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A Novel Method for Identifying the Potential Cancer Driver Genes Based on Molecular Data Integration

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Abstract

The identification of the cancer driver genes is essential for personalized therapy. The mutation frequency of most driver genes is in the middle (2–20%) or even lower range, which makes it difficult to find the driver genes with low-frequency mutations. Other forms of genomic aberrations, such as copy number variations (CNVs) and epigenetic changes, may also reflect cancer progression. In this work, a method for identifying the potential cancer driver genes (iPDG) based on molecular data integration is proposed. DNA copy number variation, somatic mutation, and gene expression data of matched cancer samples are integrated. In combination with the method of iKEEG, the "key genes" of cancer are identified, and the change in their expression levels is used for auxiliary evaluation of whether the mutated genes are potential drivers. For a mutated gene, the concept of mutational effect is defined, which takes into account the effects of copy number variation, mutation gene itself, and its neighbor genes. The method mainly includes two steps: the first step is data preprocessing. First, DNA copy number variation and somatic mutation data are integrated. Then, the integrated data are mapped to a given interaction network, and the diffusion kernel is used to form the mutation effect matrix. The second step is to obtain the key genes by using the iKGGE method, and construct the connection matrix by means of the gene expression data of the key genes and mutation impact matrix of the mutated genes. Experiments on TCGA breast cancer and Glioblastoma multiforme datasets demonstrate that iPDG is effective not only to identify the known cancer driver genes but also to discover the rare potential driver genes. When measured by functional enrichment analysis, we find that these genes are clearly associated with these two types of cancers.

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Acknowledgements

This work is supported by the National Natural Science Foundation of China (Grant Nos. 61672011, 61472467 and 61471169), and the Collaboration and Innovation Center for Digital Chinese Medicine of 2011 Project of Colleges and Universities in Hunan Province.

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Correspondence to Shu-Lin Wang.

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Zhang, W., Wang, S. A Novel Method for Identifying the Potential Cancer Driver Genes Based on Molecular Data Integration. Biochem Genet 58, 16–39 (2020). https://doi.org/10.1007/s10528-019-09924-2

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Keywords

  • Driver genes
  • DNA copy numbers variation data
  • Somatic mutation data
  • Gene expression data
  • Diffusion kernel