl. 1), i137-i144.
    • (2004) Bioinformatics , vol.20 , Issue.SUPPL. 1
    • Greenspan, G.1    Geiger, D.2
  • 17
    • 27144455205 scopus 로고    scopus 로고
    • Allegro version 2
    • Gudbjartsson, D. et al. (2005) Allegro version 2. Nat. Genet., 37, 1015-1016.
    • (2005) Nat. Genet. , vol.37 , pp. 1015-1016
    • Gudbjartsson, D.1
  • 18
    • 0034098774 scopus 로고    scopus 로고
    • Allegro, a new computer program for multipoint linkage analysis
    • Gudbjartsson, D. et al. (2000) Allegro, a new computer program for multipoint linkage analysis. Nat. Genet., 25, 12-13.
    • (2000) Nat. Genet. , vol.25 , pp. 12-13
    • Gudbjartsson, D.1
  • 19
    • 62149096354 scopus 로고    scopus 로고
    • Maximizing power in association studies
    • Halperin, E. and Stephan, D. (2009) Maximizing power in association studies. Nat. Biotecmol., 27, 255-256.
    • (2009) Nat. Biotecmol. , vol.27 , pp. 255-256
    • Halperin, E.1    Stephan, D.2
  • 20
    • 84860539286 scopus 로고    scopus 로고
    • Tag SNP selection in genotype data for maximizing SNP prediction accuracy
    • Halperin, E. et al. (2005) Tag SNP selection in genotype data for maximizing SNP prediction accuracy. Bioinformatics, 21(Suppl. 1), i195-i203.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Halperin, E.1
  • 21
    • 66349103652 scopus 로고    scopus 로고
    • Rapid and accurate multiple testing correction and power estimation for millions of correlated markers
    • Han, B. et al. (2009) Rapid and accurate multiple testing correction and power estimation for millions of correlated markers. PloS Genet., 5, e1000456.
    • (2009) PloS Genet , vol.5
    • Han, B.1
  • 22
    • 37149041369 scopus 로고    scopus 로고
    • Genetic linkage analysis, algorithms and their implementation
    • Ingolfsdottir, A. and Gudbjartsson, D. (2005) Genetic linkage analysis, algorithms and their implementation. Trans. Comput. Syst. Biol., 3737, 123-144.
    • (2005) Trans. Comput. Syst. Biol. , vol.3737 , pp. 123-144
    • Ingolfsdottir, A.1    Gudbjartsson, D.2
  • 23
    • 0031949481 scopus 로고    scopus 로고
    • Faster multipoint linkage analysis using Fourier transform
    • Kruglyak, L. and Lander, E. (1998) Faster multipoint linkage analysis using Fourier transform. J. Comput. Biol., 5, 1-7.
    • (1998) J. Comput. Biol. , vol.5 , pp. 1-7
    • Kruglyak, L.1    Lander, E.2
  • 24
    • 0028857541 scopus 로고
    • Rapid multipoint linkage analysis of recessive traits in nuclear families including homozygosity mapping
    • Kruglyak, L. et al. (1995) Rapid multipoint linkage analysis of recessive traits in nuclear families including homozygosity mapping. Am. J. Hum. Genet., 56, 519-527.
    • (1995) Am. J. Hum. Genet. , vol.56 , pp. 519-527
    • Kruglyak, L.1
  • 25
    • 0029886532 scopus 로고    scopus 로고
    • Parametric and nonparametric linkage analysis: a unified multipoint approach
    • Kruglyak, L. et al. (1996) Parametric and nonparametric linkage analysis: a unified multipoint approach. Am. J. Hum. Genet., 58, 1347-1363.
    • (1996) Am. J. Hum. Genet. , vol.58 , pp. 1347-1363
    • Kruglyak, L.1
  • 26
    • 0000803318 scopus 로고
    • Construction of multilocus genetic maps in humans
    • Lander, E. and Green, P. (1987) Construction of multilocus genetic maps in humans. Proc. Natl Acad. Sci., 84, 2363-2367.
    • (1987) Proc. Natl Acad. Sci. , vol.84 , pp. 2363-2367
    • Lander, E.1    Green, P.2
  • 28
    • 0004047518 scopus 로고    scopus 로고
    • Oxford University Press Oxford, UK
    • Lauritzen, S.L. (1996) Graphical Models. Oxford University Press, Oxford, UK.
    • (1996) Graphical Models
    • Lauritzen, S.L.1
  • 29
    • 0001006209 scopus 로고
    • Local computations with probabilities on graphical structures and their application to expert systems (with discussion)
    • Lauritzen, S.L. and Spiegelhalter, D.J. (1988) Local computations with probabilities on graphical structures and their application to expert systems (with discussion). J. Roy. Stat. Soc. Series B stat. Methodol., 50, 157-224.
    • (1988) J. Roy. Stat. Soc. Series B stat. Methodol , vol.50 , pp. 157-224
    • Lauritzen, S.L.1    Spiegelhalter, D.J.2
  • 30
    • 0035071608 scopus 로고    scopus 로고
    • Efficient multipoint linkage analysis through reduction of inheritance space
    • Markianos, K. et al. (2001) Efficient multipoint linkage analysis through reduction of inheritance space. Am. J. Hum. Genet., 68, 963-977.
    • (2001) Am. J. Hum. Genet. , vol.68 , pp. 963-977
    • Markianos, K.1
  • 31
    • 0028790963 scopus 로고
    • The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance
    • O'Connell, J. and Weeks, D. (1995) The VITESSE algorithm for rapid exact multilocus linkage analysis via genotype set-recoding and fuzzy inheritance. Nat. Genet., 11, 402-408.
    • (1995) Nat. Genet. , vol.11 , pp. 402-408
    • O'Connell, J.1    Weeks, D.2
  • 32
    • 0003408936 scopus 로고    scopus 로고
    • Johns Hopkins University Press, Baltimore, Maryland
    • Ott, J. (1999) Analysis of Human Genetic Linkage. Johns Hopkins University Press, Baltimore, Maryland.
    • (1999) Analysis of Human Genetic Linkage
    • Ott, J.1
  • 34
    • 33745279392 scopus 로고    scopus 로고
    • Evaluating and improving power in whole genome association studies using fixed marker sets
    • Peer, I. et al. (2006) Evaluating and improving power in whole genome association studies using fixed marker sets. Nat. Genet., 38, 663-667.
    • (2006) Nat. Genet. , vol.38 , pp. 663-667
    • Peer, I.1
  • 35
    • 43249125992 scopus 로고    scopus 로고
    • Estimation of the multiple testing burden for genomewide association studies of nearly all common variants
    • Peer, I. et al. (2008) Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Genet. Epidemiol., 32, 381-385.
    • (2008) Genet. Epidemiol. , vol.32 , pp. 381-385
    • Peer, I.1
  • 36
    • 34548292504 scopus 로고    scopus 로고
    • Plink: a tool set for whole-genome association and population-based linkage analyses
    • Purcell, S. et al. (2007) Plink: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet., 81, 559-575.
    • (2007) Am. J. Hum. Genet. , vol.81 , pp. 559-575
    • Purcell, S.1
  • 38
    • 0000120766 scopus 로고
    • Estimating the dimension of a model
    • Schwarz, G. (1978) Estimating the dimension of a model. Ann. Stat., 6, 461-464.
    • (1978) Ann. Stat. , vol.6 , pp. 461-464
    • Schwarz, G.1
  • 39
    • 33646887766 scopus 로고    scopus 로고
    • Online system for faster multipoint linkage analysis via parallel execution on thousands of personal computers
    • Silberstein, M. et al. (2006) Online system for faster multipoint linkage analysis via parallel execution on thousands of personal computers. Am. J. Hum. Genet., 78, 922-935.
    • (2006) Am. J. Hum. Genet. , vol.78 , pp. 922-935
    • Silberstein, M.1
  • 40
    • 0029945706 scopus 로고    scopus 로고
    • Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker sharing statistics
    • Sobel, E. and Lange, K. (1996) Descent graphs in pedigree analysis: applications to haplotyping, location scores, and marker sharing statistics. Am. J. Hum. Genet., 58, 1323-1337.
    • (1996) Am. J. Hum. Genet. , vol.58 , pp. 1323-1337
    • Sobel, E.1    Lange, K.2
  • 41
    • 84972506925 scopus 로고
    • Monte Carlo likelihood in genetic mapping
    • Thompson, E.A. (1994) Monte Carlo likelihood in genetic mapping. Stat. Sci., 9, 355-366.
    • (1994) Stat. Sci. , vol.9 , pp. 355-366
    • Thompson, E.A.1
  • 42
    • 13144265739 scopus 로고    scopus 로고
    • Genome-wide association studies: theoretical and practical concerns
    • Wang, W. et al. (2005) Genome-wide association studies: theoretical and practical concerns. Nat. Rev. Genet., 6, 109-118.
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 109-118
    • Wang, W.1


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