Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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:

  1. a true mutation
  2. an 8-oxoguanine artifact
  3. 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).

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