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iMGEins: detecting novel mobile genetic elements inserted in individual genomes

Title
iMGEins: detecting novel mobile genetic elements inserted in individual genomes
Author
박희진
Keywords
Mobile genetic elements; Paired-end sequencing; Long insertions; Structural variations
Issue Date
2018-12
Publisher
BMC
Citation
BMC GENOMICS, v. 19, Article no. 944
Abstract
BackgroundRecent advances in sequencing technology have allowed us to investigate personal genomes to find structural variations, which have been studied extensively to identify their association with the physiology of diseases such as cancer. In particular, mobile genetic elements (MGEs) are one of the major constituents of the human genomes, and cause genome instability by insertion, mutation, and rearrangement.ResultWe have developed a new program, iMGEins, to identify such novel MGEs by using sequencing reads of individual genomes, and to explore the breakpoints with the supporting reads and MGEs detected. iMGEins is the first MGE detection program that integrates three algorithmic components: discordant read-pair mapping, split-read mapping, and insertion sequence assembly. Our evaluation results showed its outstanding performance in detecting novel MGEs from simulated genomes, as well as real personal genomes. In detail, the average recall and precision rates of iMGEins are 96.67 and 100%, respectively, which are the highest among the programs compared. In the testing with real human genomes of the NA12878 sample, iMGEins shows the highest accuracy in detecting MGEs within 20bp proximity of the breakpoints annotated.ConclusionIn order to study the dynamics of MGEs in individual genomes, iMGEins was developed to accurately detect breakpoints and report inserted MGEs. Compared with other programs, iMGEins has valuable features of identifying novel MGEs and assembling the MGEs inserted.
URI
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-5290-9http://repository.hanyang.ac.kr/handle/20.500.11754/120973
ISSN
1471-2164
DOI
10.1186/s12864-018-5290-9
Appears in Collections:
COLLEGE OF ENGINEERING[S](공과대학) > COMPUTER SCIENCE(컴퓨터소프트웨어학부) > Articles
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