To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

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).

Sign In or Register to comment.