Cancer systems biology in the genome sequencing era: part 1, dissecting and modeling of tumor clones and their networks

Semin Cancer Biol. 2013 Aug;23(4):279-85. doi: 10.1016/j.semcancer.2013.06.002. Epub 2013 Jun 19.


Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has been viewed as a whole entity in cancer functional studies. With the advances of genome sequencing and computational analysis, we are able to quantify and computationally dissect clones from tumors, and then conduct clone-based analysis. Emerging technologies such as single-cell genome sequencing and RNA-Seq could profile tumor clones. Thus, we should reconsider how to conduct cancer systems biology studies in the genome sequencing era. We will outline new directions for conducting cancer systems biology by considering that genome sequencing technology can be used for dissecting, quantifying and genetically characterizing clones from tumors. Topics discussed in Part 1 of this review include computationally quantifying of tumor subpopulations; clone-based network modeling, cancer hallmark-based networks and their high-order rewiring principles and the principles of cell survival networks of fast-growing clones.

Keywords: Cancer hallmark; Genome sequencing; Molecular network; Signaling network; Systems biology; Tumor clonal network.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Apoptosis / genetics
  • Cell Cycle / genetics
  • Gene Regulatory Networks
  • Genome, Human / genetics*
  • Humans
  • Models, Genetic
  • Neoplasms / genetics*
  • Neoplasms / pathology
  • Sequence Analysis, DNA / methods*
  • Single-Cell Analysis / methods
  • Systems Biology / methods*