For de novo sequencing using capillary electrophoresis, the target DNA is fragmented and cloned into a viral or plasmid vector. Cloning provides amplification of the target DNA (by bacterial growth) and allows sequencing primers to bind to known sequence in the vector and extend the sequence into the unknown target DNA.
Researchers are not only using Ion AmpliSeq technology for less challenging research samples where available sample quantity and quality are not limiting, such as cell culture or fresh-frozen tissues, but also seeing tremendous success with challenging sample types, such as formalin-fixed paraffin-embedded (FFPE) tissue, achieved samples from fine needle aspirates, and cell-free DNA extracted from blood (cfDNA).