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