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Volumn 7, Issue 5, 2014, Pages 1740-1752

High-definition reconstruction of clonal composition in cancer

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; ARTICLE; BREAST CANCER; CANCER GROWTH; CHRONIC LYMPHATIC LEUKEMIA; CLONAL EVOLUTION; CLONE HIGH DEFINITION; CONTROLLED STUDY; DISEASE COURSE; GENE DOSAGE; GENETIC HETEROGENEITY; GERMLINE MUTATION; HETEROZYGOTE; HIGH THROUGHPUT SEQUENCING; HUMAN; PRIORITY JOURNAL; QUALITY CONTROL; SINGLE NUCLEOTIDE POLYMORPHISM; SOMATIC MUTATION; SYSTEM ANALYSIS; CANCER GENETICS; CLONAL VARIATION; CLONEHD ALGORITHM; COPY NUMBER VARIATION; DNA SEQUENCE; FUZZY SYSTEM; GENE FREQUENCY; GENETIC ALGORITHM; GENOTYPE; MALIGNANT NEOPLASTIC DISEASE; PATIENT MONITORING;

EID: 84902315822     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2014.04.055     Document Type: Article
Times cited : (137)

References (51)
  • 2
    • 84882837534 scopus 로고    scopus 로고
    • Signatures of mutational processes in human cancer
    • Australian Pancreatic Cancer Genome Initiative, ICGC Breast Cancer ConsortiumICGC Breast Cancer Consortium, ICGC MMML-Seq ConsortiumICGC MMML-Seq Consortium, ICGC PedBrainICGC PedBrain
    • Alexandrov L.B., Nik-Zainal S., Wedge D.C., Aparicio S.A.J.R., Behjati S., Biankin A.V., Bignell G.R., Bolli N., Borg Å., Børresen-Dale A.-L., et al. Signatures of mutational processes in human cancer. Nature 2013, 500:415-421. Australian Pancreatic Cancer Genome Initiative, ICGC Breast Cancer ConsortiumICGC Breast Cancer Consortium, ICGC MMML-Seq ConsortiumICGC MMML-Seq Consortium, ICGC PedBrainICGC PedBrain.
    • (2013) Nature , vol.500 , pp. 415-421
    • Alexandrov, L.B.1    Nik-Zainal, S.2    Wedge, D.C.3    Aparicio, S.A.J.R.4    Behjati, S.5    Biankin, A.V.6    Bignell, G.R.7    Bolli, N.8    Borg, Å.9    Børresen-Dale, A.-L.10
  • 4
    • 84878900455 scopus 로고    scopus 로고
    • Clinical application of targeted and genome-wide technologies: can we predict treatment responses in chronic lymphocytic leukemia?
    • Alsolami R., Knight S.J., Schuh A. Clinical application of targeted and genome-wide technologies: can we predict treatment responses in chronic lymphocytic leukemia?. Per. Med. 2013, 10:361-376.
    • (2013) Per. Med. , vol.10 , pp. 361-376
    • Alsolami, R.1    Knight, S.J.2    Schuh, A.3
  • 5
    • 84874354257 scopus 로고    scopus 로고
    • The implications of clonal genome evolution for cancer medicine
    • Aparicio S., Caldas C. The implications of clonal genome evolution for cancer medicine. N.Engl. J. Med. 2013, 368:842-851.
    • (2013) N.Engl. J. Med. , vol.368 , pp. 842-851
    • Aparicio, S.1    Caldas, C.2
  • 8
    • 84861904282 scopus 로고    scopus 로고
    • Dynamics of targeted cancer therapy
    • Bozic I., Allen B., Nowak M.A. Dynamics of targeted cancer therapy. Trends Mol. Med. 2012, 18:311-316.
    • (2012) Trends Mol. Med. , vol.18 , pp. 311-316
    • Bozic, I.1    Allen, B.2    Nowak, M.A.3
  • 10
    • 84884365015 scopus 로고    scopus 로고
    • The causes and consequences of genetic heterogeneity in cancer evolution
    • Burrell R.A., McGranahan N., Bartek J., Swanton C. The causes and consequences of genetic heterogeneity in cancer evolution. Nature 2013, 501:338-345.
    • (2013) Nature , vol.501 , pp. 338-345
    • Burrell, R.A.1    McGranahan, N.2    Bartek, J.3    Swanton, C.4
  • 12
    • 84893165480 scopus 로고    scopus 로고
    • SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing data
    • Chen M., Gunel M., Zhao H. SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing data. PLoS ONE 2013, 8:e78143.
    • (2013) PLoS ONE , vol.8
    • Chen, M.1    Gunel, M.2    Zhao, H.3
  • 13
    • 84876786068 scopus 로고    scopus 로고
    • EMu: probabilistic inference of mutational processes and their localization in the cancer genome
    • Fischer A., Illingworth C.J., Campbell P.J., Mustonen V. EMu: probabilistic inference of mutational processes and their localization in the cancer genome. Genome Biol. 2013, 14:R39.
    • (2013) Genome Biol. , vol.14
    • Fischer, A.1    Illingworth, C.J.2    Campbell, P.J.3    Mustonen, V.4
  • 14
    • 84875758730 scopus 로고    scopus 로고
    • Lessons from the cancer genome
    • Garraway L.A., Lander E.S. Lessons from the cancer genome. Cell 2013, 153:17-37.
    • (2013) Cell , vol.153 , pp. 17-37
    • Garraway, L.A.1    Lander, E.S.2
  • 16
    • 84881396090 scopus 로고    scopus 로고
    • Computational approaches to identify functional genetic variants in cancer genomes
    • International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group
    • Gonzalez-Perez A., Mustonen V., Reva B., Ritchie G.R.S., Creixell P., Karchin R., Vazquez M., Fink J.L., Kassahn K.S., Pearson J.V., et al. Computational approaches to identify functional genetic variants in cancer genomes. Nat. Methods 2013, 10:723-729. International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group.
    • (2013) Nat. Methods , vol.10 , pp. 723-729
    • Gonzalez-Perez, A.1    Mustonen, V.2    Reva, B.3    Ritchie, G.R.S.4    Creixell, P.5    Karchin, R.6    Vazquez, M.7    Fink, J.L.8    Kassahn, K.S.9    Pearson, J.V.10
  • 17
    • 84856013431 scopus 로고    scopus 로고
    • Clonal evolution in cancer
    • Greaves M., Maley C.C. Clonal evolution in cancer. Nature 2012, 481:306-313.
    • (2012) Nature , vol.481 , pp. 306-313
    • Greaves, M.1    Maley, C.C.2
  • 19
    • 84867164956 scopus 로고    scopus 로고
    • Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
    • Ha G., Roth A., Lai D., Bashashati A., Ding J., Goya R., Giuliany R., Rosner J., Oloumi A., Shumansky K., et al. Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer. Genome Res. 2012, 22:1995-2007.
    • (2012) Genome Res. , vol.22 , pp. 1995-2007
    • Ha, G.1    Roth, A.2    Lai, D.3    Bashashati, A.4    Ding, J.5    Goya, R.6    Giuliany, R.7    Rosner, J.8    Oloumi, A.9    Shumansky, K.10
  • 22
    • 84893164721 scopus 로고    scopus 로고
    • Inferring clonal evolution of tumors from single nucleotide somatic mutations
    • Jiao W., Vembu S., Deshwar A.G., Stein L., Morris Q. Inferring clonal evolution of tumors from single nucleotide somatic mutations. BMC Bioinformatics 2014, 15:35.
    • (2014) BMC Bioinformatics , vol.15 , pp. 35
    • Jiao, W.1    Vembu, S.2    Deshwar, A.G.3    Stein, L.4    Morris, Q.5
  • 23
    • 85024429815 scopus 로고
    • A new approach to linear filtering and prediction problems
    • Kalman R.E. A new approach to linear filtering and prediction problems. J.Basic Eng. 1960, 82:35-45.
    • (1960) J.Basic Eng. , vol.82 , pp. 35-45
    • Kalman, R.E.1
  • 26
    • 84880560760 scopus 로고    scopus 로고
    • PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data
    • Larson N.B., Fridley B.L. PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data. Bioinformatics 2013, 29:1888-1889.
    • (2013) Bioinformatics , vol.29 , pp. 1888-1889
    • Larson, N.B.1    Fridley, B.L.2
  • 28
    • 79960268207 scopus 로고    scopus 로고
    • GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays
    • Li A., Liu Z., Lezon-Geyda K., Sarkar S., Lannin D., Schulz V., Krop I., Winer E., Harris L., Tuck D. GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays. Nucleic Acids Res. 2011, 39:4928-4941.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 4928-4941
    • Li, A.1    Liu, Z.2    Lezon-Geyda, K.3    Sarkar, S.4    Lannin, D.5    Schulz, V.6    Krop, I.7    Winer, E.8    Harris, L.9    Tuck, D.10
  • 29
    • 84891351800 scopus 로고    scopus 로고
    • Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures
    • Lieberman T.D., Flett K.B., Yelin I., Martin T.R., McAdam A.J., Priebe G.P., Kishony R. Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures. Nat. Genet. 2014, 46:82-87.
    • (2014) Nat. Genet. , vol.46 , pp. 82-87
    • Lieberman, T.D.1    Flett, K.B.2    Yelin, I.3    Martin, T.R.4    McAdam, A.J.5    Priebe, G.P.6    Kishony, R.7
  • 30
    • 77956207880 scopus 로고    scopus 로고
    • MixHMM: inferring copy number variation and allelic imbalance using SNP arrays and tumor samples mixed with stromal cells
    • Liu Z., Li A., Schulz V., Chen M., Tuck D. MixHMM: inferring copy number variation and allelic imbalance using SNP arrays and tumor samples mixed with stromal cells. PLoS ONE 2010, 5:e10909.
    • (2010) PLoS ONE , vol.5
    • Liu, Z.1    Li, A.2    Schulz, V.3    Chen, M.4    Tuck, D.5
  • 31
    • 77955405475 scopus 로고    scopus 로고
    • Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
    • McLaren W., Pritchard B., Rios D., Chen Y., Flicek P., Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 2010, 26:2069-2070.
    • (2010) Bioinformatics , vol.26 , pp. 2069-2070
    • McLaren, W.1    Pritchard, B.2    Rios, D.3    Chen, Y.4    Flicek, P.5    Cunningham, F.6
  • 32
    • 84864751097 scopus 로고    scopus 로고
    • Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data
    • Mosén-Ansorena D., Aransay A.M., Rodríguez-Ezpeleta N. Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data. BMC Bioinformatics 2012, 13:192.
    • (2012) BMC Bioinformatics , vol.13 , pp. 192
    • Mosén-Ansorena, D.1    Aransay, A.M.2    Rodríguez-Ezpeleta, N.3
  • 36
    • 84880934918 scopus 로고    scopus 로고
    • THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data
    • Oesper L., Mahmoody A., Raphael B.J. THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. Genome Biol. 2013, 14:R80.
    • (2013) Genome Biol. , vol.14
    • Oesper, L.1    Mahmoody, A.2    Raphael, B.J.3
  • 40
    • 84869753284 scopus 로고    scopus 로고
    • Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns
    • Schuh A., Becq J., Humphray S., Alexa A., Burns A., Clifford R., Feller S.M., Grocock R., Henderson S., Khrebtukova I., et al. Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns. Blood 2012, 120:4191-4196.
    • (2012) Blood , vol.120 , pp. 4191-4196
    • Schuh, A.1    Becq, J.2    Humphray, S.3    Alexa, A.4    Burns, A.5    Clifford, R.6    Feller, S.M.7    Grocock, R.8    Henderson, S.9    Khrebtukova, I.10
  • 42
    • 84882455458 scopus 로고    scopus 로고
    • Single-cell sequencing-based technologies will revolutionize whole-organism science
    • Shapiro E., Biezuner T., Linnarsson S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat. Rev. Genet. 2013, 14:618-630.
    • (2013) Nat. Rev. Genet. , vol.14 , pp. 618-630
    • Shapiro, E.1    Biezuner, T.2    Linnarsson, S.3
  • 45
    • 84865558202 scopus 로고    scopus 로고
    • PurityEst: estimating purity of human tumor samples using next-generation sequencing data
    • Su X., Zhang L., Zhang J., Meric-Bernstam F., Weinstein J.N. PurityEst: estimating purity of human tumor samples using next-generation sequencing data. Bioinformatics 2012, 28:2265-2266.
    • (2012) Bioinformatics , vol.28 , pp. 2265-2266
    • Su, X.1    Zhang, L.2    Zhang, J.3    Meric-Bernstam, F.4    Weinstein, J.N.5
  • 49
    • 38049160116 scopus 로고    scopus 로고
    • Competitive release and facilitation of drug-resistant parasites after therapeutic chemotherapy in a rodent malaria model
    • Wargo A.R., Huijben S., de Roode J.C., Shepherd J., Read A.F. Competitive release and facilitation of drug-resistant parasites after therapeutic chemotherapy in a rodent malaria model. Proc. Natl. Acad. Sci. USA 2007, 104:19914-19919.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 19914-19919
    • Wargo, A.R.1    Huijben, S.2    de Roode, J.C.3    Shepherd, J.4    Read, A.F.5
  • 50
    • 84880063629 scopus 로고    scopus 로고
    • From human genome to cancer genome: the first decade
    • Wheeler D.A., Wang L. From human genome to cancer genome: the first decade. Genome Res. 2013, 23:1054-1062.
    • (2013) Genome Res. , vol.23 , pp. 1054-1062
    • Wheeler, D.A.1    Wang, L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.