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Identification of Cancer Driver Genes from a Custom Set of Next Generation Sequencing Data

  • Shu-Hsuan Liu
  • Wei-Chung Cheng
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1907)

Abstract

Next generation sequencing (NGS) has become the norm of cancer genomic researches. Large-scale cancer sequencing projects seek to comprehensively uncover mutated genes that confer a selective advantage for cancer cells. Numerous computational algorithms have been developed to find genes that drive cancer based on their patterns of mutation in a patient cohort. It has been noted that the distinct features of driver gene alterations in different subgroups are based on clinical characteristics. Previously, we have developed a database, DriverDB, to integrate all public cancer sequencing data and to identify cancer driver genes according to bioinformatics tools. In this chapter, we describe the use of the function “Meta-Analysis” in DriverDB that offers a list of clinical characteristics to define samples and provides a high degree of freedom for researchers to utilize the huge amounts of sequencing data. Moreover, researchers can use the “Gene” section to explore a single driver gene in all cancers by different kinds of aspects after identifying the specific driver genes by “Meta-Analysis.” DriverDB is available at http://ngs.ym.edu.tw/driverdb/.

Key words

Next generation sequencing Cancer Driver genes Subgroups Mutations 

Notes

Acknowledgments

This research is supported by the Ministry of Science and Technology of Taiwan (105-2320-B-039-006-, 106-2221-E-039-011-MY3); China Medical University (CMU 105-N-06, CMU 106-AWARD-01, CMU 106-N-05).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Shu-Hsuan Liu
    • 1
  • Wei-Chung Cheng
    • 1
    • 2
    • 3
  1. 1.Graduate Institute of Biomedical SciencesChina Medical UniversityTaichungTaiwan
  2. 2.Research Center for Tumour Medical ScienceChina Medical UniversityTaichungTaiwan
  3. 3.Drug Development CenterChina Medical UniversityTaichungTaiwan

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