메뉴 건너뛰기




Volumn 3, Issue 4, 2017, Pages

Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma

(26)  Wrzeszczynski, Kazimierz O a   Frank, Mayu O a,f   Koyama, Takahiko b   Rhrissorrakrai, Kahn b   Robine, Nicolas a   Utro, Filippo b   Emde, Anne Katrin a   Chen, Bo Juen a,h   Arora, Kanika a   Shah, Minita a   Vacic, Vladimir a,i   Norel, Raquel b   Bilal, Erhan b   Bergmann, Ewa A a,j   Moore Vogel, Julia L a   Bruce, Jeffrey N c   Lassman, Andrew B c   Canoll, Peter c   Grommes, Christian d   Harvey, Steve e   more..


Author keywords

[No Author keywords available]

Indexed keywords

BEVACIZUMAB; DNA; LOMUSTINE; RNA; TEMOZOLOMIDE;

EID: 85052665880     PISSN: None     EISSN: 23767839     Source Type: Journal    
DOI: 10.1212/NXG.0000000000000164     Document Type: Article
Times cited : (35)

References (41)
  • 2
    • 84942239424 scopus 로고    scopus 로고
    • Optimizing cancer genome sequencing and analysis
    • Griffith M, Miller CA, Griffith OL, et al. Optimizing cancer genome sequencing and analysis. Cell Syst 2015; 1: 210-223.
    • (2015) Cell Syst , vol.1 , pp. 210-223
    • Griffith, M.1    Miller, C.A.2    Griffith, O.L.3
  • 3
    • 84949536487 scopus 로고    scopus 로고
    • Precision medicine at Memorial Sloan Kettering Cancer Center: Clinical nextgeneration sequencing enabling next-generation targeted therapy trials
    • Hyman DM, Solit DB, Arcila ME, et al. Precision medicine at Memorial Sloan Kettering Cancer Center: clinical nextgeneration sequencing enabling next-generation targeted therapy trials. Drug Discov Today 2015; 20: 1422-1428.
    • (2015) Drug Discov Today , vol.20 , pp. 1422-1428
    • Hyman, D.M.1    Solit, D.B.2    Arcila, M.E.3
  • 4
    • 84885735554 scopus 로고    scopus 로고
    • Mutational landscape and significance across 12 major cancer types
    • Kandoth C, McLellan MD, Vandin F, et al. Mutational landscape and significance across 12 major cancer types. Nature 2013; 502: 333-339.
    • (2013) Nature , vol.502 , pp. 333-339
    • Kandoth, C.1    McLellan, M.D.2    Vandin, F.3
  • 5
    • 84885008220 scopus 로고    scopus 로고
    • Pan-cancer patterns of somatic copy number alteration
    • Zack TI, Schumacher SE, Carter SL, et al. Pan-cancer patterns of somatic copy number alteration. Nat Genet 2013; 45: 1134-1140.
    • (2013) Nat Genet , vol.45 , pp. 1134-1140
    • Zack, T.I.1    Schumacher, S.E.2    Carter, S.L.3
  • 6
    • 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 2009; 25: 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 7
    • 77956295988 scopus 로고    scopus 로고
    • The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
    • McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20: 1297-1303.
    • (2010) Genome Res , vol.20 , pp. 1297-1303
    • McKenna, A.1    Hanna, M.2    Banks, E.3
  • 8
    • 84874025843 scopus 로고    scopus 로고
    • Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
    • Cibulskis K, Lawrence MS, Carter SL, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 2013; 31: 213-219.
    • (2013) Nat Biotechnol , vol.31 , pp. 213-219
    • Cibulskis, K.1    Lawrence, M.S.2    Carter, S.L.3
  • 9
    • 84871227763 scopus 로고    scopus 로고
    • LoFreq: A sequencequality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-Throughput sequencing datasets
    • Wilm A, Aw PP, Bertrand D, et al. LoFreq: a sequencequality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-Throughput sequencing datasets. Nucleic Acids Res 2012; 40: 11189-11201.
    • (2012) Nucleic Acids Res , vol.40 , pp. 11189-11201
    • Wilm, A.1    Aw, P.P.2    Bertrand, D.3
  • 10
    • 84864153492 scopus 로고    scopus 로고
    • Strelka: Accurate somatic small-variant calling from sequenced tumor-normal sample pairs
    • Saunders CT, Wong WS, Swamy S, Becq J, Murray LJ, Cheetham RK. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics 2012; 28: 1811-1817.
    • (2012) Bioinformatics , vol.28 , pp. 1811-1817
    • Saunders, C.T.1    Wong, W.S.2    Swamy, S.3    Becq, J.4    Murray, L.J.5    Cheetham, R.K.6
  • 11
    • 70350694443 scopus 로고    scopus 로고
    • Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
    • Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009; 25: 2865-2871.
    • (2009) Bioinformatics , vol.25 , pp. 2865-2871
    • Ye, K.1    Schulz, M.H.2    Long, Q.3    Apweiler, R.4    Ning, Z.5
  • 12
    • 84921783122 scopus 로고    scopus 로고
    • Accurate de novo and transmitted indel detection in exome-capture data using microassembly
    • Narzisi G, O'Rawe JA, Iossifov I, et al. Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nat Methods 2014; 11: 1033-1036.
    • (2014) Nat Methods , vol.11 , pp. 1033-1036
    • Narzisi, G.1    O'Rawe, J.A.2    Iossifov, I.3
  • 13
    • 84862506964 scopus 로고    scopus 로고
    • A program for annotating and predicting the effects of single nucleotide polymorphisms SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; Iso-2; iso-3
    • Cingolani P, Platts A, Wang le L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 2012; 6: 80-92.
    • (2012) Fly (Austin , vol.6 , pp. 80-92
    • Cingolani, P.1    Platts, A.2    Wang Le, L.3
  • 15
    • 78651330430 scopus 로고    scopus 로고
    • COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
    • Forbes SA, Bindal N, Bamford S, et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 2011; 39: D945-D950.
    • (2011) Nucleic Acids Res , vol.39 , pp. D945-D950
    • Forbes, S.A.1    Bindal, N.2    Bamford, S.3
  • 16
    • 75849158230 scopus 로고    scopus 로고
    • The gene ontology in 2010 extensions and refinements
    • Gene Ontology C. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res 2010; 38: D331-D335.
    • (2010) Nucleic Acids Res , vol.38 , pp. D331-D335
    • Gene Ontology, C.1
  • 17
    • 84943171338 scopus 로고    scopus 로고
    • A global reference for human genetic variation
    • Genomes Project C, Auton A, Brooks LD, et al. A global reference for human genetic variation. Nature 2015; 526: 68-74.
    • (2015) Nature , vol.526 , pp. 68-74
    • Genomes Project, C.1    Auton, A.2    Brooks, L.D.3
  • 18
    • 81755172942 scopus 로고    scopus 로고
    • Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion
    • Xi R, Hadjipanayis AG, Luquette LJ, et al. Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc Natl Acad Sci USA 2011; 108: E1128-E1136.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. E1128-E1136
    • Xi, R.1    Hadjipanayis, A.G.2    Luquette, L.J.3
  • 19
    • 84866440781 scopus 로고    scopus 로고
    • DELLY: Structural variant discovery by integrated paired-end and split-read analysis
    • Rausch T, Zichner T, Schlattl A, Stutz AM, Benes V, Korbel JO. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 2012; 28: i333-i339.
    • (2012) Bioinformatics , vol.28 , pp. i333-i339
    • Rausch, T.1    Zichner, T.2    Schlattl, A.3    Stutz, A.M.4    Benes, V.5    Korbel, J.O.6
  • 20
    • 79961007031 scopus 로고    scopus 로고
    • CREST maps somatic structural variation in cancer genomes with basepair resolution
    • Wang J, Mullighan CG, Easton J, et al. CREST maps somatic structural variation in cancer genomes with basepair resolution. Nat Methods 2011; 8: 652-654.
    • (2011) Nat Methods , vol.8 , pp. 652-654
    • Wang, J.1    Mullighan, C.G.2    Easton, J.3
  • 21
    • 69549116107 scopus 로고    scopus 로고
    • BreakDancer: An algorithm for high-resolution mapping of genomic structural variation
    • Chen K, Wallis JW, McLellan MD, et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 2009; 6: 677-681.
    • (2009) Nat Methods , vol.6 , pp. 677-681
    • Chen, K.1    Wallis, J.W.2    McLellan, M.D.3
  • 22
    • 84857810661 scopus 로고    scopus 로고
    • Detecting genomic indel variants with exact breakpoints in single- and pairedend sequencing data using SplazerS
    • Emde AK, Schulz MH, Weese D, et al. Detecting genomic indel variants with exact breakpoints in single- And pairedend sequencing data using SplazerS. Bioinformatics 2012; 28: 619-627.
    • (2012) Bioinformatics , vol.28 , pp. 619-627
    • Emde, A.K.1    Schulz, M.H.2    Weese, D.3
  • 23
    • 84924336542 scopus 로고    scopus 로고
    • TITAN: Inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
    • Ha G, Roth A, Khattra J, et al. TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. Genome Res 2014; 24: 1881-1893.
    • (2014) Genome Res , vol.24 , pp. 1881-1893
    • Ha, G.1    Roth, A.2    Khattra, J.3
  • 25
    • 84871809302 scopus 로고    scopus 로고
    • STAR ultrafast universal RNA-seq aligner
    • Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013; 29: 15-21.
    • (2013) Bioinformatics , vol.29 , pp. 15-21
    • Dobin, A.1    Davis, C.A.2    Schlesinger, F.3
  • 26
    • 84897397058 scopus 로고    scopus 로고
    • FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features
    • Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 2014; 30: 923-930.
    • (2014) Bioinformatics , vol.30 , pp. 923-930
    • Liao, Y.1    Smyth, G.K.2    Shi, W.3
  • 28
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007; 8: 118-127.
    • (2007) Biostatistics , vol.8 , pp. 118-127
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 29
    • 73649123907 scopus 로고    scopus 로고
    • Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1
    • Verhaak RG, Hoadley KA, Purdom E, et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 2010; 17: 98-110.
    • (2010) Cancer Cell , vol.17 , pp. 98-110
    • Verhaak, R.G.1    Hoadley, K.A.2    Purdom, E.3
  • 31
    • 84979609922 scopus 로고    scopus 로고
    • Watson for genomics: Moving personalized medicine forward
    • Rhrissorrakrai K, Koyama T, Parida L. Watson for genomics: moving personalized medicine forward. Trends Cancer 2016; 2: 392-395.
    • (2016) Trends Cancer , vol.2 , pp. 392-395
    • Rhrissorrakrai, K.1    Koyama, T.2    Parida, L.3
  • 32
    • 84928761118 scopus 로고    scopus 로고
    • Cancer immunology: Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer
    • Rizvi NA, Hellmann MD, Snyder A, et al. Cancer immunology: mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 2015; 348: 124-128.
    • (2015) Science , vol.348 , pp. 124-128
    • Rizvi, N.A.1    Hellmann, M.D.2    Snyder, A.3
  • 33
    • 84938805958 scopus 로고    scopus 로고
    • Activation of MET via diverse exon 14 splicing alterations occurs in multiple tumor types and confers clinical sensitivity to MET inhibitors
    • Frampton GM, Ali SM, Rosenzweig M, et al. Activation of MET via diverse exon 14 splicing alterations occurs in multiple tumor types and confers clinical sensitivity to MET inhibitors. Cancer Discov 2015; 5: 850-859.
    • (2015) Cancer Discov , vol.5 , pp. 850-859
    • Frampton, G.M.1    Ali, S.M.2    Rosenzweig, M.3
  • 34
    • 84931004978 scopus 로고    scopus 로고
    • Identification of a novel MET mutation in high-grade glioma resulting in an auto-Active intracellular protein
    • Navis AC, van Lith SA, van Duijnhoven SM, et al. Identification of a novel MET mutation in high-grade glioma resulting in an auto-Active intracellular protein. Acta Neuropathol 2015; 130: 131-144.
    • (2015) Acta Neuropathol , vol.130 , pp. 131-144
    • Navis, A.C.1    Van Lith, S.A.2    Van Duijnhoven, S.M.3
  • 35
    • 79952113796 scopus 로고    scopus 로고
    • The regulation of class IA PI 3-kinases by inter-subunit interactions
    • Backer JM. The regulation of class IA PI 3-kinases by inter-subunit interactions. Curr Top Microbiol Immunol 2010; 346: 87-114.
    • (2010) Curr Top Microbiol Immunol , vol.346 , pp. 87-114
    • Backer, J.M.1
  • 36
    • 70749140937 scopus 로고    scopus 로고
    • Somatic mutations in p85alpha promote tumorigenesis through class IA PI3K activation
    • Jaiswal BS, Janakiraman V, Kljavin NM, et al. Somatic mutations in p85alpha promote tumorigenesis through class IA PI3K activation. Cancer Cell 2009; 16: 463-474.
    • (2009) Cancer Cell , vol.16 , pp. 463-474
    • Jaiswal, B.S.1    Janakiraman, V.2    Kljavin, N.M.3
  • 37
    • 84962609567 scopus 로고    scopus 로고
    • Next-generation sequencing of pulmonary sarcomatoid carcinoma reveals high frequency of actionable MET gene mutations
    • Liu X, Jia Y, Stoopler MB, et al. Next-generation sequencing of pulmonary sarcomatoid carcinoma reveals high frequency of actionable MET gene mutations. J Clin Oncol 2016; 34: 794-802.
    • (2016) J Clin Oncol , vol.34 , pp. 794-802
    • Liu, X.1    Jia, Y.2    Stoopler, M.B.3
  • 38
    • 35348908314 scopus 로고    scopus 로고
    • PTEN loss of expression predicts cetuximab efficacy in metastatic colorectal cancer patients
    • Frattini M, Saletti P, Romagnani E, et al. PTEN loss of expression predicts cetuximab efficacy in metastatic colorectal cancer patients. Br J Cancer 2007; 97: 1139-1145.
    • (2007) Br J Cancer , vol.97 , pp. 1139-1145
    • Frattini, M.1    Saletti, P.2    Romagnani, E.3
  • 39
    • 84928248330 scopus 로고    scopus 로고
    • Personalized genomic analyses for cancer mutation discovery and interpretation
    • 283ra253
    • Jones S, Anagnostou V, Lytle K, et al. Personalized genomic analyses for cancer mutation discovery and interpretation. Sci Transl Med 2015; 7: 283ra253.
    • (2015) Sci Transl Med , vol.7
    • Jones, S.1    Anagnostou, V.2    Lytle, K.3
  • 40
    • 84928528797 scopus 로고    scopus 로고
    • Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants
    • Belkadi A, Bolze A, Itan Y, et al. Whole-genome sequencing is more powerful than whole-exome sequencing for detecting exome variants. Proc Natl Acad Sci USA 2015; 112: 5473-5478.
    • (2015) Proc Natl Acad Sci USA , vol.112 , pp. 5473-5478
    • Belkadi, A.1    Bolze, A.2    Itan, Y.3
  • 41
    • 84954403183 scopus 로고    scopus 로고
    • Genome sequencing of autism-Affected families reveals disruption of putative noncoding regulatory DNA
    • Turner TN, Hormozdiari F, Duyzend MH, et al. Genome sequencing of autism-Affected families reveals disruption of putative noncoding regulatory DNA. Am J Hum Genet 2016; 98: 58-74.
    • (2016) Am J Hum Genet , vol.98 , pp. 58-74
    • Turner, T.N.1    Hormozdiari, F.2    Duyzend, M.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.