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DNA Isolation

DNA Isolation

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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Related Experiment Video

Updated: Apr 28, 2026

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells

Published on: April 4, 2016

Fast and accurate resolution of ecDNA sequence using Cycle-Extractor.

Mahsa Faizrahnemoon, Jens Luebeck, King L Hung

Biorxiv : the Preprint Server for Biology

|April 27, 2026

Summary

This summary is machine-generated.

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.