Tumor (all mutations)

Den

sity

(a.u

.)

VAF

Tum

or C

over

age

1 0.8 0.6 0.4 0.2 05

102050

100200500

1000

Mutation VAF on copy number 3

Mutation CCF on copy number 3

Mutation CCF on copy number 2

Den

sity

(a.u

.)

VAF

Tum

or C

over

age

1 0.8 0.6 0.4 0.2 05

102050

100200500

1000

Den

sity

(a.u

.)Tu

mor

Cov

erag

e

5102050

100200500

1000

Den

sity

(a.u

.)Tu

mor

Cov

erag

e

5102050

100200500

1000

Den

sity

(a.u

.)Tu

mor

Cov

erag

e

5102050

100200500

1000

Mutation VAF on copy number 2

VAF1 0.8 0.6 0.4 0.2 0

Cancer Cell Fraction1 0.8 0.6 0.4 0.2 0

Cancer Cell Fraction1 0.8 0.6 0.4 0.2 0

Mutation CCF (all muations)

Den

sity

(a.u

.)

Cancer Cell Fraction

Clonal mutationSubclonal mutation

Tum

or C

over

age

1 0.8 0.6 0.4 0.2 05

102050

100200500

1000

Figure 1

1/4 2/5 4/10 620/640VAF 0.13

0/20.0

0/10.0

0/10.0 0.2 0.2 0.24 0.24 0.48

VAFcellular frequency

cellular frequency

A) Mutations under positive selection

B) Mutations under neutral evolution

8/14 16/28

4/4 5/5 10/10 640/6402/21/10.5 0.5 0.5 0.5 0.5 0.5 0.5

0/10.0 0.5

14/14 28/28

1/4 2/8 160/640VAF 0.13 0.13

0/20.0

0/10.0

0/10.0 0.13 0.13

VAFcellular frequency

cellular frequency 4/16

0/4 0/8 40/640VAF 0.0 0.0

0/20.0

0/10.0

0/10.0 0.03 0.03

cellular frequency 1/16

4/4 8/8 640/6402/21/10.5 0.5 0.5 0.5 0.5

0/10.0 0.5

16/16

.....

Figure 2

evolutionary time

Therapy induced mutagenesis

Therapy as a selective pressure

Pre-existing resistant clone

Shift in clonal composition

Maintenance of clonal composition

A)

B)

C)

D)

therapy relapse

Figure 3