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Volumn 13, Issue 9, 2016, Pages 784-791

Representing genetic variation with synthetic DNA standards

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; SYNTHETIC DNA; DNA;

EID: 84981252375     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.3957     Document Type: Article
Times cited : (35)

References (46)
  • 1
    • 84879411643 scopus 로고    scopus 로고
    • Sequencing studies in human genetics: Design and interpretation
    • Goldstein, D.B. et al. Sequencing studies in human genetics: design and interpretation. Nat. Rev. Genet. 14, 460-470 (2013).
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 460-470
    • Goldstein, D.B.1
  • 2
    • 84876527918 scopus 로고    scopus 로고
    • Cancer genome-sequencing study design
    • Mwenifumbo, J.C. & Marra, M.A. Cancer genome-sequencing study design. Nat. Rev. Genet. 14, 321-332 (2013).
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 321-332
    • Mwenifumbo, J.C.1    Marra, M.A.2
  • 3
    • 83555173382 scopus 로고    scopus 로고
    • Direct mutation analysis by high-throughput sequencing: From germline to low-abundant, somatic variants
    • Gundry, M. & Vijg, J. Direct mutation analysis by high-throughput sequencing: from germline to low-abundant, somatic variants. Mutat. Res. 729, 1-15 (2012).
    • (2012) Mutat. Res. , vol.729 , pp. 1-15
    • Gundry, M.1    Vijg, J.2
  • 4
    • 84877999280 scopus 로고    scopus 로고
    • Molecular genetic testing and the future of clinical genomics
    • Katsanis, S.H. & Katsanis, N. Molecular genetic testing and the future of clinical genomics. Nat. Rev. Genet. 14, 415-426 (2013).
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 415-426
    • Katsanis, S.H.1    Katsanis, N.2
  • 5
    • 79956314887 scopus 로고    scopus 로고
    • Genotype and SNP calling from next-generation sequencing data
    • Nielsen, R., Paul, J.S., Albrechtsen, A. & Song, Y.S. Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12, 443-451 (2011).
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 443-451
    • Nielsen, R.1    Paul, J.S.2    Albrechtsen, A.3    Song, Y.S.4
  • 6
    • 84892728434 scopus 로고    scopus 로고
    • Sequencing depth and coverage: Key considerations in genomic analyses
    • Sims, D., Sudbery, I., Ilott, N.E., Heger, A. & Ponting, C.P. Sequencing depth and coverage: key considerations in genomic analyses. Nat. Rev. Genet. 15, 121-132 (2014).
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 121-132
    • Sims, D.1    Sudbery, I.2    Ilott, N.E.3    Heger, A.4    Ponting, C.P.5
  • 7
    • 84946100079 scopus 로고    scopus 로고
    • The UCSC Genome Browser database: 2015 update
    • Rosenbloom, K.R. et al. The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 43, D670-D681 (2015).
    • (2015) Nucleic Acids Res. , vol.43 , pp. D670-D681
    • Rosenbloom, K.R.1
  • 8
    • 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
  • 9
    • 84924293330 scopus 로고    scopus 로고
    • Edge effects in calling variants from targeted amplicon sequencing
    • Satya, R.V. & DiCarlo, J. Edge effects in calling variants from targeted amplicon sequencing. BMC Genomics 15, 1073-1080 (2014).
    • (2014) BMC Genomics , vol.15 , pp. 1073-1080
    • Satya, R.V.1    DiCarlo, J.2
  • 10
    • 84857145150 scopus 로고    scopus 로고
    • ART: A next-generation sequencing read simulator
    • Huang, W., Li, L., Myers, J.R. & Marth, G.T. ART: a next-generation sequencing read simulator. Bioinformatics 28, 593-594 (2012).
    • (2012) Bioinformatics , vol.28 , pp. 593-594
    • Huang, W.1    Li, L.2    Myers, J.R.3    Marth, G.T.4
  • 11
    • 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
  • 12
    • 84897387657 scopus 로고    scopus 로고
    • Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls
    • Zook, J.M. et al. Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls. Nat. Biotechnol. 32, 246-251 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 246-251
    • Zook, J.M.1
  • 13
    • 84896009017 scopus 로고    scopus 로고
    • From FastQ data to high confidence variant calls: The Genome Analysis Toolkit best practices pipeline
    • Van der Auwera, G.A. et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr. Protoc. Bioinformatics 43, 1-33 (2013).
    • (2013) Curr. Protoc. Bioinformatics , vol.43 , pp. 1-33
    • Van Der Auwera, G.A.1
  • 14
    • 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
  • 15
    • 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
  • 17
    • 84884377472 scopus 로고    scopus 로고
    • Tumour heterogeneity and cancer cell plasticity
    • Meacham, C.E. & Morrison, S.J. Tumour heterogeneity and cancer cell plasticity. Nature 501, 328-337 (2013).
    • (2013) Nature , vol.501 , pp. 328-337
    • Meacham, C.E.1    Morrison, S.J.2
  • 18
    • 84856013431 scopus 로고    scopus 로고
    • Clonal evolution in cancer
    • Greaves, M. & Maley, C.C. Clonal evolution in cancer. Nature 481, 306-313 (2012).
    • (2012) Nature , vol.481 , pp. 306-313
    • Greaves, M.1    Maley, C.C.2
  • 19
    • 84942239424 scopus 로고    scopus 로고
    • Optimizing cancer genome sequencing and analysis
    • Griffith, M. et al. Optimizing cancer genome sequencing and analysis. Cell Syst. 1, 210-223 (2015).
    • (2015) Cell Syst. , vol.1 , pp. 210-223
    • Griffith, M.1
  • 20
    • 84860782006 scopus 로고    scopus 로고
    • Absolute quantification of somatic DNA alterations in human cancer
    • Carter, S.L. et al. Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol. 30, 413-421 (2012).
    • (2012) Nat. Biotechnol. , vol.30 , pp. 413-421
    • Carter, S.L.1
  • 21
    • 84949207578 scopus 로고    scopus 로고
    • Systematic pan-cancer analysis of tumour purity
    • Aran, D., Sirota, M. & Butte, A.J. Systematic pan-cancer analysis of tumour purity. Nat. Commun. 6, 8971 (2015).
    • (2015) Nat. Commun. , vol.6 , pp. 8971
    • Aran, D.1    Sirota, M.2    Butte, A.J.3
  • 22
    • 84863229597 scopus 로고    scopus 로고
    • VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
    • Koboldt, D.C. et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 22, 568-576 (2012).
    • (2012) Genome Res. , vol.22 , pp. 568-576
    • Koboldt, D.C.1
  • 23
    • 79954672317 scopus 로고    scopus 로고
    • Genome structural variation discovery and genotyping
    • Alkan, C., Coe, B.P. & Eichler, E.E. Genome structural variation discovery and genotyping. Nat. Rev. Genet. 12, 363-376 (2011).
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 363-376
    • Alkan, C.1    Coe, B.P.2    Eichler, E.E.3
  • 24
    • 84943453909 scopus 로고    scopus 로고
    • Human structural variation: Mechanisms of chromosome rearrangements
    • Weckselblatt, B. & Rudd, M.K. Human structural variation: mechanisms of chromosome rearrangements. Trends Genet. 31, 587-599 (2015).
    • (2015) Trends Genet. , vol.31 , pp. 587-599
    • Weckselblatt, B.1    Rudd, M.K.2
  • 25
    • 84893864009 scopus 로고    scopus 로고
    • Detection of structural DNA variation from next generation sequencing data: A review of informatic approaches
    • Abel, H.J., Duncavage, E.J. & Duncavage, E.J. Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches. Cancer Genet. 206, 432-440 (2013).
    • (2013) Cancer Genet. , vol.206 , pp. 432-440
    • Abel, H.J.1    Duncavage, E.J.2    Duncavage, E.J.3
  • 26
    • 84927128250 scopus 로고    scopus 로고
    • Whole-genome CNV analysis: Advances in computational approaches
    • Pirooznia, M., Goes, F.S. & Zandi, P.P. Whole-genome CNV analysis: advances in computational approaches. Front. Genet. 6, 138 (2015).
    • (2015) Front. Genet. , vol.6 , pp. 138
    • Pirooznia, M.1    Goes, F.S.2    Zandi, P.P.3
  • 27
    • 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
  • 28
    • 84912096454 scopus 로고    scopus 로고
    • LUMPY: A probabilistic framework for structural variant discovery
    • Layer, R.M., Chiang, C., Quinlan, A.R. & Hall, I.M. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 15, R84 (2014).
    • (2014) Genome Biol. , vol.15 , pp. R84
    • Layer, R.M.1    Chiang, C.2    Quinlan, A.R.3    Hall, I.M.4
  • 29
    • 70349318211 scopus 로고    scopus 로고
    • The impact of retrotransposons on human genome evolution
    • Cordaux, R. & Batzer, M.A. The impact of retrotransposons on human genome evolution. Nat. Rev. Genet. 10, 691-703 (2009).
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 691-703
    • Cordaux, R.1    Batzer, M.A.2
  • 31
    • 77949890563 scopus 로고    scopus 로고
    • Statistical issues in the analysis of DNA copy number variations
    • Wineinger, N.E. et al. Statistical issues in the analysis of DNA copy number variations. Int. J. Comput. Biol. Drug Des. 1, 368-395 (2008).
    • (2008) Int. J. Comput. Biol. Drug Des. , vol.1 , pp. 368-395
    • Wineinger, N.E.1
  • 32
    • 84984870706 scopus 로고    scopus 로고
    • The impact of amplification on differential expression analyses by RNA-seq. Preprint at
    • Parekh, S., Ziegenhain, C., Vieth, B., Enard, W. & Hellmann, I. The impact of amplification on differential expression analyses by RNA-seq. Preprint at bioRxiv http://dx.doi.org/10.1101/035493 (2015).
    • (2015) BioRxiv
    • Parekh, S.1    Ziegenhain, C.2    Vieth, B.3    Enard, W.4    Hellmann, I.5
  • 33
    • 67649370543 scopus 로고    scopus 로고
    • Limit of blank, limit of detection and limit of quantitation
    • Armbruster, D.A. & Pry, T. Limit of blank, limit of detection and limit of quantitation. Clin. Biochem. Rev. 29 (Suppl. 1), S49-S52 (2008).
    • (2008) Clin. Biochem. Rev. , vol.29 , pp. S49-S52
    • Armbruster, D.A.1    Pry, T.2
  • 34
    • 84923378112 scopus 로고    scopus 로고
    • Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans
    • Gibbons, J.G., Branco, A.T., Yu, S. & Lemos, B. Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans. Nat. Commun. 5, 4850 (2014).
    • (2014) Nat. Commun. , vol.5 , pp. 4850
    • Gibbons, J.G.1    Branco, A.T.2    Yu, S.3    Lemos, B.4
  • 35
    • 84887804054 scopus 로고    scopus 로고
    • Identification and characterization of EBV genomes in spontaneously immortalized human peripheral blood B lymphocytes by NGS technology
    • Lei, H. et al. Identification and characterization of EBV genomes in spontaneously immortalized human peripheral blood B lymphocytes by NGS technology. BMC Genomics 14, 804 (2013).
    • (2013) BMC Genomics , vol.14 , pp. 804
    • Lei, H.1
  • 36
    • 84874446626 scopus 로고    scopus 로고
    • Genome-wide analysis of macrosatellite repeat copy number variation in worldwide populations: Evidence for differences and commonalities in size distributions and size restrictions
    • Schaap, M. et al. Genome-wide analysis of macrosatellite repeat copy number variation in worldwide populations: evidence for differences and commonalities in size distributions and size restrictions. BMC Genomics 14, 143 (2013).
    • (2013) BMC Genomics , vol.14 , pp. 143
    • Schaap, M.1
  • 37
    • 84909644283 scopus 로고    scopus 로고
    • Normalization of RNA-seq data using factor analysis of control genes or samples
    • Risso, D., Ngai, J., Speed, T.P. & Dudoit, S. Normalization of RNA-seq data using factor analysis of control genes or samples. Nat. Biotechnol. 32, 896-902 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 896-902
    • Risso, D.1    Ngai, J.2    Speed, T.P.3    Dudoit, S.4
  • 38
    • 84887491073 scopus 로고    scopus 로고
    • Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing
    • Frampton, G.M. et al. Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing. Nat. Biotechnol. 31, 1023-1031 (2013).
    • (2013) Nat. Biotechnol. , vol.31 , pp. 1023-1031
    • Frampton, G.M.1
  • 39
    • 84981274155 scopus 로고    scopus 로고
    • Spliced synthetic genes as internal controls in RNA sequencing experiments
    • Hardwick, S.A. et al. Spliced synthetic genes as internal controls in RNA sequencing experiments. Nat. Methods http://dx.doi.org/10.1038/nmeth.3958 (2016).
    • (2016) Nat. Methods
    • Hardwick, S.A.1
  • 40
    • 84954055993 scopus 로고    scopus 로고
    • Analytical validation and application of a targeted next-generation sequencing mutation-detection assay for use in treatment assignment in the NCI-MPACT trial
    • Lih, C.J. et al. Analytical validation and application of a targeted next-generation sequencing mutation-detection assay for use in treatment assignment in the NCI-MPACT trial. J. Mol. Diagn. 18, 51-67 (2016).
    • (2016) J. Mol. Diagn. , vol.18 , pp. 51-67
    • Lih, C.J.1
  • 41
    • 80052521697 scopus 로고    scopus 로고
    • Synthetic spike-in standards for RNA-seq experiments
    • Jiang, L. et al. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 21, 1543-1551 (2011).
    • (2011) Genome Res. , vol.21 , pp. 1543-1551
    • Jiang, L.1
  • 43
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A.R. & Hall, I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 44
    • 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
  • 46
    • 79951970227 scopus 로고    scopus 로고
    • CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
    • Abyzov, A., Urban, A.E., Snyder, M. & Gerstein, M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 21, 974-984 (2011).
    • (2011) Genome Res. , vol.21 , pp. 974-984
    • Abyzov, A.1    Urban, A.E.2    Snyder, M.3    Gerstein, M.4


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