Visualizing tumor evolution with the fishplot package for R

BMC Genomics

Volumn 17, Issue 1, 2016, Pages

  Miller, Christopher A ^a   McMichael, Joshua ^a   Dang, Ha X ^a   Maher, Christopher A ^a   Ding, Li ^a   Ley, Timothy J ^a   Mardis, Elaine R ^a   Wilson, Richard K ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CANCER GENETICS; CANCER MORPHOLOGY; CANCER RESEARCH; CLONAL EVOLUTION; CLONE; FISHPLOT PACKAGE; HUMAN; MEASUREMENT ACCURACY; POWER ANALYSIS; PUBLICATION; SOFTWARE; SOFTWARE DESIGN; STRUCTURE ANALYSIS; TUMOR DIAGNOSIS; BIOLOGICAL MODEL; CARCINOGENESIS; GENOMICS; PROCEDURES; WEB BROWSER;

CARCINOGENESIS; GENOMICS; MODELS, BIOLOGICAL; SOFTWARE; WEB BROWSER;

EID: 84994462665     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-3195-z     Document Type: Article

References (12)

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2. 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;11:396-8.
3. Deshwar AG, Vembu S, Yung CK, Jang GH, Stein L, Morris Q. PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome Biol. 2015;16:35.
4. Oesper L, Mahmoody A, Raphael BJ. THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. Genome Biol. 2013;14:R80.
5. Qiao Y, Quinlan AR, Jazaeri AA, Verhaak RG, Wheeler DA, Marth GT. SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome Biol. 2014;15:443.
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7. 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.
8. Engle EK, Fisher DA, Miller CA, McLellan MD, Fulton RS, Moore DM, et al. Clonal evolution revealed by whole genome sequencing in a case of primary myelofibrosis transformed to secondary acute myeloid leukemia. Leukemia. 2014. doi: 10.1038/leu.2014.289.
9. Griffith M, Miller CA, Griffith OL, Krysiak K, Skidmore ZL, Ramu A, et al. Optimizing cancer genome sequencing and analysis. Cell Syst. 2015;1:210-23.
10. Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, et al. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature. 2014;512:155-60.
11. Lundberg P, Karow A, Nienhold R, Looser R, Hao-Shen H, Nissen I, et al. Clonal evolution and clinical correlates of somatic mutations in myeloproliferative neoplasms. Blood. 2014;123:2220-8.
12. Miller CA, Gindin Y, Lu C, Griffith OL, Griffith M, Shen D, et al. Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers. Nat Commun. 2016;7:12498.