Test-drive the GATK tools and Best Practices pipelines on Terra
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OxoG oxidative artifacts
Oxidation of guanine to 8-oxoguanine is one of the most common pre-adapter artifacts associated with genomic library preparation, arising from a combination of heat, shearing, and metal contaminates in a sample (doi: 10.1093/nar/gks1443). The 8-oxoguanine base can pair with either cytosine or adenine, ultimately leading to G→T transversion mutations during PCR amplification.
This occurs when a G on the template strand is oxidized, giving it an affinity for binding to A rather than the usual C. Thus, PCR will introduce apparent G>T substitutions in read 1 and C>A in read 2. In the resulting alignments, a given G>T or C>A observation could either be:
- a true mutation
- an 8-oxoguanine artifact
- some other kind of artifact.
The variants (C→A)/(G→T) tend to occur in specific sequence contexts e.g. CCG→CAG (doi:10.1093/nar/gks1443). Although occurring at relatively low frequencies, these artifacts can have profound impacts on variant calling fidelity (doi:10.1093/nar/gks1443).