Chimera (molecular biology)

In molecular biology, and more importantly high-throughput DNA sequencing, a chimera is a single DNA sequence originating when multiple transcripts or DNA sequences get joined. Chimeras can be considered artifacts and be filtered out from the data during processing to prevent spurious inferences of biological variation. However, chimeras should not be confused with chimeric reads, who are generally used by structural variant callers to detect structural variation events and are not always an indication of the presence of a chimeric transcript or gene. In a different context, the deliberate creation of artificial chimeras can also be a useful tool in molecular biology. For example, in protein engineering, "chimeragenesis" (forming chimeras between proteins that are encoded by homologous cDNAs) is one of the "two major techniques used to manipulate cDNA sequences". For gene fusions that occur through natural processes, see chimeric genes and fusion genes. A chimera can occur as a single cDNA sequence originating from two transcripts. It is usually considered to be a contaminant in transcript and expressed sequence tag (which results in the moniker of EST chimera) databases. It is estimated that approximately 1% of all transcripts in the National Center for Biotechnology Information's Unigene database contain a "chimeric sequence". A chimera can also be an artifact of PCR amplification. It occurs when the extension of an amplicon is aborted, and the aborted product functions as a primer in the next PCR cycle. The aborted product anneals to the wrong template and continues to extend, thereby synthesizing a single sequence sourced from two different templates. PCR chimeras are an important issue to take into account during metabarcoding, where DNA sequences from environmental samples are used to determine biodiversity. A chimera is a novel sequence that will most probably not match to any known organism. Hence, it might be interpreted as a new species thereby overinflating the diversity. PCR chimeras also occur in DNA sequencing.