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Computational Prediction of Driver Missense Mutations in Melanoma

  • Haiyang Sun
  • Zhenyu Yue
  • Le Zhao
  • Junfeng Xia
  • Yannan Bin
  • Di Zhang
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10955)

Abstract

Discovering driver mutations used as the diagnostic and prognostic biomarkers is important for the treatment of cancer, including melanoma. Although during the last decade several computational methods have been developed to predict the effect of missense mutations in cancer, only a few have been specifically designed for identifying driver mutations in a specific disease context. To take into consideration of disease-specific factor, here we made efforts to prioritize missense mutations presented in melanoma. We collected 385 pathogenic mutations from the database of curated mutations (DoCM), and 392 benign mutations filtered from a benchmark neutral database (VariSnp), respectively. To evaluation of the model effect, we also selected 45 mutations from other databases. Then a random forest classifier was constructed to prioritize melanoma pathogenic mutations based on conservation, functional region annotation, protein secondary structure, protein domain, physicochemical features, and splicing information. The proposed method achieved an AUC of 0.94 on both training and test sets. When compared with previous developed algorithms, our method obtained a higher accuracy in identifying driver missense mutations in melanoma, along with a more balanced sensitivity and specificity than the other prediction methods.

Keywords

Melanoma Missense mutation Pathogenicity prediction 

Notes

Acknowledgements

The authors thank the members of our laboratory for their valuable discussions. This work has been supported by the grants from the National Natural Science Foundation of China (61672037 and 21601001) and the Anhui Provincial Outstanding Young Talent Support Plan (gxyqZD2017005), and the Young Wanjiang Scholar Program of Anhui Province, China.

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Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Haiyang Sun
    • 1
  • Zhenyu Yue
    • 2
  • Le Zhao
    • 2
  • Junfeng Xia
    • 1
  • Yannan Bin
    • 1
  • Di Zhang
    • 2
  1. 1.Institute of Physical Science and Information TechnologyAnhui UniversityHefeiChina
  2. 2.School of Computer Science and TechnologyAnhui UniversityHefeiChina

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