CNV-FB: A Feature bagging strategy-based approach to detect copy number variants from NGS data

被引:0
|
作者
Li, Chengyou [1 ]
Fan, Shiqiang [1 ]
Zhao, Haiyong [1 ]
Liu, Xiaotong [2 ]
机构
[1] Liaocheng Univ, Sch Comp Sci, Liaocheng 252000, Peoples R China
[2] Liaocheng Univ, Sch Agron & Agr Engn, Liaocheng 252000, Peoples R China
关键词
Copy number variations; next-generation sequencing; feature bagging; outlier score; median absolute deviation; EXPRESSION;
D O I
10.1142/S0219720023500269
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Copy number variation (CNV), as a type of genomic structural variation, accounts for a large proportion of structural variation and is related to the pathogenesis and susceptibility to some human diseases, playing an important role in the development and change of human diseases. The development of next-generation sequencing technology (NGS) provides strong support for the design of CNV detection algorithms. Although a large number of methods have been developed to detect CNVs using NGS data, it is still considered a difficult problem to detect CNVs with low purity and coverage. In this paper, a new calculation method CNV-FB is proposed to detect CNVs from NGS data. The core idea of CNV-FB is to randomly sample the read depth values of the genome fragment, and then each sample is individually detected for outliers, and finally combined into a final outlier score. The CNV-FB method was applied to simulation data and real data experiments and compared with the other five methods of the same type. The results show that the CNV-FB method has a better detection effect than other methods. Therefore, the CNV-FB method may be an effective algorithm for detecting genomic mutations.
引用
收藏
页数:18
相关论文
共 22 条
  • [1] Using a Targeted NGS Approach to Detect Copy Number Alterations and Gene Variants in Chronic Lymphocytic Leukemia
    Poloni, G.
    Georgieva, L.
    Milner, N.
    Pullabhatla, V.
    Reid, J.
    Holdstock, J.
    Speight, G.
    JOURNAL OF MOLECULAR DIAGNOSTICS, 2023, 25 (11): : S35 - S35
  • [2] HBOS-CNV: A New Approach to Detect Copy Number Variations From Next-Generation Sequencing Data
    Guo, Yang
    Wang, Shuzhen
    Yuan, Xiguo
    FRONTIERS IN GENETICS, 2021, 12
  • [3] CNV-CH: A Convex Hull Based Segmentation Approach to Detect Copy Number Variations (CNV) Using Next-Generation Sequencing Data
    Sinha, Rituparna
    Samaddar, Sandip
    De, Rajat K.
    PLOS ONE, 2015, 10 (08):
  • [4] CNVmap: A Method and Software To Detect and Map Copy Number Variants from Segregation Data
    Falque, Matthieu
    Jebreen, Kamel
    Paux, Etienne
    Knaak, Carsten
    Mezmouk, Sofiane
    Martin, Olivier C.
    GENETICS, 2020, 214 (03) : 561 - 576
  • [5] A Local Outlier Factor-Based Detection of Copy Number Variations From NGS Data
    Yuan, Xiguo
    Li, Junping
    Bai, Jun
    Xi, Jianing
    IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS, 2021, 18 (05) : 1811 - 1820
  • [6] An Easy-to-Use Approach to Detect CNV From Targeted NGS Data: Identification of a Novel Pathogenic Variant in MO Disease
    Corsini, Serena
    Pedrini, Elena
    Patavino, Claudio
    Gnoli, Maria
    Lanza, Marcella
    Sangiorgi, Luca
    FRONTIERS IN ENDOCRINOLOGY, 2022, 13
  • [7] CRSCNV: A Cross-Model-Based Statistical Approach to Detect Copy Number Variations in Sequence Data
    Liu, Guojun
    Yuan, Xiguo
    Zhang, Junying
    Zhao, Haiyong
    Li, Junping
    Duan, Junbo
    IEEE ACCESS, 2020, 8 (08): : 2302 - 2312
  • [8] CNVABNN: An AdaBoost algorithm and neural networks-based detection of copy number variations from NGS data
    Wang, Xuan
    Li, Junqing
    Huang, Tihao
    COMPUTATIONAL BIOLOGY AND CHEMISTRY, 2022, 99
  • [9] A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: 'rCNV', a versatile r package for paralogue and CNV detection
    Karunarathne, Piyal
    Zhou, Qiujie
    Schliep, Klaus
    Milesi, Pascal
    MOLECULAR ECOLOGY RESOURCES, 2023, 23 (08) : 1772 - 1789
  • [10] ifCNV: A novel isolation-forest-based package to detect copy-number variations from various targeted NGS datasets
    Cabello-Aguilar, Simon
    Vendrell, Julie A.
    Van Goethem, Charles
    Brousse, Mehdi
    Goze, Catherine
    Frantz, Laurent
    Solassol, Jerome
    MOLECULAR THERAPY-NUCLEIC ACIDS, 2022, 30 : 174 - 183