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PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors

Amit G Deshwar, Shankar Vembu, Christina K Yung and 3 more

Genome Biology · 2015 · CC BY

doi:10.1186/s13059-015-0602-8

Abstract

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References 49

  1. 1.

    Nowell PC. The clonal evolution of tumor cell populations. Science. 1976;194:23-8.

    Not in our library10.1126/science.959840

  2. 2.

    Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. New Engl J Med. 2012;366:883-92.

    Not in our library10.1056/nejmoa1113205

  3. 3.
  4. 4.

    Hanahan D, Weinberg RA. The hallmarks of cancer. Cell. 2000;100:57-70.

    Not in our library10.1016/s0092-8674(00)81683-9

  5. 5.

    Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144:646-74.

    Not in our library10.1016/j.cell.2011.02.013

  6. 6.

    Aparicio S, Caldas C. The implications of clonal genome evolution for cancer medicine. New Engl J Med. 2013;368:842-51.

    Not in our library10.1056/nejmra1204892

  7. 7.

    Bedard PL, Hansen AR, Ratain MJ, Siu LL. Tumour heterogeneity in the clinic. Nature. 2013;501:355-64.

    Not in our library10.1038/nature12627

  8. 8.

    Mullighan CG, Phillips LA, Su X, Ma J, Miller CB, Shurtleff SA, et al. Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia. Science. 2008;322:1377-80.

    Not in our library10.1126/science.1164266

  9. 9.

    Navin NE, Hicks J. Tracing the tumor lineage. Mol Oncol. 2010;4:267-83.

    Not in our library10.1016/j.molonc.2010.04.010

  10. 10.

    Marusyk A, Polyak K. Tumor heterogeneity: causes and consequences. Biochimica et Biophysica Acta. 2010;1805:105-17.

    Not in our library10.1016/j.bbcan.2009.11.002

  11. 11.

    Schuh A, Becq J, Humphray S, Alexa A, Burns A, Clifford R, et al. Monitoring chronic lymphocytic leukemia progression by whole genome sequencing reveals heterogeneous clonal evolution patterns. Blood. 2012;120:4191-6.

    Not in our library10.1182/blood-2012-05-433540

  12. 12.

    Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature. 2012;486:617-56.

    Not in our library10.1038/nature10933

  13. 13.

    Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, et al. Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol. 2012;30:413-21.

    Not in our library10.1038/nbt.2203

  14. 14.

    Landau DA, Carter SL, Stojanov P, McKenna A, Stevenson K, Lawrence MS, et al. Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell. 2013;152:714-26.

    Not in our library10.1016/j.cell.2013.01.019

  15. 15.
  16. 16.

    Strino F, Parisi F, Micsinai M, Kluger Y. TrAp: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Res. 2013;41:e165.

    Not in our library10.1093/nar/gkt641

  17. 17.
  18. 18.

    Roth A, Khattra J, Yap D, Wan A, Laks E, Biele J, et al. PyClone: statistical inference of clonal population structure in cancer. Nat Methods. 2014;11:396-98.

    Not in our library10.1038/nmeth.2883

  19. 19.
  20. 20.

    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.

    Not in our library10.1371/journal.pone.0078143

  21. 21.

    Larson NB, Fridley BL. PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data. Bioinformatics. 2013;29:1888-9.

    Not in our library10.1093/bioinformatics/btt293

  22. 22.

    Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, Ellrott K, et al. The cancer genome atlas pan-cancer analysis project. Nat Genet. 2013;45:1113-20.

    Not in our library10.1038/ng.2764

  23. 23.

    Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012;481:506-10.

    Not in our library10.1038/nature10738

  24. 24.

    Carter SL, Cibulskis K, Helman E, McKenna A, Shen H, Zack T, et al. Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol. 2012;30:413-21.

    Not in our library10.1038/nbt.2203

  25. 25.

    Gusnanto A, Wood HM, Pawitan Y, Rabbitts P, Berri S. Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. Bioinformatics. 2012;28:40-7.

    Not in our library10.1093/bioinformatics/btr593

  26. 26.
  27. 27.

    Fischer A, Vázquez-García I, Illingworth CJ, Mustonen V. High-definition reconstruction of clonal composition in cancer. Cell Reports. 2014;7:1740-52.

    Not in our library10.1016/j.celrep.2014.04.055

  28. 28.

    PhyloWGS. https://github.com/morrislab/phylowgs.

    Not in our library

  29. 29.

    Behjati S, Huch M, van Boxtel R, Karthaus W, Wedge DC, Tamuri AU, et al. Genome sequencing of normal cells reveals developmental lineages and mutational processes. Nature. 2014;513:422-5.

    Not in our library10.1038/nature13448

  30. 30.

    Burrell RA, McGranahan N, Bartek J, Swanton C. The causes and consequences of genetic heterogeneity in cancer evolution. Nature. 2013;501:338-45.

    Not in our library10.1038/nature12625

  31. 31.

    Klein CA. Selection and adaptation during metastatic cancer progression. Nature. 2013;501:365-72.

    Not in our library10.1038/nature12628

  32. 32.
  33. 33.

    Hajirasouliha I, Mahmoody A, Raphael BJ. A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data. Bioinformatics. 2014;30:78-86.

    Not in our library10.1093/bioinformatics/btu284

  34. 34.

    Kimura M. The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. Genetics. 1969;61:893.

    Not in our library10.1093/genetics/61.4.893

  35. 35.

    Hudson RR. Properties of a neutral allele model with intragenic recombination. Theor Popul Biol. 1983;23:183-201.

    Not in our library10.1016/0040-5809(83)90013-8

  36. 36.

    Zare H, Wang J, Hu A, Weber K, Smith J, Nickerson D, et al. Inferring clonal composition from multiple sections of a breast cancer. PLoS Comput Biol. 2014;10:e1003703.

    Not in our library10.1371/journal.pcbi.1003703

  37. 37.

    Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, Lee E, Zhang J, et al. Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc Nat Acad Sci. 2011;108:E1128-36.

    Not in our library10.1073/pnas.1110574108

  38. 38.
  39. 39.

    Miller JW, Harrison MT. A simple example of Dirichlet process mixture inconsistency for the number of components. In: Advances in neural information processing systems. 2013:199–206.

    Not in our library

  40. 40.

    Davis J, Goadrich M. The relationship between precision–recall and ROC curves. In: Proceedings of the 23rd International Conference on Machine Learning: 2006. p. 233–40.

    Not in our library

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