PTPN4 and neoplasm: Truncal mutations that occurred in all tumor subclones included chromosome losses in TP53 and NOTCH3 and gains in DMKN and GRIN3A, while early mutations included TP53, GRIN3A, PTPN4, and AKAP6. The c3 subclone was closest to the MRCA, suggesting that it was one of the earliest subclones that diverged, consistent with the clustering results, which showed that it harbored the lowest number of mutations (n = 33).