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Volumn 46, Issue 12, 2014, Pages 1350-1355

Comprehensive variation discovery in single human genomes

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA BASE COMPOSITION; FOSMID; GENETIC VARIABILITY; GENOME SIZE; GENOTYPE; HETEROZYGOSITY; HOMOZYGOSITY; HUMAN; HUMAN CELL; HUMAN GENOME; INDEL MUTATION; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; SEGMENTAL DUPLICATION; TRINUCLEOTIDE REPEAT; X CHROMOSOME; ALGORITHM; CHROMOSOME MAP; COMPUTER PROGRAM; DNA MICROARRAY; GENE FREQUENCY; GENOME; HIGH THROUGHPUT SEQUENCING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84922584295     PISSN: 10614036     EISSN: 15461718     Source Type: Journal    
DOI: 10.1038/ng.3121     Document Type: Article
Times cited : (146)

References (33)
  • 1
    • 84975742565 scopus 로고    scopus 로고
    • A map of human genome variation from population-scale sequencing
    • 1000 Genomes Project Consortium
    • 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073 (2010)
    • (2010) Nature , vol.467 , pp. 1061-1073
  • 2
    • 79957932376 scopus 로고    scopus 로고
    • Dindel: Accurate indel calls from short-read data
    • Albers, C.A. et al. Dindel: accurate indel calls from short-read data. Genome Res. 21, 961-973 (2011)
    • (2011) Genome Res. , vol.21 , pp. 961-973
    • Albers, C.A.1
  • 3
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo, M.A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491-498 (2011)
    • (2011) Nat. Genet. , vol.43 , pp. 491-498
    • Depristo, M.A.1
  • 4
    • 84861861291 scopus 로고    scopus 로고
    • LobSTR: A short tandem repeat profiler for personal genomes
    • Gymrek, M., Golan, D., Rosset, S. & Erlich, Y. lobSTR: a short tandem repeat profiler for personal genomes. Genome Res. 22, 1154-1162 (2012)
    • (2012) Genome Res. , vol.22 , pp. 1154-1162
    • Gymrek, M.1    Golan, D.2    Rosset, S.3    Erlich, Y.4
  • 5
    • 84856246802 scopus 로고    scopus 로고
    • De novo assembly and genotyping of variants using colored de Bruijn graphs
    • Iqbal, Z., Caccamo, M., Turner, I., Flicek, P. & McVean, G. De novo assembly and genotyping of variants using colored de Bruijn graphs. Nat. Genet. 44, 226-232 (2012)
    • (2012) Nat. Genet. , vol.44 , pp. 226-232
    • Iqbal, Z.1    Caccamo, M.2    Turner, I.3    Flicek, P.4    McVean, G.5
  • 6
    • 84868138663 scopus 로고    scopus 로고
    • A likelihood-based framework for variant calling and de novo mutation detection in families
    • Li, B. et al. A likelihood-based framework for variant calling and de novo mutation detection in families. PLoS Genet. 8, e1002944 (2012)
    • (2012) PLoS Genet. , vol.8 , pp. e1002944
    • Li, B.1
  • 7
    • 77956295988 scopus 로고    scopus 로고
    • The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297-1303 (2010)
    • (2010) Genome Res. , vol.20 , pp. 1297-1303
    • McKenna, A.1
  • 8
    • 84878276682 scopus 로고    scopus 로고
    • A support vector machine for identification of single-nucleotide polymorphisms from next-generation sequencing data
    • O'Fallon, B.D., Wooderchak-Donahue, W. & Crockett, D.K. A support vector machine for identification of single-nucleotide polymorphisms from next-generation sequencing data. Bioinformatics 29, 1361-1366 (2013)
    • (2013) Bioinformatics , vol.29 , pp. 1361-1366
    • Ofallon, B.D.1    Wooderchak-Donahue, W.2    Crockett, D.K.3
  • 9
    • 84857838310 scopus 로고    scopus 로고
    • Efficient de novo assembly of large genomes using compressed data structures
    • Simpson, J.T. & Durbin, R. Efficient de novo assembly of large genomes using compressed data structures. Genome Res. 22, 549-556 (2012)
    • (2012) Genome Res. , vol.22 , pp. 549-556
    • Simpson, J.T.1    Durbin, R.2
  • 10
    • 84877100867 scopus 로고    scopus 로고
    • An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data
    • Wang, Y., Lu, J., Yu, J., Gibbs, R.A. & Yu, F. An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data. Genome Res. 23, 833-842 (2013)
    • (2013) Genome Res. , vol.23 , pp. 833-842
    • Wang, Y.1    Lu, J.2    Yu, J.3    Gibbs, R.A.4    Yu, F.5
  • 11
    • 77956331627 scopus 로고    scopus 로고
    • Integrating common and rare genetic variation in diverse human populations
    • International HapMap 3 Consortium
    • International HapMap 3 Consortium. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52-58 (2010)
    • (2010) Nature , vol.467 , pp. 52-58
  • 12
    • 0025905795 scopus 로고
    • Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome
    • Verkerk, A.J. et al. Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome. Cell 65, 905-914 (1991)
    • (1991) Cell , vol.65 , pp. 905-914
    • Verkerk, A.J.1
  • 13
    • 0025868571 scopus 로고
    • DNA duplication associated with Charcot-Marie-Tooth disease type 1A
    • Lupski, J.R. et al. DNA duplication associated with Charcot-Marie-Tooth disease type 1A. Cell 66, 219-232 (1991)
    • (1991) Cell , vol.66 , pp. 219-232
    • Lupski, J.R.1
  • 14
    • 63949083912 scopus 로고    scopus 로고
    • Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes
    • Kozarewa, I. et al. Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat. Methods 6, 291-295 (2009)
    • (2009) Nat. Methods , vol.6 , pp. 291-295
    • Kozarewa, I.1
  • 15
    • 33745617710 scopus 로고    scopus 로고
    • A fast and symmetric DUST implementation to mask low-complexity DNA sequences
    • Morgulis, A., Gertz, E.M., Schaffer, A.A. & Agarwala, R. A fast and symmetric DUST implementation to mask low-complexity DNA sequences. J. Comput. Biol. 13, 1028-1040 (2006)
    • (2006) J. Comput. Biol. , vol.13 , pp. 1028-1040
    • Morgulis, A.1    Gertz, E.M.2    Schaffer, A.A.3    Agarwala, R.4
  • 16
    • 7244247384 scopus 로고    scopus 로고
    • Shotgun sequence assembly and recent segmental duplications within the human genome
    • She, X. et al. Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 431, 927-930 (2004)
    • (2004) Nature , vol.431 , pp. 927-930
    • She, X.1
  • 17
    • 84878234942 scopus 로고    scopus 로고
    • Characterizing and measuring bias in sequence data
    • Ross, M.G. et al. Characterizing and measuring bias in sequence data. Genome Biol. 14, R51 (2013)
    • (2013) Genome Biol. , vol.14 , pp. R51
    • Ross, M.G.1
  • 18
    • 79954553212 scopus 로고    scopus 로고
    • Improving SNP discovery by base alignment quality
    • Li, H. Improving SNP discovery by base alignment quality. Bioinformatics 27, 1157-1158 (2011)
    • (2011) Bioinformatics , vol.27 , pp. 1157-1158
    • Li, H.1
  • 19
    • 25844487226 scopus 로고    scopus 로고
    • Diseases of unstable repeat expansion: Mechanisms and common principles
    • Gatchel, J.R. & Zoghbi, H.Y. Diseases of unstable repeat expansion: mechanisms and common principles. Nat. Rev. Genet. 6, 743-755 (2005)
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 743-755
    • Gatchel, J.R.1    Zoghbi, H.Y.2
  • 20
    • 79954615189 scopus 로고    scopus 로고
    • Nebulin, a major player in muscle health and disease
    • Labeit, S., Ottenheijm, C.A. & Granzier, H. Nebulin, a major player in muscle health and disease. FASEB J. 25, 822-829 (2011)
    • (2011) FASEB J. , vol.25 , pp. 822-829
    • Labeit, S.1    Ottenheijm, C.A.2    Granzier, H.3
  • 21
    • 0002344794 scopus 로고
    • Bootstrap methods: Another look at the jackknife
    • Efron, B. Bootstrap methods: another look at the jackknife. Ann. Stat. 7, 1-26 (1979)
    • (1979) Ann. Stat. , vol.7 , pp. 1-26
    • Efron, B.1
  • 22
    • 84880798154 scopus 로고    scopus 로고
    • Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
    • Chin, C.S. et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10, 563-569 (2013)
    • (2013) Nat. Methods , vol.10 , pp. 563-569
    • Chin, C.S.1
  • 23
    • 77954523593 scopus 로고    scopus 로고
    • Iterative correction of reference nucleotides (iCORN) using second generation sequencing technology
    • Otto, T.D., Sanders, M., Berriman, M. & Newbold, C. Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology. Bioinformatics 26, 1704-1707 (2010)
    • (2010) Bioinformatics , vol.26 , pp. 1704-1707
    • Otto, T.D.1    Sanders, M.2    Berriman, M.3    Newbold, C.4
  • 24
    • 70349866672 scopus 로고    scopus 로고
    • Genome project standards in a new era of sequencing
    • Chain, P.S. et al. Genome project standards in a new era of sequencing. Science 326, 236-237 (2009)
    • (2009) Science , vol.326 , pp. 236-237
    • Chain, P.S.1
  • 25
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • International Human Genome Sequencing Consortium
    • International Human Genome Sequencing Consortium. Finishing the euchromatic sequence of the human genome. Nature 431, 931-945 (2004)
    • (2004) Nature , vol.431 , pp. 931-945
  • 26
    • 0034708758 scopus 로고    scopus 로고
    • A whole-genome assembly of Drosophila
    • Myers, E.W. et al. A whole-genome assembly of Drosophila. Science 287, 2196-2204 (2000)
    • (2000) Science , vol.287 , pp. 2196-2204
    • Myers, E.W.1
  • 27
    • 0035895505 scopus 로고    scopus 로고
    • The sequence of the human genome
    • Venter, J.C. et al. The sequence of the human genome. Science 291, 1304-1351 (2001)
    • (2001) Science , vol.291 , pp. 1304-1351
    • Venter, J.C.1
  • 29
    • 77949511368 scopus 로고    scopus 로고
    • Pebble and rock band: Heuristic resolution of repeats and scaffolding in the Velvet short-read de novo assembler
    • Zerbino, D.R., McEwen, G.K., Margulies, E.H. & Birney, E. Pebble and Rock Band: heuristic resolution of repeats and scaffolding in the Velvet short-read de novo assembler. PLoS ONE 4, e8407 (2009)
    • (2009) PLoS ONE , vol.4 , pp. e8407
    • Zerbino, D.R.1    McEwen, G.K.2    Margulies, E.H.3    Birney, E.4
  • 30
    • 79952178131 scopus 로고    scopus 로고
    • High-quality draft assemblies of mammalian genomes from massively parallel sequence data
    • Gnerre, S. et al. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc. Natl. Acad. Sci. USA 108, 1513-1518 (2011)
    • (2011) Proc. Natl. Acad. Sci. USA , vol.108 , pp. 1513-1518
    • Gnerre, S.1
  • 31
    • 0036144823 scopus 로고    scopus 로고
    • ARACHNE: A whole-genome shotgun assembler
    • Batzoglou, S. et al. ARACHNE: a whole-genome shotgun assembler. Genome Res. 12, 177-189 (2002)
    • (2002) Genome Res. , vol.12 , pp. 177-189
    • Batzoglou, S.1
  • 32
    • 79959867627 scopus 로고    scopus 로고
    • ECHO: A reference-free short-read error correction algorithm
    • Kao, W.C., Chan, A.H. & Song, Y.S. ECHO: a reference-free short-read error correction algorithm. Genome Res. 21, 1181-1192 (2011)
    • (2011) Genome Res. , vol.21 , pp. 1181-1192
    • Kao, W.C.1    Chan, A.H.2    Song, Y.S.3
  • 33
    • 43149086380 scopus 로고    scopus 로고
    • ALLPATHS: De novo assembly of whole-genome shotgun microreads
    • Butler, J. et al. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 18, 810-820 (2008)
    • (2008) Genome Res. , vol.18 , pp. 810-820
    • Butler, J.1


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