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Calibration 5. OV 7fdd07a4-4a27-40c3-af92-a0074e6391f5.

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Presentation on theme: "Calibration 5. OV 7fdd07a4-4a27-40c3-af92-a0074e6391f5."— Presentation transcript:

1 Calibration 5

2 OV 7fdd07a4-4a27-40c3-af92-a0074e6391f5

3 OV Chr and total CN distributionSNVs in highly amplified region

4 CITUP-single OV 7fdd07a4-4a27-40c3-af92-a0074e6391f5 Purity is predicted to be low Not many mutations in copy neutral regions Likely clonal, although not enough power to call subclones due to low purity and few mutations CITUP predictions on this sample differs when using Sanger-pipeline CNV calls, which indicates subclonal copy change

5 OV 7fdd07a4-4a27-40c3-af92-a0074e6391f5

6

7 OV 7fdd07a4-4a27-40c3-af92-a0074e6391f5: Summary PhyloWGSPhyloSub

8 OV 7fdd07a4-4a27-40c3-af92-a0074e6391f5: Cellular prevalence First cancerous population Second cancerous population Third cancerous population PhyloWGSPhyloSub

9 OV 7fdd07a4-4a27-40c3-af92-a0074e6391f5: SSM distribution First cancerous population Second cancerous population Third cancerous population PhyloWGSPhyloSub

10 OV 7fdd07a4-4a27-40c3-af92-a0074e6391f5: PhyloWGS tree

11 OV 7fdd07a4-4a27-40c3-af92-a0074e6391f5: PhyloSub tree

12 OV– 7fdd07a4 Purity used: 0.46 (from ASCAT) CCFNumber of SVs 0.5923 0.1420

13 OV 7fdd07a4-4a27-40c3-af92-a0074e6391f5

14 PACA 65d2dbc3-a163-4696-b246-47a430e66572

15 CITUP-single PACA 65d2dbc3-a163-4696-b246-47a430e66572 Purity is predicted to be very high There seems to be at least 1 subclone, possibly more Distribution of mutations to chromosomes seem homogeneous across the sucblones

16 PACA 65d2dbc3-a163-4696-b246-47a430e66572

17

18 PACA – refit 65d2dbc3-a163-4696-b246-47a430e66572

19 PACA 65d2dbc3-a163-4696-b246-47a430e66572: Summary PhyloWGSPhyloSub

20 PACA 65d2dbc3-a163-4696-b246-47a430e66572: Cellular prevalence First cancerous population Second cancerous population Third cancerous population PhyloWGSPhyloSub

21 PACA 65d2dbc3-a163-4696-b246-47a430e66572: SSM distribution First cancerous population Second cancerous population Third cancerous population PhyloWGSPhyloSub

22 PACA 65d2dbc3-a163-4696-b246-47a430e66572: PhyloWGS tree

23 PACA 65d2dbc3-a163-4696-b246-47a430e66572: PhyloSub tree

24 PACA 65d2dbc3-a163-4696-b246-47a430e66572 VAF

25 PBCA edc070db-b768-478f-ae75-4c4012bdc3fe

26 CITUP-single PBCA edc070db-b768-478f-ae75-4c4012bdc3fe Tumor purity is predicted to be high Not much going on in copy number profile (according to both BB and Sanger) except for a few chromosomes, i.e. the “high purity” is not likely to be explained by missing deletions A cross-check of dbSNP variants (v. June 2015) resulted in 127 matches, but only 43 of them are actually assigned to the clonal population

27 PBCA edc070db-b768-478f-ae75-4c4012bdc3fe

28

29 PBCA edc070db-b768-478f-ae75-4c4012bdc3fe: Summary PhyloWGSPhyloSub

30 PBCA edc070db-b768-478f-ae75-4c4012bdc3fe: Cellular prevalence First cancerous population Second cancerous population Third cancerous population PhyloWGSPhyloSub

31 PBCA edc070db-b768-478f-ae75-4c4012bdc3fe: SSM distribution First cancerous population Second cancerous population Third cancerous population PhyloWGSPhyloSub

32 PBCA edc070db-b768-478f-ae75-4c4012bdc3fe: PhyloWGS tree

33 PBCA edc070db-b768-478f-ae75-4c4012bdc3fe: PhyloSub tree

34 PBCA– edc070db Purity used: 0.97 (from ASCAT) CCFNumber of SVs 0.1427

35 PBCA edc070db-b768-478f-ae75-4c4012bdc3fe

36 CITUP-single Combined vs Sanger only Combined Sanger Only

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