Sequencing was performed using a Big Dye Terminator Ready Reaction Mix v1.1 kit and primers described in Supplementary Material, Table S3. Data were collected using an Applied Biosystems 3130xl Genetic Analyser. Data were analysed by visual inspection of electropherograms and using Mutation Surveyor software (SoftGenetics, Inc.).
For 78 of 79 tumour samples containing variants, the variant was confirmed in a second PCR using DNA that had not been whole-genome-amplified. One variant (tumour 1135) was confirmed in a second PCR from whole-genome-amplified DNA. Somatic mutation status in tumours was confirmed by analysis of normal matched blood samples except for samples 271, 595, 991, 1294, 1415 and 1434.