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| Study of CNV Detection Tools Based on Hidden Markov Model and Whole Exome Sequencing |
| Liu Ni1, Liu Han1, Zhao Aman2, Xu Fanding1, Liu Wenyu1, Duan Junbo1* |
1(The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China)
2(Department of Clinical Laboratory, Children's Hospital of Soochow University,Suzhou 215003, Jiangsu, China) |
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Received: 21 January 2021
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[1] Liang Yan, Wu Jianxin. Research progress on gene copy number variations [J]. Progress in Modern Biomedicine, 2011, 12(5): 964-967.
[2] Stranger BE, Forrest MS, Dunning M, et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes [J]. Science, 2007, 315(5813): 848-853.
[3] Barnes MR. Genetic variation analysis for biomedical researchers: A primer [J]. Methods Mol Biol, 2010, 628:1-20.
[4] Stankiewicz P, Lupski JR. Structural variation in the human genome and its role in disease[J]. Annual Review of Medicine, 2010, 61: 437-455.
[5] Wain LV, Armour JAL, Tobin MD. Genomic copy number variation, human health, and disease [J]. The Lancet, 2009, 374: 340-350.
[6] Metzker M L. Sequencing technologies—The next generation [J]. Nature Reviews Genetics, 2010, 11(1): 31-46.
[7] Saad M, Brkanac Z, Wijsman EM. Family-based genome scan for age at onset of late-onset Alzheimer's disease in whole exome sequencing data[J]. Genes, Brain and Behavior, 2015, 14(8): 607-617.
[8] 许容容,解卫平.全外显子组测序技术及其在肺癌研究中的进展[J].国际呼吸杂志,2015, 35(19):1510-1512.
[9] Amarasinghe KC, Li J, Halgamuge SK. CoNVEX: Copy number variation estimation in exome sequencing data using HMM [J].BMC Bioinformatics, 2013, 14(2): 1-9.
[10] Yue Xing, Dabney AR, Li Xiao, et al. SimulateCNVs: A novel software application for simulating CNVs in WES and WGS data [EB/OL]. https://www.biorxiv.org/content/10.1101/407486v3,2018-09/2021-01-12.
[11] Krumm N, Sudmant PH, Ko A, et al. Copy number variation detection and genotyping from exome sequence data [J]. Genome Research, 2012, 22(8): 1525-1532.
[12] Wang H, Nettleton D, Ying K. Copy number variation detection using next generation sequencing read counts [J]. BMC Bioinformatics, 2014, 15(1): 109.
[13] Tan Renjie, Wang Yadong, Kleinstein SE, et al. An evaluation of copy number variation detection tools from whole-exome sequencing data[J]. Human Mutation, 2014, 35(7): 899-907.
[14] Zare F, Dow M, Monteleone N, et al. An evaluation of copy number variation detection tools for cancer using whole exome sequencing data [J]. BMC Bioinformatics, 2017, 18(1): 286.
[15] Duan Junbo, Zhang Jigang, Deng Hongwen, et al. Comparative studies of copy number variation detection methods for next-generation sequencing technologies [J]. PLoS ONE, 2013, 8(3): e59128.
[16] Fromer M, Moran JL, Chambert K, et al. Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth[J]. The American Journal of Human Genetics, 2012, 91(4): 597-607.
[17] Amarasinghe KC, Li J, Hunter SM, et al. Inferring copy number and genotype in tumour exome data[J]. BMC Genomics, 2014, 15(1): 732.
[18] Backenroth D, Homsy J, Murillo L R, et al. CANOES: Detecting rare copy number variants from whole exome sequencing data [J]. Nucleic Acids Research, 2014, 42(12): e97.
[19] Love MI, Myšičková A, Sun R, et al. Modeling read counts for CNV detection in exome sequencing data [J]. Statistical Applications in Genetics and Molecular Biology, 2011, 10(1):1-30.
[20] Plagnol V, Curtis J, Epstein M, et al. A robust model for read count data in exome sequencing experiments and implications for copy number variant calling [J]. Bioinformatics, 2012, 28(21): 2747-2754. |
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