AluScanCNV2: An R package for copy number variation calling and cancer risk prediction with next-generation sequencing data.

Journal: Genes & diseases
Published Date: Sep 8, 2018

Abstract

The usage of next-generation sequencing (NGS) to detect copy number variation (CNV) is widely accepted in cancer research. Based on an AluScanCNV software developed by us previously, an AluScanCNV2 software has been developed in the present study as an R package that performs CNV detection from NGS data obtained through AluScan, whole-genome sequencing or other targeted NGS platforms. Its applications would include the expedited usage of somatic CNVs for cancer subtyping, and usage of recurrent germline CNVs to perform machine learning-assisted prediction of a test subject's susceptibility to cancer.

Authors

  • Taobo Hu
    Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
  • Si Chen
    Department of Pharmacy, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China.
  • Ata Ullah
    Division of Life Science, Applied Genomics Centre and Centre for Statistical Science, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.
  • Hong Xue
    International Initiative on Spatial Lifecourse Epidemiology (ISLE), the Netherlands; Department of Health Behavior and Policy, School of Medicine, Virginia Commonwealth University, Richmond, VA, 23298, USA.

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