Fig. S4.

Identification of fixed and polymorphic mutations. A total of 269 putative SNVs were found from the 23 sequenced tumor sections. Diamond, 3 SNVs were randomly chosen for validation; cross-star and star, these SNVs were chosen for validation in the whole-exome sequencing (WES) samples where they were missing, usually due to low read depth. These 269 SNVs are divided into 209 fixed and 38 polymorphic mutations. In addition, 22 SNVs are possibly fixed but have been lost occasionally (i.e., LOH in CNA regions; Materials and Methods, section 4) and 3 SNVs are possibly polymorphic but could not be reliably confirmed by Sequenom across samples due to PCR difficulties.