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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]