ClonEvol: Clonal ordering and visualization in cancer sequencing

Annals of Oncology

Volumn 28, Issue 12, 2017, Pages 3076-3082

  Dang, H X ^a   White, B S ^a,d   Foltz, S M ^a   Miller, C A ^a   Luo, J ^a,b   Fields, R C ^a,b   Maher, C A ^a,b,c  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b USA   (United States)

^c WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

^d SAGE BIONETWORKS   (United States)

Author keywords

Cancer evolution; Clonal evolution; Clonal evolution visualization; Clonality analysis; Next generation sequencing

Indexed keywords

ACCURACY; ACUTE MYELOID LEUKEMIA; ARTICLE; BOOTSTRAPPING; BREAST CANCER; CANCER GROWTH; CANCER RECURRENCE; CANCER RESISTANCE; CLONAL EVOLUTION; DATA ANALYSIS SOFTWARE; HUMAN; INTERMETHOD COMPARISON; MATHEMATICAL MODEL; NON INVASIVE PROCEDURE; PATIENT MONITORING; PERSONALIZED MEDICINE; PRIORITY JOURNAL; SOLID MALIGNANT NEOPLASM; TUMOR BIOPSY; CELL CLONE; GENETICS; HIGH THROUGHPUT SEQUENCING; PATHOLOGY; PROCEDURES;

CLONAL EVOLUTION; CLONE CELLS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LEUKEMIA, MYELOID, ACUTE; PRECISION MEDICINE;

EID: 85042151532     PISSN: 09237534     EISSN: 15698041     Source Type: Journal    
DOI: 10.1093/annonc/mdx517     Document Type: Article

References (22)

1. Roth A, Khattra J, Yap D et al. PyClone: statistical inference of clonal population structure in cancer. Nat Methods 2014; 11(4): 396-398
2. Miller CA, White BS, Dees ND et al. SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLoS Comput Biol 2014; 10(8): e1003665
3. Ding L, Ley TJ, Larson DE et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 2012; 481(7382): 506-510
4. Griffith M, Miller CA, Griffith OL et al. Optimizing cancer genome sequencing and analysis. Cell Syst 2015; 1(3): 210-223
5. Strino F, Parisi F, Micsinai M, Kluger Y. TrAp: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Res 2013; 41(17): e165
6. Popic V, Salari R, Hajirasouliha I et al. Fast and scalable inference of multi-sample cancer lineages. Genome Biol 2015; 16: 91
7. Prandi D, Baca SC, Romanel A et al. Unraveling the clonal hierarchy of somatic genomic aberrations. Genome Biol 2014; 15(8): 439
8. Niknafs N, Beleva-Guthrie V, Naiman DQ, Karchin R. SubClonal hierarchy inference from somatic mutations: automatic reconstruction of cancer evolutionary trees from multi-region next generation sequencing. PLoS Comput Biol 2015; 11(10): e1004416
9. El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinformatics 2015; 31(12): i62-i70
10. Deshwar AG, Vembu S, Yung CK et al. PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome Biol 2015; 16: 35
11. Malikic S, McPherson AW, Donmez N, Sahinalp CS. Clonality inference in multiple tumor samples using phylogeny. Bioinformatics 2015; 31(9): 1349-1356
12. Miller CA, McMichael J, Dang HX et al. Visualizing tumor evolution with the Fishplot package for R. BMC Genomics 2016; 17(1): 880
13. McPherson A, Roth A, Laks E et al. Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer. Nat Genet 2016; 48(7): 758-767
14. Gundem G, Van Loo P, Kremeyer B et al. The evolutionary history of lethal metastatic prostate cancer. Nature 2015; 520(7547): 353-357
15. Jiang Y, Qiu Y, Minn AJ, Zhang NR. Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing. Proc Natl Acad Sci USA 2016; 113(37): E5528-E5537
16. Efron B, Tibshirani RJ. An Introduction to the Bootstrap. Chapman & Hall, New York: CRC Press, 1994
17. Murtaza M, Dawson S-J, Pogrebniak K et al. Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer. Nat Commun 2015; 6: 8760
18. Aceto N, Bardia A, Miyamoto DT et al. Circulating tumor cell clusters are oligoclonal precursors of breast cancer metastasis. Cell 2014; 158(5): 1110-1122
19. Uy GL, Duncavage EJ, Chang GS et al. Dynamic changes in the clonal structure of MDS and AML in response to epigenetic therapy. Leukemia 2017; 31(4): 872-881
20. Miller CA, Gindin Y, Lu C et al. Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers. Nat Commun 2016; 7: 12498
21. Hoadley KA, Siegel MB, Kanchi KL et al. Tumor evolution in two patients with basal-like breast cancer: a retrospective genomics study of multiple metastases. PLoS Med 2016; 13(12): e1002174
22. Johanns TM, Miller CA, Dorward IG et al. Immunogenomics of hypermutated glioblastoma: a patient with germline POLE deficiency treated with checkpoint blockade immunotherapy. Cancer Discov 2016; 6(11): 1230-1236