Method comparison for discovering copy number variation with next-generation sequencing in target exome regions

• Main Authors: Chen Li-Jing, 陳莉靜
• Other Authors: Huang Guan-Hua
• Format: Others
• Language: zh-TW
• Published: 2014
• Online Access: http://ndltd.ncl.edu.tw/handle/46254639984812006869

碩士 === 國立交通大學 === 統計學研究所 === 102 === Exome sequencing using next-generation sequencing technologies is a cost-efficient approach for detection of disease variants. One of the important applications of exome sequencing data is to identify copy number variations (CNVs). During the last several years, there have been many exome CNV softwares developed , but the accuracy and performance of these programs have not been thoroughly evaluated. In this thesis, we will review the theory of four popular exome CNV softwares (exomeCopy, ExomeDepth, cn.MOPS and CoNIFER) and uses the data of UK10K project (http://www.uk10k.org/) (214 samples with schizophrenia in Scotland) to systematically compare and evaluate four softwares. Although some preprocess of four software are equal, the results of detecting copy number variation are still different due to some different analysis methods. We further calculate the concordance, sensitivity and bias of these four software to systematically evaluate their performance and give some suggestions for the usage of them.