Related Experiment Video
Updated: May 31, 2026
08:29
Long-term Live-cell Imaging to Assess Cell Fate in Response to Paclitaxel
Published on: May 14, 2018
Multiplicity: an organizing principle for cancers and somatic mutations
Lewis J Frey1, Stephen R Piccolo, Mary E Edgerton
1Department of Biomedical Informatics, University of Utah, 26 South 2000 East, Salt Lake City, UT 84112, USA. lewis.frey@hsc.utah.edu
BMC Medical Genomics
|July 1, 2011
Summary
We developed multiplicity measures to organize cancer genomic data, revealing similarities in mutations across cancer types. This method effectively clusters causal genes and segregates blood tumors, aiding in understanding cancer progression.
Area of Science:
- Genomics
- Cancer Biology
- Bioinformatics
Background:
- Whole-genome analysis generates vast amounts of tumor genomic data.
- Organizing this data requires principled methods for clinical relevance.
- Multiplicity measures are proposed to organize cancer and gene networks.
Purpose of the Study:
- To introduce multiplicity measures for organizing somatic mutations and cancers.
- To identify clinically meaningful clusters of cancer types and genes.
- To extend the multi-hit genetic model across diverse cancers.
Main Methods:
- Constructed cancer and gene networks using the Catalogue of Somatic Mutations in Cancer (COSMIC).
- Calculated multiplicity based on linked cancers and genes per somatic mutation.
- Employed the Kamada-Kawai algorithm for network visualization and hierarchical clustering in 3D.
Main Results:
- Gene clustering revealed shared mutations across cancer types and separated known causal mutations.
- Multiplicity clustering identified causal genes with high accuracy (AUC 0.84).
- Cancer type clustering segregated blood tumors, indicating distinct mutation patterns.
Conclusions:
- Multiplicity measures effectively organize somatic mutations and cancers into clinically relevant clusters.
- These clusters highlight key genes driving cancer progression.
- The approach provides a framework for understanding inter-cancer mutation similarities.
Related Concept Videos
02:21Cancers Originate from Somatic Mutations in a Single Cell
Cancer arises from mutations in the critical genes that allow healthy cells to escape cell cycle regulation and acquire the ability to proliferate indefinitely. Though originating from a single mutation event in one of the originator cells, cancer progresses when the mutant cell lines continue to gain more and more mutations, and finally, become malignant. For example, chronic myelogenous leukemia (CML) develops initially as a non-lethal increase in white blood cells, which progressively...
02:21Cancers Originate from Somatic Mutations in a Single Cell
Cancer arises from mutations in the critical genes that allow healthy cells to escape cell cycle regulation and acquire the ability to proliferate indefinitely. Though originating from a single mutation event in one of the originator cells, cancer progresses when the mutant cell lines continue to gain more and more mutations, and finally, become malignant. For example, chronic myelogenous leukemia (CML) develops initially as a non-lethal increase in white blood cells, which progressively...
02:18Cancer
Cancers arise due to mutations in genes involved in the regulation of cell division, which leads to unrestricted cell proliferation. Modern science and medicine have made great strides in the understanding and treatment of cancer, including eradicating cancer in some patients. However, there is still no cure for cancer. This is largely due to the fact that cancer is a large group of many diseases.
01:33Cancer-Critical Genes I: Proto-oncogenes
Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
01:33Cancer-Critical Genes I: Proto-oncogenes
Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
02:53Adaptive Mechanisms in Cancer Cells
Cancer cells accumulate genetic changes at an abnormally rapid rate due to the defects in the DNA repair mechanisms. From an evolutionary perspective, such genetic instability is advantageous for cancer development. Mutant cell lines accumulate a series of beneficial mutations that contribute to their progression into cancer.
Some of the advantages that cancer cells have on normal cells include - enhanced ability to divide without terminally differentiating, induce new blood vessel formation,...
Some of the advantages that cancer cells have on normal cells include - enhanced ability to divide without terminally differentiating, induce new blood vessel formation,...