amplicon

An amplicon is a DNA fragment that has been amplified by polymerase chain reaction (PCR) or another in vitro amplification method. The term is commonly used to refer to the amplified product intended for downstream analysis.

In PCR, primers flank the region of interest and, through cycles of denaturation, annealing, and extension, copies of the target sequence are synthesized. In ideal conditions, each cycle doubles the number of copies, so after n cycles roughly 2^n more amplicon is present than the starting template. Amplicons usually range from about 100 to 1,000 base pairs, depending on primer design and sequencing needs.

Amplicons are central to amplicon sequencing, in which the amplified region is sequenced to determine genetic variation or to profile microbial communities by marker genes such as 16S rRNA. They also underpin targeted resequencing panels, SNP genotyping, and diagnostics in which real-time PCR monitors the accumulation of amplicons to infer target presence.

Challenges include amplification bias, preferential amplification of certain sequences, and the formation of chimeric sequences or primer-dimers. Contamination and off-target amplification can also affect results. Because amplicons represent only a subset of the genome, analyses must account for biases and artifacts when interpreting sequence data.

In sequencing workflows, dedicated primers and protocols enrich for specific loci, yielding amplicon libraries that enable high-depth, targeted analysis on short-read platforms. Amplicon data are commonly processed with quality filtering, primer trimming, and, in microbial studies, clustering into operational taxonomic units or amplicon sequence variants.