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Cas9 targeted enrichment of mobile elements using nanopore sequencing
Torrin L McDonald1, Weichen Zhou2, Christopher P Castro2
1Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
Nature Communications
|June 12, 2021
Summary
This study introduces Cas9-targeted nanopore sequencing to efficiently detect mobile element insertions (MEIs) in human genomes. This method significantly enriches for these repetitive sequences, aiding in the discovery of genetic variations.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Mobile element insertions (MEIs) are repetitive genomic sequences contributing to genetic variation and disorders.
- Short-read sequencing methods struggle to detect MEIs in complex genomic regions due to limited read length.
Purpose of the Study:
- To develop and validate a novel method for capturing active MEIs in human genomes.
- To enhance the detection of mobile element insertions, particularly in challenging genomic areas.
Main Methods:
- Utilized Cas9-targeted nanopore sequencing combined with computational analysis.
- Achieved parallel enrichment for distinct classes of MEIs, significantly increasing on-target read percentages.
Main Results:
- Demonstrated substantial enrichment (13.4-54x) for MEIs compared to whole-genome approaches.
- Recovered a high percentage of major MEI classes (e.g., 97% L1Hs, 93% AluYb) in a single flow cell.
- Identified seventeen novel non-reference MEIs in GM12878, including those missed by existing long-read pipelines, primarily in repetitive regions.
Conclusions:
- Cas9-targeted nanopore sequencing is a powerful tool for MEI enrichment and discovery.
- This approach facilitates the rapid identification of elusive repetitive genetic elements, advancing the study of genetic variation and disorders.
