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

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Presentation transcript:

Calibration 5

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

OV Chr and total CN distributionSNVs in highly amplified region

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

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

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

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

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

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

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

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

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

PACA 65d2dbc3-a b246-47a430e66572

CITUP-single PACA 65d2dbc3-a 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

PACA 65d2dbc3-a b246-47a430e66572

PACA – refit 65d2dbc3-a b246-47a430e66572

PACA 65d2dbc3-a b246-47a430e66572: Summary PhyloWGSPhyloSub

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

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

PACA 65d2dbc3-a b246-47a430e66572: PhyloWGS tree

PACA 65d2dbc3-a b246-47a430e66572: PhyloSub tree

PACA 65d2dbc3-a b246-47a430e66572 VAF

PBCA edc070db-b f-ae75-4c4012bdc3fe

CITUP-single PBCA edc070db-b f-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

PBCA edc070db-b f-ae75-4c4012bdc3fe

PBCA edc070db-b f-ae75-4c4012bdc3fe: Summary PhyloWGSPhyloSub

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

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

PBCA edc070db-b f-ae75-4c4012bdc3fe: PhyloWGS tree

PBCA edc070db-b f-ae75-4c4012bdc3fe: PhyloSub tree

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

PBCA edc070db-b f-ae75-4c4012bdc3fe

CITUP-single Combined vs Sanger only Combined Sanger Only