Detection of copy number variations based on a local distance using next-generation sequencing data

Frontiers in Genetics

Genetics

Hongzhi Yang¹  Guojun Liu²  Zongzhen He² 

[1] Department of Radiology, XD Group Hospital, Xi’an, China;School of Mathematics, Xi’an University of Finance and Economics, Xi’an, China;

关键词: copy number variation;    next-generation sequencing;    read depth;    local distance;    normal distribution;   

DOI  :  10.3389/fgene.2023.1147761

 received in 2023-02-01, accepted in 2023-09-14,  发布年份 2023

来源: Frontiers

【 摘 要 】

As one of the main types of structural variation in the human genome, copy number variation (CNV) plays an important role in the occurrence and development of human cancers. Next-generation sequencing (NGS) technology can provide base-level resolution, which provides favorable conditions for the accurate detection of CNVs. However, it is still a very challenging task to accurately detect CNVs from cancer samples with different purity and low sequencing coverage. Local distance-based CNV detection (LDCNV), an innovative computational approach to predict CNVs using NGS data, is proposed in this work. LDCNV calculates the average distance between each read depth (RD) and its k nearest neighbors (KNNs) to define the distance of KNNs of each RD, and the average distance between the KNNs for each RD to define their internal distance. Based on the above definitions, a local distance score is constructed using the ratio between the distance of KNNs and the internal distance of KNNs for each RD. The local distance scores are used to fit a normal distribution to evaluate the significance level of each RDS, and then use the hypothesis test method to predict the CNVs. The performance of the proposed method is verified with simulated and real data and compared with several popular methods. The experimental results show that the proposed method is superior to various other techniques. Therefore, the proposed method can be helpful for cancer diagnosis and targeted drug development.

【 授权许可】

Unknown   
Copyright © 2023 Liu, Yang and He.