Fast and accurate resolution of ecDNA sequence using Cycle-Extractor

Area of Science:

• Genomics
• Bioinformatics
• Cancer Research

Background:

• Extrachromosomal DNA (ecDNA) is crucial in cancer, driving oncogene amplification and poor patient outcomes.
• Accurate reconstruction of ecDNA structures from sequencing data is vital for understanding their function but remains a challenge.

Purpose of the Study:

• To introduce Cycle-Extractor (CE), a novel computational tool for reconstructing ecDNA cycles.
• To evaluate CE's performance against existing methods using simulated and real cancer data.

Main Methods:

• CE accepts breakpoint graphs from short or long-read sequencing data.
• It employs a mixed-integer linear program (MILP) and a traversal procedure for efficient cycle extraction.
• Performance was compared to CoRAL, Decoil, and AmpliconArchitect (AA).

Main Results:

• CE achieved performance comparable to CoRAL and outperformed AA and Decoil on simulated ecDNA.
• On real cancer cell lines, CE identified longer and higher-copy ecDNA structures than AA.
• CE demonstrated significantly faster processing times (40x) compared to CoRAL.

Conclusions:

• CE accurately reconstructs ecDNA from both short and long-read sequencing data.
• Long-read sequencing with CE enables recovery of more complete and higher-confidence ecDNA structures.
• CE successfully reconstructed a large, high-copy MYC-containing ecDNA in PC3 cells, validated by CRISPR-CATCH experiments.