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The chromosomal DNA flanking regions used to construct the relevant suicide vectors for ΔPfur81 TT araC PBAD fur, ΔasdA33, and Δ tviABCDE10 mutations were amplified from the S. Typhi Ty2 chromosome.

The samples screened for BRCA1 and BRCA2 mutations were amplified using the BRCA MASTR kit v2.1.

The fragments containing the pre-defined mutations were amplified and sequenced using specific primers (Additional File 9).

Clones carrying the desired mutations were amplified and plasmids were extracted using NucleoBond Xtra Maxi EF (Macherey-Nagel, Bethlehem, PA).

Fragments of genomic DNA containing point mutations were amplified by PCR using the original purified fosmid as the template.

BRAF exon 15, which contains the V600E mutation, and KRAS codon 12/13 mutations were amplified using primers reported in Supplementary Table 1.

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Each fragment containing mutations was amplified by PCR and sequenced a second time to confirm that the identified mutations were not due to PCR artifacts.

Fragments in regions suspected to contain the mutation were amplified by PCR and sequenced.

Myc-tagged full length KREPA3 WT and mutant genes with one or both zinc fingers mutation were amplified from the plasmids pLEW79-A3-TAP, pLEW79-A3ZFm1-TAP, pLEW-A3ZFm2-TAP and pLEW79-A3ZFm1&2-TAP [49], respectively, by using the primers 5'-CCTCGAGCCACCATGAAGCGTGTTACTTCAC-3' and 5'-ATTCATGATCACAGGTCTTCTTCAGAGATCAG-3'.

Selected variant regions (~125pb flanking the identified somatic mutation) were amplified and PCR products were sequenced on the Ion PGM Sequencer (Life Technologies) according to the manufacturer's protocol with a mean coverage >1,800X.

Importantly, although Kras is a single oncogene, several studies show that Kras codon 12 GAT mutation is amplified during carcinogenesis, even when the mutational specificity of the mutagen is other than the G to A mutation being measured.

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