Table 1.

Efficiency of germline filtering in identifying somatic mutations

Sample ID	No. coding variants	No. xenograft nov-SNVs	No. true somatic mutations	No. true somatic mutations observed within set of xenograft nov-SNVs
LuCaP 92	17,092	193	56	51
LuCaP 145.2*	18,455	281	122	106
LuCaP 147*	22,458	2,122	2,045	1,823

We sequenced the exomes of normal and metastatic cancer tissue corresponding to three xenografts (LuCaP 92, LuCap 145.2, and LuCaP 147), and, for this analysis, considered only those positions called at high confidence across all three tissues. The first two columns represent the number of coding variants and nov-SNVs (variants observed in xenograft exome that remained after filtering) occurring at coordinates that could be confidently base-called in all three samples. The next two columns describe the number of true somatic mutations (defined by comparison of the exomes of normal and metastatic cancer tissue) within the set of all variants and the set of nov-SNVs. For example, filtering reduced the number of variants in LuCaP 92 from 17,092 to 193 while preserving 51 of 56 somatic mutations (sensitivity of 91%).

*Original tumor sample could not be identified, so a neighboring metastasis was used.