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Related Concept Videos

DNA Isolation01:24

DNA Isolation

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DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
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Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
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Fast and accurate resolution of ecDNA sequence using Cycle-Extractor.

Mahsa Faizrahnemoon, Jens Luebeck, King L Hung

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    Cycle-Extractor (CE) accurately reconstructs extrachromosomal DNA (ecDNA) structures from sequencing data. This tool enables better understanding of ecDNA

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    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.