OxoG Filter

Overview

The OxoG filter removes oxidative DNA damage artifacts from somatic variant calls, specifically C>A transversions arising from 8-oxoguanine (OxoG) lesions introduced during DNA extraction or library preparation. These artifacts can masquerade as somatic mutations, particularly in samples with older or FFPE-derived DNA. The filter operates on variant allele frequencies and strand bias signals.

Used by

• Applied as one of eight named filters in the TCGA MC3 pipeline; run on the ISB Cancer Genomics Cloud and Broad FireCloud; targeted low-VAF G>T strand-biased artifacts particularly prevalent in WashU samples PMID:29596782

Notes

• Primarily targets C>A (G>T) transversions with strand bias — a hallmark of oxidative damage.
• Especially important for fresh-frozen samples with any degradation and for high-throughput pipelines where many samples are processed together.
• Part of the standard Broad Institute variant-calling quality-control suite.

Sources

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