SeqURE - a new copy-capture based method for sequencing of unknown Retroposition events

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Retroelements (REs) comprise a significant portion of eukaryotic genomes.
• Active RE copies are typically repressed but can mobilize in specific tissues or cancer.
• Detecting rare, subclonal RE insertions is challenging due to artifacts and validation issues.

Purpose of the Study:

• To develop a novel method for efficient and reliable identification of new genomic RE insertions.
• To enable the detection of rare RE insertions present in a small fraction of cells.
• To provide a basis for quantitative assessment of RE insertions.

Main Methods:

• Implementation of a copy-capture technique within the SeqURE method.
• Selective amplification and sequencing of genomic regions flanking RE insertions.
• Development of a system to precisely test method sensitivity.

Main Results:

• SeqURE allows efficient and reliable identification of new genomic RE insertions.
• The method can detect insertions present in 1 out of 100 cells and a substantial portion in 1 out of 1000 cells.
• Absence of somatic Alu insertions was shown in colorectal cancer samples with tumor-specific L1HS insertions.

Conclusions:

• The study introduces the first copy-capture technique for RE insertion analysis.
• Provides a methodological basis for quantitative assessment of rare RE insertions.
• Enables validation of detected insertions using the intact template DNA.