In consistent with conventional belief7, we found benign nodules are genetically unrelated to PTC as define by: few overlapping mutations and distinct branched evolutionary relationships in the paired benign nodule and PTC samples, especially for those PTC with BRAF mutation; PTC-related mutations detected in benign nodules did not exist in the paired PTC tumour; and distinct transcriptome clustering and functional pathways between benign nodules and PTCs. Here, BRAF is linked to neoplasm.