vafSOMA: Detecting cell-layer-fixed somatic mutations in plants

vafSOMA detects layer-fixed somatic mutations in plants by modeling tissue composition, recovering branch meristem–fixed mutations with estimates close to the simulated stem-cell mutation rate.

• Why it matters: Bulk plant sequencing mixes DNA from multiple meristem layers, making variant allele frequencies depend on tissue contributions and obscuring which fixed somatic mutations are present.
• What they did: The model uses tissue composition to infer mutation counts and assign mutations to layers, handling bulk and layer-enriched samples, and it was evaluated in simulations and on apricot sequencing data.
• The result: In simulations it matched the best hindsight variant allele frequency cutoff without a user-chosen threshold, and diagnostics flagged unsupported layers; in apricot, dominant-layer mutations were recovered from fruit mixtures at high depth while epidermal mutations stayed unresolvable, implying bulk studies may miss fixed mutations by about two- to threefold when layer-specific rates are similar.

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