iMGEins: detecting novel mobile genetic elements inserted in individual genomes SCIE SCOPUS

Cited 1 time in WEB OF SCIENCE Cited 1 time in Scopus
Title
iMGEins: detecting novel mobile genetic elements inserted in individual genomes
Author(s)
Bae, Junwoo; Lee, Kyeong Won; Islam, Mohammad Nazrul; Yim, Hyung-Soon; Park, Heejin; Rho, Mina
KIOST Author(s)
Lee, Kyeong Won(이경원)Yim, Hyung Soon(임형순)
Publication Year
2018-12-18
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.
ISSN
1471-2164
URI
https://sciwatch.kiost.ac.kr/handle/2020.kiost/776
DOI
10.1186/s12864-018-5290-9
Bibliographic Citation
BMC GENOMICS, v.19, 2018
Publisher
BMC
Subject
WHOLE-GENOME; SOMATIC RETROTRANSPOSITION; READ ALIGNMENT; DISCOVERY; ACCURATE; IDENTIFICATION; TOOLS
Keywords
Mobile genetic elements; Paired-end sequencing; Long insertions; Structural variations
Type
Article
Language
English
Document Type
Article
Publisher
BMC
Related Researcher
Research Interests

marine genomics,biochemistry,molecular cell biology,해양 유전체,생화학,세포분자 생물학

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