Systematic artifacts from Illumina two-color chemistry confound variant identification and actionability in clinical panels

Illumina short-read sequencing underpins clinical cancer genomics, with targeted panels widely used to detect actionable variants. Newer Illumina platforms employ a two-color chemistry to accelerate sequencing, but its impact on variant identification has not been systematically evaluated. Here we show that two-color platforms generate recurrent T>G artifacts in targeted panels at low variant allele fractions, predominantly occurring in specific trinucleotide contexts. These artifacts can produce spurious pathogenic variants in key cancer genes such as TP53 and KIT, and inflate tumor mutational burden, a metric considered when assessing patient eligibility for immunotherapy. Accounting for such artifacts is therefore essential for accurate interpretation of clinical panel data.