DNA was extracted from patient’s tumor, early passage tumorgrafts developed from liver metastases, normal samples (adjacent non-cancerous liver or peripheral blood), and from normal tissue of the same mouse strain as those used to grow the xenografts using the Qiagen DNA FFPE tissue kit or Qiagen DNA blood mini kit (Qiagen, CA). Additional analyses were performed for CRC334 after afatinib anti-EGFR therapy and tumorgraft regrowth (indicated in footnote of Supplementary Table 4). Genomic DNA from tumor and normal samples were fragmented and used for Illumina TruSeq library construction (Illumina, San Diego, CA) according to the manufacturer’s instructions or as previously described33 (link). Exonic or targeted regions were captured in solution using the Agilent SureSelect v.4 kit or a custom targeted panel according to the manufacturer’s instructions (Agilent, Santa Clara, CA) (Supplementary Table 9). The captured library was then purified with a Qiagen MinElute column purification kit and eluted in 17 μl of 70°C EB to obtain 15 μl of captured DNA library. The captured DNA library was amplified in the following way: Eight 30uL PCR reactions each containing 19 μl of H2O, 6 μl of 5 × Phusion HF buffer, 0.6 μl of 10 mM dNTP, 1.5 μl of DMSO, 0.30 μl of Illumina PE primer #1, 0.30μl of Illumina PE primer #2, 0.30 μl of Hotstart Phusion polymerase, and 2 μl of captured exome library were set up. The PCR program used was: 98°C for 30 seconds; 14 cycles (exome) or 16 cycles (targeted) of 98°C for 10 seconds, 65°C for 30 seconds, 72°C for 30 seconds; and 72°C for 5 min. To purify PCR products, a NucleoSpin Extract II purification kit (Macherey-Nagel, PA) was used following the manufacturer’s instructions. Paired-end sequencing, resulting in 100 bases from each end of the fragments for exome libraries and 100 or 150 bases from each end of the fragment for targeted libraries, was performed using Illumina HiSeq 2000/2500 and Illumina MiSeq instrumentation (Illumina, San Diego, CA).