1. Supplemental Data

2. Mutation % Concordance
Supplement 1: Allele Frequency R2, Copy Number R2, and Mutation Percent Concordance for all samples in each tumor
Tumor
Samples
Allele frequency R2
Copy number R2
Mutation % Concordance T1
1 v 2
0.938
0.906
98.7% T4
0.910
0.802
96.3%
T11
0.690
0.933
84.3%
1 v 3
0.812
0.920
87.0%
2 v 3
0.748
0.902
88.2%
T20
0.845
0.817
92.7%
0.887
0.795
93.4%
0.903
0.868
94.2%
T204
0.886
0.740
89.9%
NP1
0.894
0.864
96.6%
0.897
0.929
0.958
0.856
100.0%
corr to allele freq R2 1
-0.393 p
0.206
4.8E-05
corr to copy# R2
-0.159
0.621
corr to concordance

3. Supplemental Data 2
Allele Frequency Plots for all tumors

4. Patient 1
Ca1 MATH = 22
Ca2 MATH = 20

5. Patient 4
Ca1 MATH = 7
Ca2 MATH = 9

6. Patient 11
Ca1 MATH = 11
Ca2 MATH = 11
Ca3 MATH = 11

7. Patient 20
Ca1 MATH = 42
Ca2 MATH = 40
Ca3 MATH = 40

8. Patient 204
Ca1 MATH = 22
Ca2 MATH = 16

9. Patient NP1
Ca1 MATH = 24
Ca2 MATH = 14
Ca3 MATH = 19

10. Supplemental Data 3
Copy Number Changes in all samples.

11. TuScan %aberrant: 55%
TuScan Ploidy: 4

12. TuScan %aberrant: 40%
TuScan Ploidy: 4

15. TuScan %aberrant: NA
TuScan Ploidy: NA
57%

16. TuScan %aberrant: 70%
TuScan Ploidy: 2

17. TuScan %aberrant: 65%
TuScan Ploidy: 2

18. TuScan %aberrant: 65%
TuScan Ploidy: 2

19. TuScan %aberrant: NA
TuScan Ploidy: NA
45%

21. TuScan %aberrant: 55%
TuScan Ploidy: 2
70%

22. TuScan %aberrant: 80%
TuScan Ploidy: 4
90%

23. TuScan %aberrant: NA
TuScan Ploidy: NA
50%

24. TuScan %aberrant: NA
TuScan Ploidy: NA
40%

25. TuScan %aberrant: NA
TuScan Ploidy: NA
30%

26. TuScan %aberrant: NA
TuScan Ploidy: NA
45%

27. TuScan %aberrant: 50%
TuScan Ploidy: 2
66%

28. TuScan %aberrant: NA
TuScan Ploidy: NA
45%

29. Supplemental Data 4
SciClone plots

30. P1: Three individual subclones were identified in the 2 copy number state and are all in both spatially distinct samples.

31. P4: Three individual subclones were identified in the 2 copy number state and are all in both spatially distinct samples.

32. P11: Six individual subclones were identified in the 2 copy number state. Subclones 1 and 2 are shared between samples but subclones 3 and 4 are just in sample 1, subclone 5 is just in sample 2 and subclone 6 is just in sample 3.

33. P20: Eight subclones were identified in the 2 copy number state and they were shared between samples.

34. P204: Two subclones were identified in the 2 copy number state and they were shared between samples but more prevelent in Sample 1 than 2.

35. NP1: Three subclones were identified in the 2 copy number state and all are shared between the different tumor samples.