Figure 3. Comparison of kataegic mutations in yeast AID/APOBEC transformants with those in breast cancers.

(A) Comparison of the length, number of mutations and polarity of yeast kataegic clusters with those in breast cancers. The degree of strand polarity is indicated by colour intensity. The breast cancer data (Nik-Zainal et al., 2012) are a compilation from three tumours (PD4103a, PD4107a, PD4199a) chosen for their large number of clusters. (B) Context of the genome wide mutated C bases in yeast AID/APOBEC transformants with total numbers of mutations in each dataset indicated. (C) Context of the kataegic and singlet mutated C bases in selected breast cancers. Analyses of all sequenced breast cancers are presented in Figure 3—figure supplements 2–4. (D) Similarity of sequence contexts of C mutations in breast cancer kataegic stretches compared to those of deaminase-induced C mutations in yeast. (D1) Identity of the base at the −2 position of TC mutations in cancer kataegic regions and in APOBEC3A/B yeast transformants. The base compositions were normalised to the genomic base composition of the −2 base at TC dinucleotides. (D2) Sequence contexts similarity p-value at positions (−1 plus −2) to the mutated Cs. The contexts of all Cs throughout the yeast and human genomes are included for comparison. Mutation context of wild type versions of AID and APOBEC3G are shown in Figure 3—figure supplement 1. Analysis of additional yeast transformants and breast cancers is shown in Figure 3—figure supplements 2–4.

DOI: http://dx.doi.org/10.7554/eLife.00534.009

Figure 3—figure supplement 1. Mutation context of hyperactive APOBEC3G and AID are identical to the wild type proteins.

Mutation context of Can^R transformants expressing APOBEC3G and AID.

DOI: http://dx.doi.org/10.7554/eLife.00534.010

Figure 3—figure supplement 2. Analysis of kataegic stretches and mutation distributions of 21 breast cancers.

Analysis of tumours PD3851a to PD4086a. For each tumour, somatic mutations are displayed as intermutational distance (IMD) plots (top left), as described in Figure 1B. Dots are coloured according to kataegic mutations (black) or singlet mutations (red). The sequence context of C mutations in unclustered and kataegic locations are shown (lower plots), with the number of mutations indicated, coloured as in Figure 3B. The length and number of mutations within each cluster is displayed (top right), with the dot colour intensity indicating polarity. Data are taken from Nik-Zainal et al. (2012).

DOI: http://dx.doi.org/10.7554/eLife.00534.011

Figure 3—figure supplement 3. Analysis of kataegic stretches and mutation distributions of 21 breast cancers.

Analysis of tumours PD4088a to PD4194a. For each tumour, somatic mutations are displayed as intermutational distance (IMD) plots (top left), as described in Figure 1B. Dots are coloured according to kataegic mutations (black) or singlet mutations (red). The sequence context of C mutations in unclustered and kataegic locations are shown (lower plots), with the number of mutations indicated, coloured as in Figure 3B. The length and number of mutations within each cluster is displayed (top right), with the dot colour intensity indicating polarity. Data are taken from Nik-Zainal et al. (2012).

DOI: http://dx.doi.org/10.7554/eLife.00534.012

Figure 3—figure supplement 4. Analysis of kataegic stretches and mutation distributions of 21 breast cancers.

Analysis of tumours PD4198a to PD4248a. For each tumour, somatic mutations are displayed as intermutational distance (IMD) plots (top left), as described in Figure 1B. Dots are coloured according to kataegic mutations (black) or singlet mutations (red). The sequence context of C mutations in unclustered and kataegic locations are shown (lower plots), with the number of mutations indicated, coloured as in Figure 3B. The length and number of mutations within each cluster is displayed (top right), with the dot colour intensity indicating polarity. Data are taken from Nik-Zainal et al. (2012).

DOI: http://dx.doi.org/10.7554/eLife.00534.013