Files and links (1)
Accepted (AM)Open Access (License Unspecified), Open
Journal article
Characterization of full-length LINE-1 insertions in 154 genomes
Genomics (San Diego, Calif.), v 113(6), pp 3804-3810
Nov 2021
PMID: 34534648
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Long interspersed nuclear elements (LINEs) are retrotransposons that contribute to genetic variation in the human genome. LINE-1 elements in larger-scale studies are challenging to identify using sequencing technologies due to cost and scalability. We developed an approach using optical mapping for detection of full-length LINE-1 insertions and 10× sequencing for confirmation. We found 51 true positive full-length LINE-1 insertions, of which 4 are novel insertions, in NA12878. Repeating our analysis on a larger sample set representing 26 populations, we identified 329 full-length LINE-1 elements, of which 123 are novel. 24.8% of these 329 LINE-1 insertions were shared amongst all 5 superpopulations (AFR, AMR, EUR, EAS, SAS). The African superpopulation has a higher percentage of population-specific LINE-1 insertions than any other superpopulation. These data indicate that our approach can provide high-speed, cost-effective, and increased accuracy for LINE-1 detection. These data also provide an insight into variations of LINE-1 elements between different populations.
•Method of detecting full-length LINE1 insertions by whole-genome optical mapping in conjunction with 10× genomics sequencing.•Identified 329 full-length LINE-1 insertions (123 novel) in 154 genomes and their distribution across 26 populations.•Population analysis shows a higher percentage of population-specific LINE-1 s present in the African superpopulation.
Metrics
Details
- Title
- Characterization of full-length LINE-1 insertions in 154 genomes
- Creators
- Jessica S. Wong - Drexel UniversityTanaya Jadhav - Drexel UniversityEleanor Young - Drexel UniversityYilin Wang - Drexel UniversityMing Xiao - Drexel University
- Publication Details
- Genomics (San Diego, Calif.), v 113(6), pp 3804-3810
- Publisher
- Elsevier
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000709491200008
- Scopus ID
- 2-s2.0-85122548826
- Other Identifier
- 991019167735104721
UN Sustainable Development Goals (SDGs)
This publication has contributed to the advancement of the following goals:
InCites Highlights
Data related to this publication, from InCites Benchmarking & Analytics tool:
- Web of Science research areas
- Biotechnology & Applied Microbiology
- Genetics & Heredity