메뉴 건너뛰기




Volumn 548, Issue 7665, 2017, Pages 87-91

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

(59)  Maretty, Lasse a   Jensen, Jacob Malte b   Petersen, Bent c   Sibbesen, Jonas Andreas a   Liu, Siyang a,d   Villesen, Palle b   Skov, Laurits b   Belling, Kirstine c   Theil Have, Christian e   Izarzugaza, Jose M G c   Grosjean, Marie c   Bork Jensen, Jette e   Grove, Jakob b,f   Als, Thomas D b,f   Huang, Shujia g,h   Chang, Yuqi g   Xu, Ruiqi d   Ye, Weijian d   Rao, Junhua d   Guo, Xiaosen a,g   more..


Author keywords

[No Author keywords available]

Indexed keywords

CHROMOSOME; GENETIC ANALYSIS; GENETIC VARIATION; GENOME; MAJOR HISTOCOMPATIBILITY COMPLEX; PHENOTYPE;

EID: 85026856426     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature23264     Document Type: Article
Times cited : (106)

References (54)
  • 1
    • 84943171338 scopus 로고    scopus 로고
    • A global reference for human genetic variation
    • The 1000 Genomes Project Consortium
    • The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature 526, 68-74 (2015).
    • (2015) Nature , vol.526 , pp. 68-74
  • 2
    • 84929132687 scopus 로고    scopus 로고
    • Large-scale whole-genome sequencing of the Icelandic population
    • Gudbjartsson, D. F. et al. Large-scale whole-genome sequencing of the Icelandic population. Nat. Genet. 47, 435-444 (2015).
    • (2015) Nat. Genet. , vol.47 , pp. 435-444
    • Gudbjartsson, D.F.1
  • 3
    • 84923223571 scopus 로고    scopus 로고
    • Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes
    • Hoehe, M. R. et al. Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes. Nat. Commun. 5, 5569 (2014).
    • (2014) Nat. Commun. , vol.5 , pp. 5569
    • Hoehe, M.R.1
  • 4
    • 84991628639 scopus 로고    scopus 로고
    • Deep sequencing of 10, 000 human genomes
    • Telenti, A. et al. Deep sequencing of 10, 000 human genomes. Proc. Natl Acad. Sci. USA 113, 11901-11906 (2016).
    • (2016) Proc. Natl Acad. Sci. USA , vol.113 , pp. 11901-11906
    • Telenti, A.1
  • 5
    • 84923112396 scopus 로고    scopus 로고
    • Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios
    • Besenbacher, S. et al. Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios. Nat. Commun. 6, 5969 (2015).
    • (2015) Nat. Commun. , vol.6 , pp. 5969
    • Besenbacher, S.1
  • 6
    • 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, (2015).
    • (2015) Science , vol.349
    • Sudmant, P.H.1
  • 7
    • 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
  • 8
    • 84897965254 scopus 로고    scopus 로고
    • Reconstructing complex regions of genomes using long-read sequencing technology
    • Huddleston, J. et al. Reconstructing complex regions of genomes using long-read sequencing technology. Genome Res. 24, 688-696 (2014).
    • (2014) Genome Res. , vol.24 , pp. 688-696
    • Huddleston, J.1
  • 9
    • 84913600842 scopus 로고    scopus 로고
    • Single haplotype assembly of the human genome from a hydatidiform mole
    • Steinberg, K. M. et al. Single haplotype assembly of the human genome from a hydatidiform mole. Genome Res. 24, 2066-2076 (2014).
    • (2014) Genome Res. , vol.24 , pp. 2066-2076
    • Steinberg, K.M.1
  • 10
    • 84930946770 scopus 로고    scopus 로고
    • De novo assembly of a haplotype-resolved human genome
    • Cao, H. et al. De novo assembly of a haplotype-resolved human genome. Nat. Biotechnol. 33, 617-622 (2015).
    • (2015) Nat. Biotechnol. , vol.33 , pp. 617-622
    • Cao, H.1
  • 11
    • 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
  • 12
    • 84938423867 scopus 로고    scopus 로고
    • Assembly and diploid architecture of an individual human genome via single-molecule technologies
    • Pendleton, M. et al. Assembly and diploid architecture of an individual human genome via single-molecule technologies. Nat. Methods 12, 780-786 (2015).
    • (2015) Nat. Methods , vol.12 , pp. 780-786
    • Pendleton, M.1
  • 13
    • 84991738269 scopus 로고    scopus 로고
    • De novo assembly and phasing of a Korean human genome
    • Seo, J. S. et al. De novo assembly and phasing of a Korean human genome. Nature 538, 243-247 (2016).
    • (2016) Nature , vol.538 , pp. 243-247
    • Seo, J.S.1
  • 14
    • 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
  • 15
    • 85019127944 scopus 로고    scopus 로고
    • Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
    • Schneider, V. A. et al. Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly. Genome Res. 27, 849-864 (2017).
    • (2017) Genome Res. , vol.27 , pp. 849-864
    • Schneider, V.A.1
  • 16
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
    • Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1, 18 (2012).
    • (2012) Gigascience , vol.1 , pp. 18
    • Luo, R.1
  • 17
    • 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
  • 18
    • 84991529236 scopus 로고    scopus 로고
    • Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale
    • Liu, S. et al. Discovery, genotyping and characterization of structural variation and novel sequence at single nucleotide resolution from de novo genome assemblies on a population scale. Gigascience 4, 64 (2015).
    • (2015) Gigascience , vol.4 , pp. 64
    • Liu, S.1
  • 19
    • 84905579746 scopus 로고    scopus 로고
    • Whole-genome sequence variation, population structure and demographic history of the Dutch population
    • The Genome of the Netherlands Consortium.
    • The 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
  • 20
    • 80052260252 scopus 로고    scopus 로고
    • A copy number variation morbidity map of developmental delay
    • Cooper, G. M. et al. A copy number variation morbidity map of developmental delay. Nat. Genet. 43, 838-846 (2011).
    • (2011) Nat. Genet. , vol.43 , pp. 838-846
    • Cooper, G.M.1
  • 21
    • 84982253941 scopus 로고    scopus 로고
    • Analysis of protein-coding genetic variation in 60, 706 humans
    • Lek, M. et al. Analysis of protein-coding genetic variation in 60, 706 humans. Nature 536, 285-291 (2016).
    • (2016) Nature , vol.536 , pp. 285-291
    • Lek, M.1
  • 22
    • 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
  • 23
    • 84865208871 scopus 로고    scopus 로고
    • Rate of de novo mutations and the importance of father's age to disease risk
    • Kong, A. et al. Rate of de novo mutations and the importance of father's age to disease risk. Nature 488, 471-475 (2012).
    • (2012) Nature , vol.488 , pp. 471-475
    • Kong, A.1
  • 24
    • 84955601029 scopus 로고    scopus 로고
    • New observations on maternal age effect on germline de novo mutations
    • Wong, W. S. et al. New observations on maternal age effect on germline de novo mutations. Nat. Commun. 7, 10486 (2016).
    • (2016) Nat. Commun. , vol.7 , pp. 10486
    • Wong, W.S.1
  • 25
    • 0026468664 scopus 로고
    • Shared polymorphism between gorilla and human major histocompatibility complex DRB loci
    • Kupfermann, H., Mayer, W. E., O'hUigin, C., Klein, D. & Klein, J. Shared polymorphism between gorilla and human major histocompatibility complex DRB loci. Hum. Immunol. 34, 267-278 (1992).
    • (1992) Hum. Immunol. , vol.34 , pp. 267-278
    • Kupfermann, H.1    Mayer, W.E.2    O'Huigin, C.3    Klein, D.4    Klein, J.5
  • 26
    • 84964284907 scopus 로고    scopus 로고
    • Punctuated bursts in human Male demography inferred from 1, 244 worldwide Y-chromosome sequences
    • Poznik, G. D. et al. Punctuated bursts in human male demography inferred from 1, 244 worldwide Y-chromosome sequences. Nat. Genet. 48, 593-599 (2016).
    • (2016) Nat. Genet. , vol.48 , pp. 593-599
    • Poznik, G.D.1
  • 27
    • 80052840370 scopus 로고    scopus 로고
    • Genome-wide population-based association study of extremely overweight young adults-the GOYA study
    • Paternoster, L. et al. Genome-wide population-based association study of extremely overweight young adults-the GOYA study. PLoS ONE 6, e24303 (2011).
    • (2011) PLoS ONE , vol.6 , pp. e24303
    • Paternoster, L.1
  • 28
    • 85019117090 scopus 로고    scopus 로고
    • Genome graphs
    • Novak, A. M. et al. Genome graphs. bioRxiv http://dx. doi. org/10. 1101/101378 (2017).
    • (2017) BioRxiv
    • Novak, A.M.1
  • 29
    • 0024603179 scopus 로고
    • Linkage between serum cholinesterase 2 (CHE2) and gamma-crystallin gene cluster (CRYG): Assignment to chromosome 2
    • Eiberg, H. et al. Linkage between serum cholinesterase 2 (CHE2) and gamma-crystallin gene cluster (CRYG): assignment to chromosome 2. Clin. Genet. 35, 313-321 (1989).
    • (1989) Clin. Genet. , vol.35 , pp. 313-321
    • Eiberg, H.1
  • 30
    • 84894557694 scopus 로고    scopus 로고
    • Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci
    • Borglum, A. D. et al. Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci. Mol. Psychiatry 19, 325-333 (2014).
    • (2014) Mol. Psychiatry , vol.19 , pp. 325-333
    • Borglum, A.D.1
  • 31
    • 84867401413 scopus 로고    scopus 로고
    • Imaging and cognitive genetics: The Norwegian Cognitive NeuroGenetics sample
    • Espeseth, T. et al. Imaging and cognitive genetics: the Norwegian Cognitive NeuroGenetics sample. Twin Res. Hum. Genet. 15, 442-452 (2012).
    • (2012) Twin Res. Hum. Genet. , vol.15 , pp. 442-452
    • Espeseth, T.1
  • 32
    • 84885020424 scopus 로고    scopus 로고
    • Genome-wide association analysis identifies 13 new risk loci for schizophrenia
    • Ripke, S. et al. Genome-wide association analysis identifies 13 new risk loci for schizophrenia. Nat. Genet. 45, 1150-1159 (2013).
    • (2013) Nat. Genet. , vol.45 , pp. 1150-1159
    • Ripke, S.1
  • 34
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 35
    • 79956307251 scopus 로고    scopus 로고
    • Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
    • Lunter, G. & Goodson, M. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res. 21, 936-939 (2011).
    • (2011) Genome Res. , vol.21 , pp. 936-939
    • Lunter, G.1    Goodson, M.2
  • 36
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009).
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 38
    • 80054913451 scopus 로고    scopus 로고
    • FLASH: Fast length adjustment of short reads to improve genome assemblies
    • Magoc?, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957-2963 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 2957-2963
    • Magoc, T.1    Salzberg, S.L.2
  • 41
    • 80054915847 scopus 로고    scopus 로고
    • A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
    • Li, H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27, 2987-2993 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 2987-2993
    • Li, H.1
  • 42
    • 85019687237 scopus 로고    scopus 로고
    • Edlib: A C/C ++ library for fast, exact sequence alignment using edit distance
    • Šošic, M. & Šikic, M. Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance. Bioinformatics btw753 (2017).
    • (2017) Bioinformatics btw753
    • Šošic, M.1    Šikic, M.2
  • 43
    • 84976871290 scopus 로고    scopus 로고
    • The Dfam database of repetitive DNA families
    • Hubley, R. et al. The Dfam database of repetitive DNA families. Nucleic Acids Res. 44 (D1), D81-D89 (2016).
    • (2016) Nucleic Acids Res. , vol.44 , Issue.D1 , pp. D81-D89
    • Hubley, R.1
  • 44
    • 84866482104 scopus 로고    scopus 로고
    • SeqTrace: A graphical tool for rapidly processing DNA sequencing chromatograms
    • Stucky, B. J. SeqTrace: a graphical tool for rapidly processing DNA sequencing chromatograms. J. Biomolec. Techniq. 23, 90-93 (2012).
    • (2012) J. Biomolec. Techniq. , vol.23 , pp. 90-93
    • Stucky, B.J.1
  • 45
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The european molecular biology open software suite
    • Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16, 276-277 (2000).
    • (2000) Trends Genet. , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 46
    • 85009151993 scopus 로고    scopus 로고
    • A reference data set of 5. 4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree
    • Eberle, M. A. et al. A reference data set of 5. 4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree. Genome Res. 27, 157-164 (2016).
    • (2016) Genome Res , vol.27 , pp. 157-164
    • Eberle, M.A.1
  • 47
    • 84868502906 scopus 로고    scopus 로고
    • Imputation of exome sequence variants into population-based samples and blood-cell-trait-associated loci in African Americans: NHLBI GO Exome Sequencing Project
    • Auer P. L. et al. Imputation of exome sequence variants into population-based samples and blood-cell-trait-associated loci in African Americans: NHLBI GO Exome Sequencing Project. Am. J. Hum. Genet. 91, 794-808 (2012).
    • (2012) Am. J. Hum. Genet. , vol.91 , pp. 794-808
    • Auer, P.L.1
  • 51
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: Improvements in performance and usability
    • Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772-780 (2013).
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 52
    • 84891946246 scopus 로고    scopus 로고
    • Seeing the wood for the trees: A minimal reference phylogeny for the human y chromosome
    • Oven, M., Geystelen, A., Kayser, M., Decorte, R. & Larmuseau, M. H. D. Seeing the wood for the trees: a minimal reference phylogeny for the human Y chromosome. Hum. Mutat. 35, 187-191 (2014).
    • (2014) Hum. Mutat. , vol.35 , pp. 187-191
    • Oven, M.1    Geystelen, A.2    Kayser, M.3    Decorte, R.4    Larmuseau, M.H.D.5
  • 54
    • 84929132937 scopus 로고    scopus 로고
    • The Y-chromosome point mutation rate in humans
    • Helgason, A. et al. The Y-chromosome point mutation rate in humans. Nat. Genet. 47, 453-457 (2015).
    • (2015) Nat. Genet. , vol.47 , pp. 453-457
    • Helgason, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.