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Table 2 Overview of methods for eccDNA investigation

From: Small extrachromosomal circular DNA (eccDNA): major functions in evolution and cancer

Methods

Description

Advantage or Limitation

References

Electron microscopy

Localization, identification, quantification

No sequence information

[9]

Karyotype

Localization, identification, quantification

No sequence information

[7]

2D gel electrophoresis

Identification

No sequence information

[98, 100]

Southern blotting

Quantification

Little sequence information

[98]

Inverse PCR

Quantification, identification

Little but useful sequence information

[15, 42]

FISH

Localization, identification, quantification

Little sequence information

[7,8,9]

Density gradient centrifugation

Isolation and purification

Laborious

[47]

Methods based on next-generation sequencing

Localization, quantification, high resolution, (1) tagmentation method is more sensitive than (2) nuclease digestion (Msp); (3) exonuclease III digestion; (4) exonuclease V digestion; (5) rolling-amplification

High throughput, high resolution, sensitive, expensive

[4,5,6,7,8,9, 26, 34]