Amplicon sequencing is when a DNA or RNA sequence is amplified, or copied many times, using PCR. The amplified sequences are converted to libraries, pooled and sequenced. Amplicon sequencing has been used for biomonitoring, diet analysis and microbial metagenomics. Amplicons commonly targeted for sequencing include 16s ribosomal RNA (rRNA), 18s rRNA and ITS (internal transcribed spacer). The ITS sequence is a nonfunctional RNA located between structural rRNA of a common precursor transcript. 16s, 18s and ITS sequencing are used for taxonomy and identifying the relationships between species and genera in bacteria and fungi because these regions are highly variable in sequence.
Amplicon sequencing is based on Next Generation Sequencing (NGS) technology or PacBio SMRT sequencing. This technique has a wide range of applications including 16S/18S/ITS gene sequencing, SNP genotyping, CRISPR sequencing, somatic/complex variant discovery, antibody screening sequencing, and immune repertoire sequencing.