ABSTRACT
Copy number variation (CNV) is a non-negligible structural variation on the genome. And next-generation sequencing (NGS) technology is widely used to detect CNVs due to the feature of high throughput and low cost on the whole genome. Based on the original MFCNV method, this paper proposes an improved CNV detection method, which is called CNVABNN. In comparison to the MFCNV method, CNVABNN has three advantages: (1) It adds detectable categories, and refines the categories of loss into hemi_loss and homo_loss. (2) It utilizes the idea of integrated learning. The AdaBoost algorithm is used as the core framework and neural networks are used as weak classifiers, then CNVABNN combines all of the weak classifiers into a strong classifier. The overall performance of CNV detection is improved by using the strong classifier. (3) The detection is optimized by predicting CNVs twice through neural networks and voting mechanisms. To evaluate the performance of CNVABNN, six existing detection methods are used for comparison. The experimental results show that CNVABNN achieves better results in terms of precision, sensitivity, and F1-score for both simulated and real samples.
Subject(s)
DNA Copy Number Variations , High-Throughput Nucleotide Sequencing , Algorithms , DNA Copy Number Variations/genetics , High-Throughput Nucleotide Sequencing/methods , Neural Networks, Computer , Sequence Analysis, DNA/methodsABSTRACT
Copy number variation (CNV), is defined as repetitions or deletions of genomic segments of 1 Kb to 5 Mb, and is a major trigger for human disease. The high-throughput and low-cost characteristics of next-generation sequencing technology provide the possibility of the detection of CNVs in the whole genome, and also greatly improve the clinical practicability of next-generation sequencing (NGS) testing. However, current methods for the detection of CNVs are easily affected by sequencing and mapping errors, and uneven distribution of reads. In this paper, we propose an improved approach, CNV-MEANN, for the detection of CNVs, involving changing the structure of the neural network used in the MFCNV method. This method has three differences relative to the MFCNV method: (1) it utilizes a new feature, mapping quality, to replace two features in MFCNV, (2) it considers the influence of the loss categories of CNV on disease prediction, and refines the output structure, and (3) it uses a mind evolutionary algorithm to optimize the backpropagation (neural network) neural network model, and calculates individual scores for each genome bin to predict CNVs. Using both simulated and real datasets, we tested the performance of CNV-MEANN and compared its performance with those of seven widely used CNV detection methods. Experimental results demonstrated that the CNV-MEANN approach outperformed other methods with respect to sensitivity, precision, and F1-score. The proposed method was able to detect many CNVs that other approaches could not, and it reduced the boundary bias. CNV-MEANN is expected to be an effective method for the analysis of changes in CNVs in the genome.
ABSTRACT
Copy number variation (CNV) is a very important phenomenon in tumor genomes and plays a significant role in tumor genesis. Accurate detection of CNVs has become a routine and necessary procedure for a deep investigation of tumor cells and diagnosis of tumor patients. Next-generation sequencing (NGS) technique has provided a wealth of data for the detection of CNVs at base-pair resolution. However, such task is usually influenced by a number of factors, including GC-content bias, sequencing errors, and correlations among adjacent positions within CNVs. Although many existing methods have dealt with some of these artifacts by designing their own strategies, there is still a lack of comprehensive consideration of all the factors. In this paper, we propose a new method, MFCNV, for an accurate detection of CNVs from NGS data. Compared with existing methods, the characteristics of the proposed method include the following: (1) it makes a full consideration of the intrinsic correlations among adjacent positions in the genome to be analyzed, (2) it calculates read depth, GC-content bias, base quality, and correlation value for each genome bin and combines them as multiple features for the evaluation of genome bins, and (3) it addresses the joint effect among the factors via training a neural network algorithm for the prediction of CNVs. We test the performance of the MFCNV method by using simulation and real sequencing data and make comparisons with several peer methods. The results demonstrate that our method is superior to other methods in terms of sensitivity, precision, and F1-score and can detect many CNVs that other methods have not discovered. MFCNV is expected to be a complementary tool in the analysis of mutations in tumor genomes and can be extended to be applied to the analysis of single-cell sequencing data.
