In this study, SOX2 amplification was also associated with increased risk of malignant progression; combining PIK3CA and SOX2 amplification allowed for distinction of three cancer risk subgroups, and PIK3CA and SOX2 co-amplification was the strongest predictor (HR = 2.64, 95% CI 1.09–6.37, p = 0.031). Here, SOX2 is linked to cancer.