메뉴 건너뛰기




Volumn 19, Issue 9, 2009, Pages 1553-1561

Identification of deleterious mutations within three human genomes

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID;

EID: 69749122314     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.092619.109     Document Type: Article
Times cited : (822)

References (50)
  • 2
    • 38049024773 scopus 로고    scopus 로고
    • Analysis of sequence conservation at nucleotide resolution
    • doi: 10.1371/journal.pcbi.0030254
    • Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S. 2007. Analysis of sequence conservation at nucleotide resolution. PLoS Comput Biol 3: e254. doi: 10.1371/journal.pcbi.0030254.
    • (2007) PLoS Comput Biol , vol.3
    • Asthana, S.1    Roytberg, M.2    Stamatoyannopoulos, J.3    Sunyaev, S.4
  • 5
    • 34547100092 scopus 로고    scopus 로고
    • SNAP: Predict effect of non-synonymous polymorphisms on function
    • DOI 10.1093/nar/gkm238
    • Bromberg Y, Rost B. 2007. Snap: Predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res 35: 3823-3835. (Pubitemid 47244674)
    • (2007) Nucleic Acids Research , vol.35 , Issue.11 , pp. 3823-3835
    • Bromberg, Y.1    Rost, B.2
  • 7
    • 0035937259 scopus 로고    scopus 로고
    • Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: Structure-based assessment of amino acid variation
    • DOI 10.1006/jmbi.2001.4510
    • Chasman D, Adams RM. 2001. Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: Structure-based assessment of amino acid variation. J Mol Biol 307: 683-706. (Pubitemid 33027685)
    • (2001) Journal of Molecular Biology , vol.307 , Issue.2 , pp. 683-706
    • Chasman, D.1    Adams, R.M.2
  • 8
    • 24344500211 scopus 로고    scopus 로고
    • Initial sequence of the chimpanzee genome and comparison with the human genome
    • DOI 10.1038/nature04072, PII N04072
    • Chimpanzee Sequencing and Analysis Consortium. 2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87. (Pubitemid 41613428)
    • (2005) Nature , vol.437 , Issue.7055 , pp. 69-87
  • 9
    • 3843056691 scopus 로고    scopus 로고
    • Multiple rare alleles contribute to low plasma levels of HDL cholesterol
    • DOI 10.1126/science.1099870
    • Cohen JC, Kiss RS, Pertsemlidis A, Marcel YL, McPherson R, Hobbs HH. 2004. Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 305: 869-872. (Pubitemid 39038422)
    • (2004) Science , vol.305 , Issue.5685 , pp. 869-872
    • Cohen, J.C.1    Kiss, R.S.2    Pertsemlidis, A.3    Marcel, Y.L.4    McPherson, R.5    Hobbs, H.H.6
  • 10
    • 22244452677 scopus 로고    scopus 로고
    • Distribution and intensity of constraint in mammalian genomic sequence
    • DOI 10.1101/gr.3577405
    • Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A. 2005. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res 15: 901-913. (Pubitemid 40994210)
    • (2005) Genome Research , vol.15 , Issue.7 , pp. 901-913
    • Cooper, G.M.1    Stone, E.A.2    Asimenos, G.3    Green, E.D.4    Batzoglou, S.5    Sidow, A.6
  • 11
    • 0018343295 scopus 로고
    • Efficiency of truncation selection
    • Crow JF, Kimura M. 1979. Efficiency of truncation selection. Proc Natl Acad Sci 76: 396-399.
    • (1979) Proc Natl Acad Sci , vol.76 , pp. 396-399
    • Crow, J.F.1    Kimura, M.2
  • 12
    • 0035986857 scopus 로고    scopus 로고
    • Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection
    • Dagan T, Talmor Y, Graur D. 2002. Ratios of radical to conservative amino acid replacement are affected by mutational and compositional factors and may not be indicative of positive Darwinian selection. Mol Biol Evol 19: 1022-1025. (Pubitemid 34743227)
    • (2002) Molecular Biology and Evolution , vol.19 , Issue.7 , pp. 1022-1025
    • Dagan, T.1    Talmor, Y.2    Graur, D.3
  • 14
    • 14644390333 scopus 로고    scopus 로고
    • A model of the statistical power of comparative genome sequence analysis
    • doi: 10.1371/journal.pbio.0030010
    • Eddy SR. 2005. A model of the statistical power of comparative genome sequence analysis. PLoS Biol 3: e10. doi: 10.1371/journal.pbio.0030010.
    • (2005) PLoS Biol , vol.3
    • Eddy, S.R.1
  • 15
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • DOI 10.1093/nar/gkh340
    • Edgar RC. 2004. Muscle: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797. (Pubitemid 38832724)
    • (2004) Nucleic Acids Research , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 16
    • 0034924997 scopus 로고    scopus 로고
    • Positive and negative selection on the human genome
    • Fay JC, Wyckoff GJ, Wu C-I. 2001. Positive and negative selection on the human genome. Genetics 158: 1227-1234. (Pubitemid 32667107)
    • (2001) Genetics , vol.158 , Issue.3 , pp. 1227-1234
    • Fay, J.C.1    Wyckoff, G.J.2    Wu, C.-I.3
  • 17
    • 0037186608 scopus 로고    scopus 로고
    • Testing the neutral theory of molecular evolution with genomic data from Drosophila
    • Fay JC, Wyckoff GJ, Wu C-I. 2002. Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415: 1024-1026.
    • (2002) Nature , vol.415 , pp. 1024-1026
    • Fay, J.C.1    Wyckoff, G.J.2    Wu, C.-I.3
  • 18
    • 23744486255 scopus 로고    scopus 로고
    • The scale of mutational variation in the murid genome
    • Gaffney DJ, Keightley PD. 2005. The scale of mutational variation in the murid genome. Genome Res 15: 1086-1094.
    • (2005) Genome Res , vol.15 , pp. 1086-1094
    • Gaffney, D.J.1    Keightley, P.D.2
  • 19
    • 0016197604 scopus 로고
    • Amino acid difference formula to help explain protein evolution
    • Grantham R. 1974. Amino acid difference formula to help explain protein evolution. Science 185: 862-864.
    • (1974) Science , vol.185 , pp. 862-864
    • Grantham, R.1
  • 20
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • DOI 10.1007/BF02101694
    • Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174. (Pubitemid 16227864)
    • (1985) Journal of Molecular Evolution , vol.22 , Issue.2 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 22
    • 61349141884 scopus 로고    scopus 로고
    • Cryptic variation in the human mutation rate
    • doi: 10.1371/journal.pbio.1000027
    • Hodgkinson A, Ladoukakis E, Eyre-Walker A. 2009. Cryptic variation in the human mutation rate. PLoS Biol 7: e27. doi: 10.1371/journal.pbio.1000027.
    • (2009) PLoS Biol , vol.7
    • Hodgkinson, A.1    Ladoukakis, E.2    Eyre-Walker, A.3
  • 23
    • 35348983887 scopus 로고    scopus 로고
    • A second generation human haplotype map of over 3.1 million SNPs
    • The International HapMap Consortium
    • The International HapMap Consortium. 2007. A second generation human haplotype map of over 3.1 million SNPs. Nature 449: 851-861.
    • (2007) Nature , vol.449 , pp. 851-861
  • 24
    • 37249042614 scopus 로고    scopus 로고
    • Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies
    • DOI 10.1534/genetics.107.080663
    • Keightley PD, Eyre-Walker A. 2007. Joint inference of the distribution of fitness effects of deleteriousmutations and population demography based on nucleotide polymorphism frequencies. Genetics 177: 2251-2261. (Pubitemid 350277004)
    • (2007) Genetics , vol.177 , Issue.4 , pp. 2251-2261
    • Keightley, P.D.1    Eyre-Walker, A.2
  • 25
    • 0037069428 scopus 로고    scopus 로고
    • Dobzhansky-Muller incompatibilities in protein evolution
    • Kondrashov A, Sunyaev S, Kondrashov F. 2002. Dobzhansky-Muller incompatibilities in protein evolution. Proc Natl Acad Sci 99: 14878-14883.
    • (2002) Proc Natl Acad Sci , vol.99 , pp. 14878-14883
    • Kondrashov, A.1    Sunyaev, S.2    Kondrashov, F.3
  • 26
    • 34147116715 scopus 로고    scopus 로고
    • Most rare missense alleles are deleterious in humans: Implications for complex disease and association studies
    • Kryukov GV, Pennacchio LA, Sunyaev SR. 2007. Most rare missense alleles are deleterious in humans: Implications for complex disease and association studies. Am J Hum Genet 80: 727-739.
    • (2007) Am J Hum Genet , vol.80 , pp. 727-739
    • Kryukov, G.V.1    Pennacchio, L.A.2    Sunyaev, S.R.3
  • 28
    • 0033972072 scopus 로고    scopus 로고
    • The probability of duplicate gene preservation by subfunctionalization
    • Lynch M, Force A. 2000. The probability of duplicate gene preservation by subfunctionalization. Genetics 154: 459-473. (Pubitemid 30045935)
    • (2000) Genetics , vol.154 , Issue.1 , pp. 459-473
    • Lynch, M.1    Force, A.2
  • 29
    • 0027428093 scopus 로고
    • The mutational meltdown in asexual populations
    • Lynch M, Bürger R, Butcher D, GabrielW. 1993. The mutational meltdown in asexual populations. J Hered 84: 339-344.
    • (1993) J Hered , vol.84 , pp. 339-344
    • Lynch, M.1    Bürger, R.2    Butcher, D.3    Gabriel, W.4
  • 30
    • 0001386654 scopus 로고
    • An estimate of the mutational damage in man from data on consanguineous marriages
    • Morton NE, Crow JF, Muller HJ. 1956. An estimate of the mutational damage in man from data on consanguineous marriages. Proc Natl Acad Sci 42: 855-863.
    • (1956) Proc Natl Acad Sci , vol.42 , pp. 855-863
    • Morton, N.E.1    Crow, J.F.2    Muller, H.J.3
  • 31
    • 1542802459 scopus 로고
    • Our load of mutations
    • Muller HJ. 1950. Our load of mutations. Am J Hum Genet 2: 111-176.
    • (1950) Am J Hum Genet , vol.2 , pp. 111-176
    • Muller, H.J.1
  • 32
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • Muse SV, Gaut BS. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11: 715-724.
    • (1994) Mol Biol Evol , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 33
    • 0035026704 scopus 로고    scopus 로고
    • Predicting deleterious amino acid substitutions
    • DOI 10.1101/gr.176601
    • Ng P, Henikoff S. 2001. Predicting deleterious amino acid substitutions. Genome Res 11: 863-874. (Pubitemid 32447869)
    • (2001) Genome Research , vol.11 , Issue.5 , pp. 863-874
    • Ng, P.C.1    Henikoff, S.2
  • 34
    • 0036119504 scopus 로고    scopus 로고
    • Accounting for human polymorphisms predicted to affect protein function
    • DOI 10.1101/gr.212802
    • Ng P, Henikoff S. 2002. Accounting for human polymorphisms predicted to affect protein function. Genome Res 12: 436-446. (Pubitemid 34233019)
    • (2002) Genome Research , vol.12 , Issue.3 , pp. 436-446
    • Ng, P.C.1    Henikoff, S.2
  • 35
    • 0043122919 scopus 로고    scopus 로고
    • SIFT: Predicting amino acid changes that affect protein function
    • DOI 10.1093/nar/gkg509
    • Ng P, Henikoff S. 2003. Sift: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31: 3812-3814. (Pubitemid 37442253)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3812-3814
    • Ng, P.C.1    Henikoff, S.2
  • 36
    • 33750353461 scopus 로고    scopus 로고
    • Predicting the effects of amino acid substitutions on protein function
    • DOI 10.1146/annurev.genom.7.080505.115630
    • Ng PC, Henikoff S. 2006. Predicting the effects of amino acid substitutions on protein function. Annu Rev Genomics Hum Genet 7: 61-80. (Pubitemid 44627922)
    • (2006) Annual Review of Genomics and Human Genetics , vol.7 , pp. 61-80
    • Ng, P.C.1    Henikoff, S.2
  • 38
    • 0015722319 scopus 로고
    • Slightly deleterious mutant substitutions in evolution
    • Ohta T. 1973. Slightly deleterious mutant substitutions in evolution. Nature 246: 96-98.
    • (1973) Nature , vol.246 , pp. 96-98
    • Ohta, T.1
  • 39
    • 15844406550 scopus 로고    scopus 로고
    • HyPhy: Hypothesis testing using phylogenies
    • DOI 10.1093/bioinformatics/bti079
    • Pond S, Frost S, Muse S. 2005. HyPhy: Hypothesis testing using phylogenies. Bioinformatics 21: 676-679. (Pubitemid 40424796)
    • (2005) Bioinformatics , vol.21 , Issue.5 , pp. 676-679
    • Kosakovsky Pond, S.L.1    Frost, S.D.W.2    Muse, S.V.3
  • 40
    • 0034969437 scopus 로고    scopus 로고
    • Are rare variants responsible for susceptibility to complex diseases?
    • Pritchard J. 2001. Are rare variants responsible for susceptibility to complex diseases? Am J Hum Genet 69: 124-137.
    • (2001) Am J Hum Genet , vol.69 , pp. 124-137
    • Pritchard, J.1
  • 41
    • 0036713510 scopus 로고    scopus 로고
    • Human non-synonymous SNPs: Server and survey
    • Ramensky V, Bork P, Sunyaev S. 2002. Human non-synonymous SNPs: Server and survey. Nucleic Acids Res 30: 3894-3900. (Pubitemid 35012462)
    • (2002) Nucleic Acids Research , vol.30 , Issue.17 , pp. 3894-3900
    • Ramensky, V.1    Bork, P.2    Sunyaev, S.3
  • 43
    • 0017634248 scopus 로고
    • Mutations affecting fitness in Drosophila populations
    • Simmons MJ, Crow JF. 1977. Mutations affecting fitness in Drosophila populations. Annu Rev Genet 11: 49-78.
    • (1977) Annu Rev Genet , vol.11 , pp. 49-78
    • Simmons, M.J.1    Crow, J.F.2
  • 44
    • 22244437614 scopus 로고    scopus 로고
    • Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity
    • DOI 10.1101/gr.3804205
    • Stone E, Sidow A. 2005. Physicochemical constraint violation by missense substitutions mediates impairment of protein function and disease severity. Genome Res 15: 978-986. (Pubitemid 40994218)
    • (2005) Genome Research , vol.15 , Issue.7 , pp. 978-986
    • Stone, E.A.1    Sidow, A.2
  • 45
    • 25844498846 scopus 로고    scopus 로고
    • Trade-offs in detecting evolutionarily constrained sequence by comparative genomics
    • DOI 10.1146/annurev.genom.6.080604.162146
    • Stone EA, Cooper GM, Sidow A. 2005. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. Annu Rev Genomics Hum Genet 6: 143-164. (Pubitemid 41397079)
    • (2005) Annual Review of Genomics and Human Genetics , vol.6 , pp. 143-164
    • Stone, E.A.1    Cooper, G.M.2    Sidow, A.3
  • 47
    • 59949096873 scopus 로고    scopus 로고
    • EnsemblCompara Genetrees: Complete, duplication-aware phylogenetic trees in vertebrates
    • Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. 2009. EnsemblCompara Genetrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 19: 327-335.
    • (2009) Genome Res , vol.19 , pp. 327-335
    • Vilella, A.J.1    Severin, J.2    Ureta-Vidal, A.3    Heng, L.4    Durbin, R.5    Birney, E.6
  • 48
    • 0035065485 scopus 로고    scopus 로고
    • SNPs, protein structure, and disease
    • Wang Z, Moult J. 2001. SNPs, protein structure, and disease. Hum Mutat 17: 263-270.
    • (2001) Hum Mutat , vol.17 , pp. 263-270
    • Wang, Z.1    Moult, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.