CNV-seq: a new method to detect copy number variation using high-throughput sequencing. Background: DNA copy number variation (CNV) has been recognized as an important source of genetic variation. Array comparative genomic hybridization (aCGH) is commonly used for CNV detection, but the microarray platform has a number of inherent limitations. Results: Here, we describe a method to detect copy number variation using shotgun sequencing, CNV-seq. The method is based on a robust statistical model that describes the complete analysis procedure and allows the computation of essential confidence values for detection of CNV. Our results show that the number of reads, not the length of the reads is the key factor determining the resolution of detection. This favors the next-generation sequencing methods that rapidly produce large amount of short reads. Conclusion: Simulation of various sequencing methods with coverage between 0.1× to 8× show overall specificity between 91.7 – 99.9%, and sensitivity between 72.2 – 96.5%. We also show the results for assessment of CNV between two individual human genomes.

References in zbMATH (referenced in 11 articles )

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  1. Lee, Jaeeun; Chen, Jie: A penalized regression approach for DNA copy number study using the sequencing data (2019)
  2. Yang, Shengping; Fang, Zhide: Beta approximation of ratio distribution and its application to next generation sequencing read counts (2017)
  3. Chen, Jie; Li, Hua: A statistical change-point analysis approach for modeling the ratio of next generation sequencing reads (2016)
  4. Greenman, C. D.; Cooke, S. L.; Marshall, J.; Stratton, M. R.; Campbell, P. J.: Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process (2016)
  5. Malekpour, Seyed Amir; Pezeshk, Hamid; Sadeghi, Mehdi: MGP-HMM: detecting genome-wide CNVs using an HMM for modeling mate pair insertion sizes and read counts (2016)
  6. Ji, Tieming; Chen, Jie: Modeling the next generation sequencing read count data for DNA copy number variant study (2015)
  7. Yiğiter, Ayten; Chen, Jie; An, Lingling; Danacioğlu, Nazan: An online copy number variant detection method for short sequencing reads (2015)
  8. Shen, Jeremy J.; Zhang, Nancy R.: Change-point model on nonhomogeneous Poisson processes with application in copy number profiling by next-generation DNA sequencing (2012)
  9. Love, Michael I.; Myšičková, Alena; Sun, Ruping; Kalscheuer, Vera; Vingron, Martin; Haas, Stefan A.: Modeling read counts for CNV detection in exome sequencing data (2011)
  10. Rueda, Oscar M.; Díaz-Uriarte, Ramón: Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously (2009) ioport
  11. Xie, Chao; Tammi, Martti T.: CNV-seq, a new method to detect copy number variation using high-throughput sequencing (2009) ioport