Sample-Index Misassignment Impacts Tumor Exome Sequencing

Sample pooling enabled by dedicated indexes is a common and cost-effective strategy used in high-throughput DNA sequencing. Index misassignment leading to cross-sample contamination has however been described as a general problem of sequencing instruments which utilize exclusion amplification. Using real-life data from multiple tumor sequencing projects, we demonstrate that co-multiplexed samples can induce artifactual calls closely resembling high-quality somatic variant calls, and argue that dual indexing is the most reliable countermeasure.