Analysis of amplicons has been made possible by the development of amplification methods such as PCR, and increasingly by cheaper and more high-throughput technologies for DNA sequencing or next-generation sequencing, such as ion semiconductor sequencing, popularly referred to as the brand of the developer, Ion Torrent.
DNA sequencing technologies such as next-generation sequencing have made it possible to study amplicons in genome biology and genetics, including cancer genetics research, phylogenetic research, and human genetics. For example, using the 16S rRNA gene, which is part of every bacterial and archaeal genome and is highly conserved, bacteria can be taxonomically classified by comparison of the amplicon sequence to known sequences. This works similarly in the fungal domain with the 18S rRNA gene as well as the ITS1 non-coding region.
Irrespective of the approach used to amplify the amplicons, some technique must be used to quantitate the amplified product. Generally, these techniques incorporate a capture step and a detection step, although how these steps are incorporated depends on the individual assay.
Examples include the Amplicor HIV-1 Monitor Assay (RT-PCR), which has the capacity to recognize HIV in plasma; the HIV-1 QT (NASBA), which is used to measure plasma viral load by amplifying a segment of the HIV RNA; and transcription mediated amplification, which employs a hybridization protection assay to distinguish Chlamydia trachomatis infections. Various detection and capture steps are involved in each approach to assess the amplification product, or amplicon. With amplicon sequencing the high number of different amplicons resulting from amplification of a usual sample are concatenated and sequenced. After quality control classification is done by different methods, the counts of identical taxa representing their relative abundance in the sample.