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Volumn 11, Issue 10, 2014, Pages 1071-1075

SeqControl: Process control for DNA sequencing

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BLOOD SAMPLING; CLINICAL ARTICLE; COMPUTER PREDICTION; CONTROLLED STUDY; DNA EXTRACTION; DNA LIBRARY; DNA SEQUENCE; EXPERIMENTAL DESIGN; GENE FREQUENCY; GENOTYPE; HUMAN; HUMAN GENOME; HUMAN TISSUE; PRIORITY JOURNAL; PROCESS CONTROL; PROSTATE CANCER; RANDOM FOREST; SEQCONTROL; SEQUENCE ALIGNMENT; TUMOR MODEL; ALGORITHM; AREA UNDER THE CURVE; BIOLOGY; COMPUTER PROGRAM; GENOME; MALE; METABOLISM; MULTIVARIATE ANALYSIS; PROCEDURES; PROSTATE TUMOR; QUALITY CONTROL; STATISTICAL MODEL;

EID: 84921758024     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.3094     Document Type: Article
Times cited : (8)

References (37)
  • 1
    • 84975742565 scopus 로고    scopus 로고
    • The 1000 genomes project consortium. a map of human genome variation from population-scale sequencing
    • The 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
    • 84867331947 scopus 로고    scopus 로고
    • A high-coverage genome sequence from an archaic Denisovan individual
    • Meyer, M. et al. A high-coverage genome sequence from an archaic Denisovan individual. Science 338, 222-226 (2012).
    • (2012) Science , vol.338 , pp. 222-226
    • Meyer, M.1
  • 3
    • 84864576715 scopus 로고    scopus 로고
    • Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers
    • Lachance, J. et al. Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers. Cell 150, 457-469 (2012).
    • (2012) Cell , vol.150 , pp. 457-469
    • Lachance, J.1
  • 4
    • 84862980012 scopus 로고    scopus 로고
    • The bonobo genome compared with the chimpanzee and human genomes
    • Prüfer, K. et al. The bonobo genome compared with the chimpanzee and human genomes. Nature 486, 527-531 (2012).
    • (2012) Nature , vol.486 , pp. 527-531
    • Prüfer, K.1
  • 5
    • 84867875610 scopus 로고    scopus 로고
    • A map of rice genome variation reveals the origin of cultivated rice
    • Huang, X. et al. A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497-501 (2012).
    • (2012) Nature , vol.490 , pp. 497-501
    • Huang, X.1
  • 6
    • 84869003221 scopus 로고    scopus 로고
    • Analyses of pig genomes provide insight into porcine demography and evolution
    • Groenen, M.A.M. et al. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491, 393-398 (2012).
    • (2012) Nature , vol.491 , pp. 393-398
    • Groenen, M.A.M.1
  • 7
    • 84864696893 scopus 로고    scopus 로고
    • The banana (Musa acuminata) genome and the evolution of monocotyledonous plants
    • D'Hont, A. et al. The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature 488, 213-217 (2012).
    • (2012) Nature , vol.488 , pp. 213-217
    • D'hont, A.1
  • 8
    • 58449137410 scopus 로고    scopus 로고
    • The Sorghum bicolor genome and the diversification of grasses
    • Paterson, A.H. et al. The Sorghum bicolor genome and the diversification of grasses. Nature 457, 551-556 (2009).
    • (2009) Nature , vol.457 , pp. 551-556
    • Paterson, A.H.1
  • 9
    • 84863954202 scopus 로고    scopus 로고
    • Non-invasive prenatal measurement of the fetal genome
    • Fan, H.C. et al. Non-invasive prenatal measurement of the fetal genome. Nature 487, 320-324 (2012).
    • (2012) Nature , vol.487 , pp. 320-324
    • Fan, H.C.1
  • 10
    • 84862647180 scopus 로고    scopus 로고
    • Three-dimensional structures of membrane proteins from genomic sequencing
    • Hopf, T.A. et al. Three-dimensional structures of membrane proteins from genomic sequencing. Cell 149, 1607-1621 (2012).
    • (2012) Cell , vol.149 , pp. 1607-1621
    • Hopf, T.A.1
  • 11
    • 84863922124 scopus 로고    scopus 로고
    • Comprehensive molecular characterization of human colon and rectal cancer
    • Cancer Genome Atlas Network.
    • Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330-337 (2012).
    • (2012) Nature , vol.487 , pp. 330-337
  • 12
    • 84866434919 scopus 로고    scopus 로고
    • Genomic landscape of non-small cell lung cancer in smokers and never-smokers
    • Govindan, R. et al. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell 150, 1121-1134 (2012).
    • (2012) Cell , vol.150 , pp. 1121-1134
    • Govindan, R.1
  • 13
    • 77950475726 scopus 로고    scopus 로고
    • Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy
    • Lupski, J.R. et al. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N. Engl. J. Med. 362, 1181-1191 (2010).
    • (2010) N. Engl. J. Med. , vol.362 , pp. 1181-1191
    • Lupski, J.R.1
  • 14
    • 84862605504 scopus 로고    scopus 로고
    • Use of next-generation sequencing and other whole-genome strategies to dissect neurological disease
    • Bras, J., Guerreiro, R. & Hardy, J. Use of next-generation sequencing and other whole-genome strategies to dissect neurological disease. Nat. Rev. Neurosci. 13, 453-464 (2012).
    • (2012) Nat. Rev. Neurosci. , vol.13 , pp. 453-464
    • Bras, J.1    Guerreiro, R.2    Hardy, J.3
  • 15
    • 84873093569 scopus 로고    scopus 로고
    • Feasibility of real time next generation sequencing of cancer genes linked to drug response: Results from a clinical trial
    • Tran, B. et al. Feasibility of real time next generation sequencing of cancer genes linked to drug response: results from a clinical trial. Int. J. Cancer 132, 1547-1555 (2013).
    • (2013) Int. J. Cancer , vol.132 , pp. 1547-1555
    • Tran, B.1
  • 16
    • 84865833740 scopus 로고    scopus 로고
    • High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing
    • Wagle, N. et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov. 2, 82-93 (2012).
    • (2012) Cancer Discov. , vol.2 , pp. 82-93
    • Wagle, N.1
  • 17
    • 84893473154 scopus 로고    scopus 로고
    • Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations
    • Fu, G.K. et al. Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations. Proc. Natl. Acad. Sci. USA 111, 1891-1896 (2014).
    • (2014) Proc. Natl. Acad. Sci. USA , vol.111 , pp. 1891-1896
    • Fu, G.K.1
  • 18
    • 80054757012 scopus 로고    scopus 로고
    • Performance comparison of exome DNA sequencing technologies
    • Clark, M.J. et al. Performance comparison of exome DNA sequencing technologies. Nat. Biotechnol. 29, 908-914 (2011).
    • (2011) Nat. Biotechnol. , vol.29 , pp. 908-914
    • Clark, M.J.1
  • 19
    • 77954139210 scopus 로고    scopus 로고
    • Incorporating sequence quality data into alignment improves DNA read mapping
    • Frith, M.C., Wan, R. & Horton, P. Incorporating sequence quality data into alignment improves DNA read mapping. Nucleic Acids Res. 38, e100 (2010).
    • (2010) Nucleic Acids Res. , vol.38 , pp. e100
    • Frith, M.C.1    Wan, R.2    Horton, P.3
  • 21
    • 84866461485 scopus 로고    scopus 로고
    • Accurate estimation of short read mapping quality for next-generation genome sequencing
    • Ruffalo, M., Koyutürk, M., Ray, S. & LaFramboise, T. Accurate estimation of short read mapping quality for next-generation genome sequencing. Bioinformatics 28, i349-i355 (2012).
    • (2012) Bioinformatics , vol.28 , pp. i349-i355
    • Ruffalo, M.1    Koyutürk, M.2    Ray, S.3    Laframboise, T.4
  • 22
    • 84866554191 scopus 로고    scopus 로고
    • ESTclean: A cleaning tool for next-gen transcriptome shotgun sequencing
    • Tae, H., Ryu, D., Sureshchandra, S. & Choi, J.-H. ESTclean: A cleaning tool for next-gen transcriptome shotgun sequencing. BMC Bioinformatics 13, 247 (2012).
    • (2012) BMC Bioinformatics , vol.13 , pp. 247
    • Tae, H.1    Ryu, D.2    Sureshchandra, S.3    Choi, J.-H.4
  • 23
    • 84875700725 scopus 로고    scopus 로고
    • Predicting the molecular complexity of sequencing libraries
    • Daley, T. & Smith, A.D. Predicting the molecular complexity of sequencing libraries. Nat. Methods 10, 325-327 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 325-327
    • Daley, T.1    Smith, A.D.2
  • 24
    • 0034812285 scopus 로고    scopus 로고
    • Unlocking the archive-gene expression in paraffin-embedded tissue
    • Lewis, F., Maughan, N.J., Smith, V., Hillan, K. & Quirke, P. Unlocking the archive-gene expression in paraffin-embedded tissue. J. Pathol. 195, 66-71 (2001).
    • (2001) J. Pathol. , vol.195 , pp. 66-71
    • Lewis, F.1    Maughan, N.J.2    Smith, V.3    Hillan, K.4    Quirke, P.5
  • 25
    • 0035710433 scopus 로고    scopus 로고
    • Real-time PCR analysis of DNA and RNA extracted from formalin-fixed and paraffin-embedded biopsies
    • Lehmann, U. & Kreipe, H. Real-time PCR analysis of DNA and RNA extracted from formalin-fixed and paraffin-embedded biopsies. Methods 25, 409-418 (2001).
    • (2001) Methods , vol.25 , pp. 409-418
    • Lehmann, U.1    Kreipe, H.2
  • 26
    • 77951115122 scopus 로고    scopus 로고
    • International network of cancer genome projects
    • International Cancer Genome Consortium.
    • International Cancer Genome Consortium. International network of cancer genome projects. Nature 464, 993-998 (2010).
    • (2010) Nature , vol.464 , pp. 993-998
  • 27
    • 0000506838 scopus 로고
    • Tests for rank correlation coefficients. i
    • Fieller, E.C., Hartley, H.O. & Pearson, E.S. Tests for rank correlation coefficients. I. Biometrika 44, 470-481 (1957).
    • (1957) Biometrika , vol.44 , pp. 470-481
    • Fieller, E.C.1    Hartley, H.O.2    Pearson, E.S.3
  • 28
    • 0035478854 scopus 로고    scopus 로고
    • Random forests
    • Breiman, L. Random forests. Mach. Learn. 45, 5-32 (2001).
    • (2001) Mach. Learn. , vol.45 , pp. 5-32
    • Breiman, L.1
  • 29
    • 84861550476 scopus 로고    scopus 로고
    • The life history of 21 breast cancers
    • Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994-1007 (2012).
    • (2012) Cell , vol.149 , pp. 994-1007
    • Nik-Zainal, S.1
  • 30
    • 78751683468 scopus 로고    scopus 로고
    • Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: Large scale validity study
    • Chiu, R.W.K. et al. Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. Br. Med. J. 342, c7401 (2011).
    • (2011) Br. Med. J. , vol.342 , pp. c7401
    • Chiu, R.W.K.1
  • 31
    • 84861746437 scopus 로고    scopus 로고
    • Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA
    • Forshew, T. et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci. Transl. Med. 4, 136ra68 (2012).
    • (2012) Sci. Transl. Med. , vol.4 , pp. 136ra68
    • Forshew, T.1
  • 33
    • 84866700697 scopus 로고    scopus 로고
    • Qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles
    • Song, S. et al. qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles. PLoS ONE 7, e45835 (2012).
    • (2012) PLoS ONE , vol.7 , pp. e45835
    • Song, S.1
  • 34
    • 78650762588 scopus 로고    scopus 로고
    • A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries
    • Fisher, S. et al. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol. 12, R1 (2011).
    • (2011) Genome Biol. , vol.12 , pp. R1
    • Fisher, S.1
  • 35
    • 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
  • 36
    • 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
  • 37
    • 79952709519 scopus 로고    scopus 로고
    • PROC: An open-source package for R and S+ to analyze and compare ROC curves
    • Robin, X. et al. pROC: An open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinformatics 12, 77 (2011).
    • (2011) BMC Bioinformatics , vol.12 , pp. 77
    • Robin, X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.