Volume 43 Issue 1
Jan.  2022
Turn off MathJax
Article Contents
Xi-Guo Yuan, Yuan Zhao, Yang Guo, Lin-Mei Ge, Wei Liu, Shi-Yu Wen, Qi Li, Zhang-Bo Wan, Pei-Na Zheng, Tao Guo, Zhi-Da Li, Martin Peifer, Yu-Peng Cun. COSINE: A web server for clonal and subclonal structure inference and evolution in cancer genomics. Zoological Research, 2022, 43(1): 75-77. doi: 10.24272/j.issn.2095-8137.2021.250
Citation: Xi-Guo Yuan, Yuan Zhao, Yang Guo, Lin-Mei Ge, Wei Liu, Shi-Yu Wen, Qi Li, Zhang-Bo Wan, Pei-Na Zheng, Tao Guo, Zhi-Da Li, Martin Peifer, Yu-Peng Cun. COSINE: A web server for clonal and subclonal structure inference and evolution in cancer genomics. Zoological Research, 2022, 43(1): 75-77. doi: 10.24272/j.issn.2095-8137.2021.250

COSINE: A web server for clonal and subclonal structure inference and evolution in cancer genomics

doi: 10.24272/j.issn.2095-8137.2021.250
Funds:  This work was supported by the CAS Pioneer Hundred Talents Program and National Natural Science Foundation of China (32070683) to Y.P.C.; the Science and Technology Planning Project of XI'AN (GXYD6.2) and National Natural Science Foundation of China (61771369) to X.G.Y.
More Information
  • Corresponding author: E-mail: cunyp@cqmu.edu.cn
  • Received Date: 2021-09-25
  • Accepted Date: 2021-11-19
  • Published Online: 2021-11-26
  • Publish Date: 2022-01-18
  • loading
  • [1]
    Cmero M, Yuan K, Ong CS, Schröder J, Adams DJ, Anur P, et al. 2020. Inferring structural variant cancer cell fraction. Nature Communications, 11(1): 730. doi: 10.1038/s41467-020-14351-8
    [2]
    Cun YP, Yang TP, Achter V, Lang U, Peifer M. 2018. Copy-number analysis and inference of subclonal populations in cancer genomes using Sclust. Nature Protocols, 13(6): 1488−1501. doi: 10.1038/nprot.2018.033
    [3]
    Gerstung M, Jolly C, Leshchiner I, Dentro SC, Gonzalez S, Rosebrock D, et al. 2020. The evolutionary history of 2, 658 cancers. Nature, 578(7793): 122−128. doi: 10.1038/s41586-019-1907-7
    [4]
    Malikic S, Mcpherson AW, Donmez N, Sahinalp CS. 2015. Clonality inference in multiple tumor samples using phylogeny. Bioinformatics, 31(9): 1349−1356. doi: 10.1093/bioinformatics/btv003
    [5]
    Mcgranahan N, Swanton C. 2017. Clonal heterogeneity and tumor evolution: past, present, and the future. Cell, 168(4): 613−628. doi: 10.1016/j.cell.2017.01.018
    [6]
    Miller CA, White BS, Dees ND, Griffith M, Welch JS, Griffith OL, et al. 2014. SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLoS Computational Biology, 10(8): e1003665. doi: 10.1371/journal.pcbi.1003665
    [7]
    Miura S, Gomez K, Murillo O, Huuki LA, Vu T, Buturla T, et al. 2018. Predicting clone genotypes from tumor bulk sequencing of multiple samples. Bioinformatics, 34(23): 4017−4026.
    [8]
    Nik-Zainal S, Van Loo P, Wedge DC, Alexandrov LB, Greenman CD, Lau KW, et al. 2012. The life history of 21 breast cancers. Cell, 149(5): 994−1007. doi: 10.1016/j.cell.2012.04.023
    [9]
    Salcedo A, Tarabichi M, Espiritu SMG, Deshwar AG, David M, Wilson NM, et al. 2020. A community effort to create standards for evaluating tumor subclonal reconstruction. Nature Biotechnology, 38(1): 97−107. doi: 10.1038/s41587-019-0364-z
    [10]
    Strino F, Parisi F, Micsinai M, Kluger Y. 2013. TrAp: a tree approach for fingerprinting subclonal tumor composition. Nucleic Acids Research, 41(17): e165. doi: 10.1093/nar/gkt641
    [11]
    Xiao Y, Wang XQ, Zhang HJ, Ulintz PJ, Li HY, Guan YF. 2020. FastClone is a probabilistic tool for deconvoluting tumor heterogeneity in bulk-sequencing samples. Nature Communications, 11(1): 4469. doi: 10.1038/s41467-020-18169-2
  • ZR-2021-250 Supplementary Materials.zip
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(1)

    Article Metrics

    Article views (1769) PDF downloads(180) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return