Penalized weighted low-rank approximation for robust recovery of recurrent copy number variations

Robust Recurrent CNV Detection in the Presence of Inter-Subject Variability

The study of recurrent copy number variations (CNVs) plays an important role in understanding the onset and evolution of complex diseases such as cancer. Array-based comparative genomic hybridization (aCGH) is a widely used microarray based technology for identifying CNVs. However, due to high noise levels and inter-sample variability, detecting recurrent CNVs from aCGH data remains a challenging topic. This paper proposes a novel method for identification of the recurrent CNVs. In the proposed method, the noisy aCGH data is modeled as the superposition of three matrices: a full-rank matrix of weighted piece-wise generating signals accounting for the clean aCGH data, a Gaussian noise matrix to model the inherent experimentation errors and other sources of error, and a sparse matrix to capture the sparse inter-sample (sample-specific) variations. We demonstrated the ability of our method to separate accurately recurrent CNVs from sample-specific variations and noise in both simulated (artificial) data and real data. The proposed method produced more accurate results than current state-of-the-art methods used in recurrent CNV detection and exhibited robustness to noise and sample-specific variations.

A Projection Neural Network for Identifying Copy Number Variants

The identification of copy number variations (CNVs) helps the diagnosis of many diseases. One major hurdle in the path of CNVs discovery is that the boundaries of normal and aberrant regions cannot be distinguished from the raw data, since various types of noise contaminate them. To tackle this challenge, the total variation regularization is mostly used in the optimization problems to approximate the noise-free data from corrupted observations. The minimization using such regularization is challenging to deal with since it is non-differentiable. In this paper, we propose a projection neural network to solve the non-smooth problem. The proposed neural network has a simple one-layer structure and is theoretically assured to have the global exponential convergence to the solution of the total variation-regularized problem. The experiments on several real and simulated datasets illustrate the reasonable performance of the proposed neural network and show that its performance is comparable with those of more sophisticated algorithms.