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A penalized regression approach for DNA copy number study using the sequencing data

Author

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  • Lee Jaeeun
  • Chen Jie

    (Division of Biostatistics and Data Science, Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA 30912, USA)

Abstract

Modeling the high-throughput next generation sequencing (NGS) data, resulting from experiments with the goal of profiling tumor and control samples for the study of DNA copy number variants (CNVs), remains to be a challenge in various ways. In this application work, we provide an efficient method for detecting multiple CNVs using NGS reads ratio data. This method is based on a multiple statistical change-points model with the penalized regression approach, 1d fused LASSO, that is designed for ordered data in a one-dimensional structure. In addition, since the path algorithm traces the solution as a function of a tuning parameter, the number and locations of potential CNV region boundaries can be estimated simultaneously in an efficient way. For tuning parameter selection, we then propose a new modified Bayesian information criterion, called JMIC, and compare the proposed JMIC with three different Bayes information criteria used in the literature. Simulation results have shown the better performance of JMIC for tuning parameter selection, in comparison with the other three criterion. We applied our approach to the sequencing data of reads ratio between the breast tumor cell lines HCC1954 and its matched normal cell line BL 1954 and the results are in-line with those discovered in the literature.

Suggested Citation

  • Lee Jaeeun & Chen Jie, 2019. "A penalized regression approach for DNA copy number study using the sequencing data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 18(4), pages 1-14, August.
    • Handle: RePEc:bpj:sagmbi:v:18:y:2019:i:4:p:14:n:1
    DOI: 10.1515/sagmb-2018-0001
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    References listed on IDEAS

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    1. Robert Tibshirani & Michael Saunders & Saharon Rosset & Ji Zhu & Keith Knight, 2005. "Sparsity and smoothness via the fused lasso," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 67(1), pages 91-108, February.
    2. Qian, Junhui & Su, Liangjun, 2016. "Shrinkage Estimation Of Regression Models With Multiple Structural Changes," Econometric Theory, Cambridge University Press, vol. 32(6), pages 1376-1433, December.
    3. Pan, Jianmin & Chen, Jiahua, 2006. "Application of modified information criterion to multiple change point problems," Journal of Multivariate Analysis, Elsevier, vol. 97(10), pages 2221-2241, November.
    4. Nancy R. Zhang & David O. Siegmund, 2007. "A Modified Bayes Information Criterion with Applications to the Analysis of Comparative Genomic Hybridization Data," Biometrics, The International Biometric Society, vol. 63(1), pages 22-32, March.
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