Several lines of evidence support the validity of these subclonal mutations, including Illumina resequencing of an independent whole genome amplification aliquot, which confirmed both their presence (Supplementary Fig. 8a,b), and that their allelic fractions corresponded to subclonal multiplicity values (Supplementary Fig. 8c,d). In addition, the mutation spectrum seen for clonal and subclonal mutations was similar (RMSE = 0.02, Fig. 4c), consistent with a common mechanism of origin. Power calculations showed that these samples were at least 80% powered for detection of subclonal mutations occurring in cancer-cell fractions ranging from 10% to 53%, with a median of 19% (Supplementary Fig. 7e).
