Detecting low-allele-fraction mosaic mutations: A multi-institution benchmarking with cell-line mixtures.

Detection of low-allele-fraction mosaic mutations with VAFs above 2% achieves nearly 80% sensitivity and precision at 300× sequencing depth across multiple centers.

• Why it matters: Accurate identification of mosaic mutations in normal tissues is challenging due to their low VAFs, which hampers reliable detection and understanding of their biological significance.
• What they did: The SMaHT Network created a cell-line mixture and generated ultra-deep sequencing data at five centers, applying twelve variant-calling pipelines to assess detection performance and expose limitations.
• The result: Findings suggest that for VAFs above 2%, increasing sequencing depth beyond 300× offers little benefit, and the study provides a framework and resources to improve low-VAF mutation detection.