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Volumn 7, Issue , 2016, Pages

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

(67)  Hehir Kwa, Jayne Y a   Marschall, Tobias b,c   Kloosterman, Wigard P d   Francioli, Laurent C d,e,f,g   Baaijens, Jasmijn A h   Dijkstra, Louis J h   Abdellaoui, Abdel i   Koval, Vyacheslav j   Thung, Djie Tjwan a   Wardenaar, René k,l   Renkens, Ivo d   Coe, Bradley P m   Deelen, Patrick k   De Ligt, Joep d   Lameijer, Eric Wubbo n   Van Dijk, Freerk k   Hormozdiari, Fereydoun m   Uitterlinden, André G j   Van Duijn, Cornelia M j   Eichler, Evan E m   more..


Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXITY; GENETIC ANALYSIS; GENETIC VARIATION; GENOMICS; HUMAN ACTIVITY; PHENOTYPE; SPECTRUM;

EID: 84990859114     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms12989     Document Type: Article
Times cited : (80)

References (42)
  • 1
    • 84905579746 scopus 로고    scopus 로고
    • Whole-genome sequence variation, population structure and demographic history of the Dutch population
    • Genome of the Netherlands Consortium
    • Genome of the Netherlands Consortium. Whole-genome sequence variation, population structure and demographic history of the Dutch population. Nat. Genet. 46, 818-825 (2014).
    • (2014) Nat. Genet , vol.46 , pp. 818-825
  • 2
    • 84908551473 scopus 로고    scopus 로고
    • Improved imputation quality of low-frequency and rare variants in European samples using the 'Genome of the Netherlands'
    • Deelen, P. et al. Improved imputation quality of low-frequency and rare variants in European samples using the 'Genome of The Netherlands'. Eur. J. Hum. Genet. 22, 1321-1326 (2014).
    • (2014) Eur. J. Hum. Genet , vol.22 , pp. 1321-1326
    • Deelen, P.1
  • 3
    • 79959503826 scopus 로고    scopus 로고
    • The international hapmap project
    • International HapMap Consortium
    • International HapMap Consortium. The international hapmap project. Nature 426, 789-796 (2003).
    • (2003) Nature , vol.426 , pp. 789-796
  • 4
    • 77956331627 scopus 로고    scopus 로고
    • Integrating common and rare genetic variation in diverse human populations
    • International HapMap 3 Consortium et al
    • International HapMap 3 Consortium et al. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52-58 (2010).
    • (2010) Nature , vol.467 , pp. 52-58
  • 5
    • 77950461601 scopus 로고    scopus 로고
    • Origins and functional impact of copy number variation in the human genome
    • Conrad, D. F. et al. Origins and functional impact of copy number variation in the human genome. Nature 464, 704-712 (2010).
    • (2010) Nature , vol.464 , pp. 704-712
    • Conrad, D.F.1
  • 6
    • 59149098800 scopus 로고    scopus 로고
    • Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis
    • De Cid, R. et al. Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasis. Nat. Genet. 41, 211-215 (2009).
    • (2009) Nat. Genet , vol.41 , pp. 211-215
    • De Cid, R.1
  • 7
    • 34249815834 scopus 로고    scopus 로고
    • FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity
    • Fanciulli, M. et al. FCGR3B copy number variation is associated with susceptibility to systemic, but not organ-specific, autoimmunity. Nat. Genet. 39, 721-723 (2007).
    • (2007) Nat. Genet , vol.39 , pp. 721-723
    • Fanciulli, M.1
  • 8
    • 81755183108 scopus 로고    scopus 로고
    • Relative burden of large CNVs on a range of neurodevelopmental phenotypes
    • Girirajan, S. et al. Relative burden of large CNVs on a range of neurodevelopmental phenotypes. PLOS Genet. 7, e1002334 (2011).
    • (2011) PLOS Genet , vol.7 , pp. e1002334
    • Girirajan, S.1
  • 9
    • 61649100746 scopus 로고    scopus 로고
    • Genomic microarrays in mental retardation: A practical workflow for diagnostic applications
    • Koolen, D. A. et al. Genomic microarrays in mental retardation: a practical workflow for diagnostic applications. Hum. Mutat. 30, 283-292 (2009).
    • (2009) Hum. Mutat , vol.30 , pp. 283-292
    • Koolen, D.A.1
  • 10
    • 43049107147 scopus 로고    scopus 로고
    • The functional impact of structural variation in humans
    • Hurles, M. E., Dermitzakis, E. T. & Tyler-Smith, C. The functional impact of structural variation in humans. Trends Genet. 24, 238-245 (2008).
    • (2008) Trends Genet , vol.24 , pp. 238-245
    • Hurles, M.E.1    Dermitzakis, E.T.2    Tyler-Smith, C.3
  • 11
    • 31144469134 scopus 로고    scopus 로고
    • Structural variation in the human genome
    • Feuk, L., Carson, A. R. & Scherer, S. W. Structural variation in the human genome. Nat. Rev. Genet. 7, 85-97 (2006).
    • (2006) Nat. Rev. Genet , vol.7 , pp. 85-97
    • Feuk, L.1    Carson, A.R.2    Scherer, S.W.3
  • 12
    • 84943171338 scopus 로고    scopus 로고
    • A global reference for human genetic variation
    • 1,000 Genomes Project Consortium et al
    • 1,000 Genomes Project Consortium et al. A global reference for human genetic variation. Nature 526, 68-74 (2015).
    • (2015) Nature , vol.526 , pp. 68-74
  • 13
    • 84942436432 scopus 로고    scopus 로고
    • Global diversity, population stratification, and selection of human copy-number variation
    • Sudmant, P. H. et al. Global diversity, population stratification, and selection of human copy-number variation. Science 349, aab3761 (2015).
    • (2015) Science , vol.349 , pp. aab3761
    • Sudmant, P.H.1
  • 14
    • 84943182461 scopus 로고    scopus 로고
    • An integrated map of structural variation in 2,504 human genomes
    • Sudmant, P. H. et al. An integrated map of structural variation in 2,504 human genomes. Nature 526, 75-81 (2015).
    • (2015) Nature , vol.526 , pp. 75-81
    • Sudmant, P.H.1
  • 15
    • 84945370533 scopus 로고    scopus 로고
    • Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers
    • Sidore, C. et al. Genome sequencing elucidates Sardinian genetic architecture and augments association analyses for lipid and blood inflammatory markers. Nat. Genet. 47, 1272-1281 (2015).
    • (2015) Nat. Genet , vol.47 , pp. 1272-1281
    • Sidore, C.1
  • 16
    • 84923112396 scopus 로고    scopus 로고
    • Novel variation and de novo mutation rates in populationwide de novo assembled Danish trios
    • Besenbacher, S. et al. Novel variation and de novo mutation rates in populationwide de novo assembled Danish trios. Nat. Commun. 6, 5969 (2015).
    • (2015) Nat. Commun , vol.6 , pp. 5969
    • Besenbacher, S.1
  • 17
    • 84943182742 scopus 로고    scopus 로고
    • The UK10K project identifies rare variants in health and disease
    • UK10K Consortium et al
    • UK10K Consortium et al. The UK10K project identifies rare variants in health and disease. Nature 526, 82-90 (2015).
    • (2015) Nature , vol.526 , pp. 82-90
  • 18
    • 84872333179 scopus 로고    scopus 로고
    • Deep whole-genome sequencing of 100 southeast Asian Malays
    • Wong, L.-P. et al. Deep whole-genome sequencing of 100 southeast Asian Malays. Am. J. Hum. Genet. 92, 52-66 (2013).
    • (2013) Am. J. Hum. Genet , vol.92 , pp. 52-66
    • Wong, L.-P.1
  • 19
    • 84892798985 scopus 로고    scopus 로고
    • The Genome of the Netherlands: Design, and project goals
    • Boomsma, D. I. et al. The Genome of the Netherlands: design, and project goals. Eur. J. Hum. Genet. 22, 221-227 (2013).
    • (2013) Eur. J. Hum. Genet , vol.22 , pp. 221-227
    • Boomsma, D.I.1
  • 20
    • 84937191220 scopus 로고    scopus 로고
    • Genome-wide patterns and properties of de novo mutations in humans
    • Francioli, L. C. et al. Genome-wide patterns and properties of de novo mutations in humans. Nat. Genet. 47, 822-826 (2015).
    • (2015) Nat. Genet , vol.47 , pp. 822-826
    • Francioli, L.C.1
  • 21
    • 84931833875 scopus 로고    scopus 로고
    • Characteristics of de novo structural changes in the human genome
    • Kloosterman, W. P. et al. Characteristics of de novo structural changes in the human genome. Genome Res. 25, 792-801 (2015).
    • (2015) Genome Res , vol.25 , pp. 792-801
    • Kloosterman, W.P.1
  • 22
    • 84912535591 scopus 로고    scopus 로고
    • GINDEL: Accurate genotype calling of insertions and deletions from low coverage population sequence reads
    • Chu, C., Zhang, J. & Wu, Y. GINDEL: accurate genotype calling of insertions and deletions from low coverage population sequence reads. PLOS ONE 9, e113324 (2014).
    • (2014) PLOS ONE , vol.9 , pp. e113324
    • Chu, C.1    Zhang, J.2    Wu, Y.3
  • 23
    • 84900348313 scopus 로고    scopus 로고
    • MATE-CLEVER: Mendelianinheritance-aware discovery and genotyping of midsize and long indels
    • Marschall, T., Hajirasouliha, I. & Schönhuth, A. MATE-CLEVER: Mendelianinheritance-aware discovery and genotyping of midsize and long indels. Bioinformatics 29, 3143-3150 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 3143-3150
    • Marschall, T.1    Hajirasouliha, I.2    Schönhuth, A.3
  • 24
    • 33344458848 scopus 로고    scopus 로고
    • A comparison of phasing algorithms for trios and unrelated individuals
    • Marchini, J. et al. A comparison of phasing algorithms for trios and unrelated individuals. Am. J. Hum. Genet. 78, 437-450 (2006).
    • (2006) Am. J. Hum. Genet , vol.78 , pp. 437-450
    • Marchini, J.1
  • 25
    • 84871736050 scopus 로고    scopus 로고
    • Genotype calling and phasing using nextgeneration sequencing reads and a haplotype scaffold
    • Menelaou, A. & Marchini, J. Genotype calling and phasing using nextgeneration sequencing reads and a haplotype scaffold. Bioinformatics 29, 84-91 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 84-91
    • Menelaou, A.1    Marchini, J.2
  • 26
    • 84925497196 scopus 로고    scopus 로고
    • Resolving the complexity of the human genome using single-molecule sequencing
    • Chaisson, M. J. P. et al. Resolving the complexity of the human genome using single-molecule sequencing. Nature 517, 608-611 (2015).
    • (2015) Nature , vol.517 , pp. 608-611
    • Chaisson, M.J.P.1
  • 27
    • 0035173378 scopus 로고    scopus 로고
    • DbSNP: The NCBI database of genetic variation
    • Sherry, S. T. et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29, 308-311 (2001).
    • (2001) Nucleic Acids Res , vol.29 , pp. 308-311
    • Sherry, S.T.1
  • 28
    • 84891783452 scopus 로고    scopus 로고
    • The Database of Genomic Variants: A curated collection of structural variation in the human genome
    • MacDonald, J. R., Ziman, R., Yuen, R. K. C., Feuk, L. & Scherer, S. W. The Database of Genomic Variants: a curated collection of structural variation in the human genome. Nucleic Acids Res. 42, D986-D992 (2014).
    • (2014) Nucleic Acids Res , vol.42 , pp. D986-D992
    • MacDonald, J.R.1    Ziman, R.2    Yuen, R.K.C.3    Feuk, L.4    Scherer, S.W.5
  • 29
    • 84873487706 scopus 로고    scopus 로고
    • Gene copy-number polymorphism caused by retrotransposition in humans
    • Schrider, D. R. et al. Gene copy-number polymorphism caused by retrotransposition in humans. PLOS Genet. 9, e1003242 (2013).
    • (2013) PLOS Genet , vol.9 , pp. e1003242
    • Schrider, D.R.1
  • 30
    • 84954358158 scopus 로고    scopus 로고
    • Identification of a 2Mb human ortholog of Drosophila eyes shut/spacemaker that is mutated in patients with retinitis pigmentosa
    • Collin, R. W. J. et al. Identification of a 2Mb human ortholog of Drosophila eyes shut/spacemaker that is mutated in patients with retinitis pigmentosa. Am. J. Hum. Genet. 83, 594-603 (2008).
    • (2008) Am. J. Hum. Genet , vol.83 , pp. 594-603
    • Collin, R.W.J.1
  • 31
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memory-efficient shortread de novo assembler
    • Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient shortread de novo assembler. Gigascience 1, 18 (2012).
    • (2012) Gigascience , vol.1 , pp. 18
    • Luo, R.1
  • 32
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • 1,000 Genomes Project Consortium et al
    • 1,000 Genomes Project Consortium et al. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56-65 (2012).
    • (2012) Nature , vol.491 , pp. 56-65
  • 33
    • 84929224491 scopus 로고    scopus 로고
    • EQTL mapping identifies insertion-and deletion-specific eQTLs in multiple tissues
    • Huang, J. et al. eQTL mapping identifies insertion-and deletion-specific eQTLs in multiple tissues. Nat. Commun. 6, 6821 (2015).
    • (2015) Nat. Commun , vol.6 , pp. 6821
    • Huang, J.1
  • 34
    • 84891790401 scopus 로고    scopus 로고
    • The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
    • Welter, D. et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 42, D1001-D1006 (2014).
    • (2014) Nucleic Acids Res , vol.42 , pp. D1001-D1006
    • Welter, D.1
  • 35
    • 84865822182 scopus 로고    scopus 로고
    • Systematic localization of common disease-associated variation in regulatory DNA
    • Maurano, M. T. et al. Systematic localization of common disease-associated variation in regulatory DNA. Science 337, 1190-1195 (2012).
    • (2012) Science , vol.337 , pp. 1190-1195
    • Maurano, M.T.1
  • 36
    • 78649489009 scopus 로고    scopus 로고
    • Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci
    • Franke, A. et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci. Nat. Genet. 42, 1118-1125 (2010).
    • (2010) Nat. Genet , vol.42 , pp. 1118-1125
    • Franke, A.1
  • 37
    • 84868336049 scopus 로고    scopus 로고
    • Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease
    • Jostins, L. et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491, 119-124 (2012).
    • (2012) Nature , vol.491 , pp. 119-124
    • Jostins, L.1
  • 38
    • 84873348443 scopus 로고    scopus 로고
    • Common genetic variation and antidepressant efficacy in major depressive disorder: A meta-analysis of three genome-wide pharmacogenetic studies
    • GENDEP Investigators and MARS Investigators & STAR∗D Investigators
    • GENDEP Investigators, MARS Investigators & STAR∗D Investigators. Common genetic variation and antidepressant efficacy in major depressive disorder: a meta-analysis of three genome-wide pharmacogenetic studies. Am. J. Psychiatry 170, 207-217 (2013).
    • (2013) Am. J. Psychiatry , vol.170 , pp. 207-217
  • 39
    • 77953808087 scopus 로고    scopus 로고
    • Genotype imputation for genome-wide association studies
    • Marchini, J. & Howie, B. Genotype imputation for genome-wide association studies. Nat. Rev. Genet. 11, 499-511 (2010).
    • (2010) Nat. Rev. Genet , vol.11 , pp. 499-511
    • Marchini, J.1    Howie, B.2
  • 40
    • 33846978695 scopus 로고    scopus 로고
    • Relative impact of nucleotide and copy number variation on gene expression phenotypes
    • Stranger, B. E. et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315, 848-853 (2007).
    • (2007) Science , vol.315 , pp. 848-853
    • Stranger, B.E.1
  • 41
    • 84940521469 scopus 로고    scopus 로고
    • Population-specific genotype imputations using minimac or IMPUTE2
    • Van Leeuwen, E. M. et al. Population-specific genotype imputations using minimac or IMPUTE2. Nat. Protoc. 10, 1285-1296 (2015).
    • (2015) Nat. Protoc , vol.10 , pp. 1285-1296
    • Van Leeuwen, E.M.1
  • 42
    • 84856478855 scopus 로고    scopus 로고
    • A linear complexity phasing method for thousands of genomes
    • Delaneau, O., Marchini, J. & Zagury, J.-F. A linear complexity phasing method for thousands of genomes. Nat. Methods 9, 179-181 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 179-181
    • Delaneau, O.1    Marchini, J.2    Zagury, J.-F.3


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