Detection Copy Number Variants from NGS with Sparse and Smooth Constraints

Yue Zhang, Yiu Ming CHEUNG*, Bo Xu, Weifeng Su

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

7 Citations (Scopus)

Abstract

It is known that copy number variations (CNVs) are associated with complex diseases and particular tumor types, thus reliable identification of CNVs is of great potential value. Recent advances in next generation sequencing (NGS) data analysis have helped manifest the richness of CNV information. However, the performances of these methods are not consistent. Reliably finding CNVs in NGS data in an efficient way remains a challenging topic, worthy of further investigation. Accordingly, we tackle the problem by formulating CNVs identification into a quadratic optimization problem involving two constraints. By imposing the constraints of sparsity and smoothness, the reconstructed read depth signal from NGS is anticipated to fit the CNVs patterns more accurately. An efficient numerical solution tailored from alternating direction minimization (ADM) framework is elaborated. We demonstrate the advantages of the proposed method, namely ADM-CNV, by comparing it with six popular CNV detection methods using synthetic, simulated, and empirical sequencing data. It is shown that the proposed approach can successfully reconstruct CNV patterns from raw data, and achieve superior or comparable performance in detection of the CNVs compared to the existing counterparts.

Original languageEnglish
Article number7464276
Pages (from-to)856-867
Number of pages12
JournalIEEE/ACM Transactions on Computational Biology and Bioinformatics
Volume14
Issue number4
DOIs
Publication statusPublished - 1 Jul 2017

Scopus Subject Areas

  • Biotechnology
  • Genetics
  • Applied Mathematics

User-Defined Keywords

  • Copy number variants
  • read depth
  • sparsity
  • total variation

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