Related Experiment Video
Updated: Nov 4, 2025
11:02
Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
19.6K
driveR: a novel method for prioritizing cancer driver genes using somatic genomics data
1Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey. egeulgen@gmail.com.
BMC Bioinformatics
|May 25, 2021
Summary
We developed driveR, a new computational tool for identifying cancer driver genes using somatic genomics data. driveR accurately prioritizes driver genes in both personalized and batch analyses, outperforming existing methods.
Area of Science:
- Genomics
- Computational Biology
- Cancer Research
Background:
- Cancer development is driven by specific genetic alterations.
- Existing methods for identifying cancer drivers primarily focus on cohort-scale data.
- Personalized analysis of driver genes remains an underdeveloped area.
Purpose of the Study:
- To develop a novel computational approach for driver gene prioritization.
- To enable both personalized and batch analysis of cancer driver genes.
- To improve the accuracy and usability of driver gene identification.
Main Methods:
- Developed driveR, a multi-task learning model.
- Integrated genomics data with prior biological knowledge.
- Validated driveR on 28 batch and 5157 personalized analysis datasets.
Main Results:
- driveR achieved a median AUC of 0.684 for batch analysis and 0.773 for personalized analysis.
- driveR significantly outperformed existing methods including MutSigCV, DriverNet, OncodriveFML, MutPanning, DawnRank, and PRODIGY.
- The model demonstrated robust performance across diverse datasets.
Conclusions:
- driveR is an accurate and user-friendly tool for prioritizing cancer driver genes.
- The method is effective for both personalized and batch analysis scenarios.
- The driveR software package is publicly available on CRAN.
Related Concept Videos
02:21Cancers Originate from Somatic Mutations in a Single Cell
13.4K
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...
13.4K
01:05Cancer-Critical Genes II: Tumor Suppressor Genes
8.5K
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...
8.5K
01:33Cancer-Critical Genes I: Proto-oncogenes
9.5K
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...
9.5K
01:21Cancer Survival Analysis
493
Cancer survival analysis focuses on quantifying and interpreting the time from a key starting point, such as diagnosis or the initiation of treatment, to a specific endpoint, such as remission or death. This analysis provides critical insights into treatment effectiveness and factors that influence patient outcomes, helping to shape clinical decisions and guide prognostic evaluations. A cornerstone of oncology research, survival analysis tackles the challenges of skewed, non-normally...
493
02:57Targeted Cancer Therapies
8.0K
The targeted cancer therapies, also known as “molecular targeted therapies,” take advantage of the molecular and genetic differences between the cancer cells and the normal cells. It needs a thorough understanding of the cancer cells to develop drugs that can target specific molecular aspects that drive the growth, progression, and spread of cancer cells without affecting the growth and survival of other normal cells in the body.
There are several types of targeted therapies against...
There are several types of targeted therapies against...
8.0K