1. ICGC PCAWG WG-11 Data Calibration Round 3 – 2015-08-07

2. Overview A brief update from last week 3 selected samples

3. PBCA ac1bd179-8285-468c-ab9f-7f91151ca0f2

4. fraction of subclonal copy numbers: 0.1343 number of subclonal populations: 0 PBCA: ac1bd179-8285-468c-ab9f-7f91151ca0f2

5. PBCA: ac1bd179-8285-468c-ab9f-7f91151ca0f2 discussion 1 2 3 raw copy number BAF normal BAF tumor Is the diploid (purity=45%) or tetraploid (purity=85%) correct? genomic loss + BAF  purity > 50% and is compatible with 85% Leaving out chr18 or under-segmenting the sample yields the diploid solution: the tetraploid solution is likely to be correct, thus chromosome doubling occurred probably before most copy number changes.

6. PBCA ac1bd179-8285-468c-ab9f-7f91151ca0f2

7. Conclusion: – This is a tetraploid sample – Still a bit ofuncertainty about the subclonal copy number segments

8. 3 new samples

9. BOCA f86e2d80-911b-7a19-e040-11ac0d486900

13. CITUP-single - data calibration

14. BOCA Battenberg Interestingly, in Battenberg calls chromosome X is mostly neutral but in Sanger, there are large CNV regions CITUP-single - data calibration

15. BOCA f86e2d80-911b-7a19-e040- 11ac0d486900 Battenberg Sanger Battenberg: 199 X 1,455,089 2,699,246 0.503947351500281 1 0.19222126988525 3.59577066099121 2 2 1 200 X 154,933,612 155,233,098 0.641222214024068 0.0535333794525915 -0.0396146835282881 2.93818768414796 2 1 1 Sanger: X 169804. C.. SVTYPE=CNV;END=31,637,696 GT:TCN:MCN./.:2:1./.:2:0 X 31,646,868. C.. SVTYPE=CNV;END=31,824,663 GT:TCN:MCN./.:2:1./.:1:0 X 31,824,849. T.. SVTYPE=CNV;END=31,971,839 GT:TCN:MCN./.:2:1./.:0:0 X 31,974,706. A.. SVTYPE=CNV;END=32,382,035 GT:TCN:MCN./.:2:1./.:1:0 X 32,383,033. A.. SVTYPE=CNV;END=32,612,038 GT:TCN:MCN./.:2:1./.:0:0 X 32,614,102. C.. SVTYPE=CNV;END=32,707,631 GT:TCN:MCN./.:2:1./.:1:0 X 32,712,356. G.. SVTYPE=CNV;END=33,074,990 GT:TCN:MCN./.:2:1./.:0:0 X 33,078,993. A.. SVTYPE=CNV;END=33,998,554 GT:TCN:MCN./.:2:1./.:1:0 X 33,999,187. G.. SVTYPE=CNV;END=155,233,846 GT:TCN:MCN./.:2:1./.:2:0 CITUP-single - data calibration

16. f86e2d80-911b-7a19-e040-11ac0d486900: Summary PhyloWGSPhyloSub

17. f86e2d80-911b-7a19-e040-11ac0d486900: Cellular prevalence First cancerous population Second cancerous population Third cancerous population PhyloWGSPhyloSub

18. f86e2d80-911b-7a19-e040-11ac0d486900: SSM distribution First cancerous population Second cancerous population Third cancerous population PhyloWGSPhyloSub

19. BOCA f86e2d80-911b-7a19-e040-11ac0d486900

20. BOCA – F86e2d80 Purity used: 0.71 (from ASCAT) CCFNumber of SVs 1.2930 0.41155

21. CESC 047f9e4d-86b5-4943-aef5-68199bf29e8c

23. CITUP-single - data calibration

24. CESC Battenberg Overlap between usable SNVs in Battenberg and Sanger calls are high (94-98%) Purity estimate using Battenberg calls is similar Probably only 1 subclone CITUP-single - data calibration

25. CESC 047f9e4d-86b5-4943-aef5-68199bf29e8c Battenberg Sanger CITUP-single - data calibration

26. CESC 047f9e4d-86b5-4943-aef5-68199bf29e8c Sanger When run with stricter parameters, CITUP merges the two close-by clusters though the purity estimate is somewhat smaller There is still a small subclone around 0.5 though (with some evidence) CITUP-single - data calibration

27. 047f9e4d-86b5-4943-aef5-68199bf29e8c: Summary PhyloWGSPhyloSub

28. 047f9e4d-86b5-4943-aef5-68199bf29e8c: Cellular prevalence First cancerous population Second cancerous population Third cancerous population PhyloWGSPhyloSub

29. 047f9e4d-86b5-4943-aef5-68199bf29e8c: SSM distribution First cancerous population Second cancerous population Third cancerous population PhyloWGSPhyloSub

30. CESC 047f9e4d-86b5-4943-aef5-68199bf29e8c

31. GBM 56ffaa35-814c-4c0b-b3c6-d4514d34fec2

33. CITUP-single - data calibration

34. GBM Battenberg Little overlap between usable Battenberg SNVs and Sanger SNVs: 167 out of 308 (54% in Sanger) and out of 271 (61% in Battenberg) CITUP-single - data calibration

35. GBM 56ffaa35-814c-4c0b-b3c6-d4514d34fec2 Battenberg Sanger Little overlap between usable Battenberg SNVs and Sanger SNVs: 167 out of 308 (54% in Sanger) and out of 271 (61% in Battenberg) CITUP-single - data calibration

36. 56ffaa35-814c-4c0b-b3c6-d4514d34fec2: Summary PhyloWGSPhyloSub

37. 56ffaa35-814c-4c0b-b3c6-d4514d34fec2: Cellular prevalence First cancerous population Second cancerous population Third cancerous population PhyloWGSPhyloSub

38. 56ffaa35-814c-4c0b-b3c6-d4514d34fec2: SSM distribution First cancerous population Second cancerous population Third cancerous population PhyloWGSPhyloSub

39. GBM 56ffaa35-814c-4c0b-b3c6-d4514d34fec2

40. GBM– 56ffaa35 Purity used: 0.62 (from ASCAT) CCFNumber of SVs 1.25 0.3947