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. 2016 Jan 13;24(8):1167–1174. doi: 10.1038/ejhg.2015.281

Table 1. Tumour staging data for 23 patients with UBC together with information on TARGET aberrations identified.

Patient number Tumour stage Grade DNA source Number of TARGET aberrations identified Sensitivity for TARGET mutations present in FFPE (%) Details of TARGET aberrations Comments
1 pT2+ G3 FFPE tumour sections 2 NA KIT amp; CDKN2A/B biallelic loss  
      Urine supernatant 2 100 KIT amp; CDKN2A/B biallelic loss  
      Urine cell pellet NA NA NA DNA insufficient for OncoScan
2 pT2+ G3 FFPE tumour sections 5 NA AKT2 amp; CDK4 amp; MCL1 amp; MDM2 amp; RAF1 amp  
      Urine supernatant 5 100 AKT2 amp; CDK4 amp; MCL1 amp; MDM2 amp; RAF1 amp  
      Urine cell pellet 0 0 NA  
3 pT2+ G3 FFPE tumour sections 3 NA PIK3CA:c.1633G>A (p.(E545K)); PIK3CA:c.1624G>A (p.(E542K)); CDKN2A/B biallelic loss Differences in somatic mutations identified in urine and FFPE samples highlights tumour heterogeneity. Mutations in urine cfDNA consistent with FFPE sections from deeper tumour material (data not shown)
      Urine supernatant 3 67 PIK3CA:c.1633G>A (p.(E545K)); TP53:c.524G>A (p.(R175H)); CDKN2A/B biallelic loss  
      Urine cell pellet 3 67 PIK3CA:c.1633G>A (p.(E545K)); TP53:p.R175H; TP53:c.524G>A (p.(R175H)) CDKN2A/B biallelic loss  
4 pT2+ G3 FFPE tumour sections 0 NA   Clear and consistent CN aberrations evident for both cfDNA and FFPE DNA
      Urine supernatant 0 NA    
      Urine cell pellet 0 NA    
5 pT2+ G3 FFPE tumour sections 12 NA AKT2 amp; AURKA amp; BRAF amp; CCND3 amp; CCNE1 amp; CDK6 amp; CRKL amp; EGFR amp; FGFR1 amp; MAPK1 amp; MCL1 amp; MET amp  
      Urine supernatant 12 100 AKT2 amp; AURKA amp; BRAF amp; CCND3 amp; CCNE1 amp; CDK6 amp; CRKL amp; EGFR amp; FGFR1 amp; MAPK1 amp; MCL1 amp; MET amp  
      Urine cell pellet 0 0   Apparently representative of germline genome only
6 pT2+ G3 FFPE tumour sections NA NA   DNA insufficient for OncoScan
      Urine supernatant 1 100 MCL1 amp In absence of FFPE results, assume cfDNA to be representative of tumour
      Urine cell pellet 0 0   Apparently representative of germline genome only
7 pT2+ G3 FFPE tumour sections 0 NA Quality insufficient to call aberrations  
      Urine supernatant 2 100 CCND1 amp; CCNE1 amp In absence of FFPE results, assume urine DNA aberrations to be representative of tumour
      Urine cell pellet 2 100 CCND1 amp; CCNE1 amp In absence of FFPE results, assume urine DNA aberrations to be representative of tumour
8 pT2+ G3 FFPE tumour sections 3 NA FGFR1 amp; MYC amp; PIK3CA:c.3140A>G (p.(H1047R))  
      Urine supernatant 3 100 FGFR1 amp; MYC amp; PIK3CA:c.3140A>G (p.(H1047R))  
      Urine cell pellet 1 33 PIK3CA:c.3140A>G (p.(H1047R))  
9 pTa G1 FFPE tumour sections 0 NA    
      Urine supernatant 0 NA    
      Urine cell pellet 0 NA    
10 pT2+ G3 FFPE tumour sections 0 NA    
      Urine supernatant 0 NA    
      Urine cell pellet NA NA   DNA insufficient for OncoScan
11 pTa G2 FFPE tumour sections 1 NA CDKN2A biallelic loss  
      Urine supernatant NA NA   Quality of OncoScan data too poor for accurate analysis
      Urine cell pellet NA NA   DNA insufficient for OncoScan
12 pT2+ G3 FFPE tumour sections 1 NA TP53:c.844C>T (p.(R282W))  
      Urine supernatant 1 100 TP53:c.844C>T (p.(R282W))  
      Urine cell pellet 1 100 TP53:c.844C>T (p.(R282W))  
13 pT2+ G3 FFPE tumour sections 3 NA CCND1 amp; CDK4 amp; MDM2 amp  
      Urine supernatant 3 100 CCND1 amp; CDK4 amp; MDM2 amp  
      Urine cell pellet 3 100 CCND1 amp; CDK4 amp; MDM2 amp  
14 pTa G1 FFPE tumour sections 1 NA PIK3CA:c.3140A>G (p.(H1047R))  
      Urine supernatant 1 100 PIK3CA:c.3140A>G (p.(H1047R))  
      Urine cell pellet 1 100 PIK3CA:c.3140A>G (p.(H1047R))  
15 pT2+ G3 FFPE tumour sections 1 NA EGFR amp  
      Urine supernatant 0 0    
      Urine cell pellet 0 0    
16 pT1 G3 FFPE tumour sections 8 NA BRAF amp; CCND3 amp; CDK6 amp; EGFR amp; MAPK3 amp; MET amp; MYC amp; RAF1 amp  
      Urine supernatant 8 100 BRAF amp; CCND3 amp; CDK6 amp; EGFR amp; MAPK3 amp; MET amp; MYC amp; RAF1 amp  
      Urine cell pellet 4 50 CCND3 amp; MAPK3 amp; MYC amp; RAF1 amp  
17 pT1 G2 FFPE tumour sections 1 NA CCND1 amp  
      Urine supernatant 1 100 CCND1 amp  
      Urine cell pellet 1 100 CCND1 amp  
18 pT2+ G3 FFPE tumour sections 4 NA CCNE1 amp; RAF1 amp; CDKN2A/B biallelic loss; PIK3CA:c.1624G>A (p.(E542K))  
      Urine supernatant 4 100 CCNE1 amp; RAF1 amp; CDKN2A/B biallelic loss; PIK3CA:c.1624G>A (p.(E542K))  
      Urine cell pellet 4 100 CCNE1 amp; RAF1 amp; CDKN2A/B biallelic loss; PIK3CA:c.1624G>A (p.(E542K))  
19 pT2+ G2 FFPE tumour sections 3 NA CCND1 amp; CDKN2A/B biallelic loss; TSC1 biallelic loss  
      Urine supernatant 2 67 CCND1 amp; CDKN2A/B biallelic loss  
      Urine cell pellet 2 67 CCND1 amp; CDKN2A/B biallelic loss  
20 pTa G3 FFPE tumour sections 0 NA    
      Urine supernatant 0 NA    
      Urine cell pellet NA NA   DNA insufficient for OncoScan
21 pTa G1 FFPE tumour sections 0 NA    
      Urine supernatant 0 NA    
      Urine cell pellet 0 NA    
22 pTa G3 FFPE tumour sections 1 NA CDKN2A/B biallelic loss  
      Urine supernatant 1 100 CDKN2A/B biallelic loss  
      Urine cell pellet NA NA   DNA insufficient for OncoScan
23 pT1 G2 FFPE tumour sections 1 NA CDKN2A/B biallelic loss  
      Urine supernatant 1 100 CDKN2A/B biallelic loss  
      Urine cell pellet 1 100 CDKN2A/B biallelic loss  

Abbreviations: FFPE, formalin-fixed paraffin embedded; NA, not applicable.

Analytical sensitivity (for detection of FFPE-identified aberrations) is indicated. CN probes are mapped to Genome Reference Consortium human genome build 37 (GRCh37). Reference sequences used for somatic mutations listed are TP53 (NM_000546.5) and PIK3CA (NM_006218.2).