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MDAGenera: An Efficient and Accurate Simulator for Multiple Displacement Amplification

  • Weiheng Huang
  • Hongmin CaiEmail author
  • Wei Shao
  • Bo Xu
  • Fuqiang Li
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9771)

Abstract

The advance of single cell sequencing advocates a new era to delineate intratumor heterogeneity and traces the evolution of single cells at molecular level. However, current single cell technology is hindered by an indispensable step of genome amplification to accumulate enough samples to reach the sequencing requirement. Multiple Displacement Amplification (MDA) method is the major technology adopted for genome amplification. But it suffers from a major drawback of large amplification bias, resulting in time and label consuming. To fulfill this gap, we have presented a simulation software for the MDA process in this paper. The proposed simulator was based on an original hypothesis for catering to empirical MDA process. It was implemented to achieve high efficiency with affordable computational cost, thus allowing for an individual MDA experiment to be simulated quickly. Surprising nice experiments demonstrated the simulator is promising in providing guidance and cross-validation for experimental MDA.

Keywords

Single cell sequencing Multiple Displacement Amplification (MDA) DNA amplification simulator 

Notes

Acknowledgments

This work was supported by National Nature Science Foundation of China (61372141), Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund (the second phase), Science and Technology Planning Project of Guangdong Province, and the Fundamental Research Fund for the Central Universities (2015ZZ025).

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • Weiheng Huang
    • 1
  • Hongmin Cai
    • 1
    Email author
  • Wei Shao
    • 1
  • Bo Xu
    • 1
  • Fuqiang Li
    • 2
  1. 1.School of Computer Science and EngineeringSouth China University of TechnologyGuangzhouChina
  2. 2.Beijing Genomics InstituteShenzhenChina

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