Table 1 Tumour staging data for 23 patients with UBC together with information on TARGET aberrations identified
From: Genomic complexity of urothelial bladder cancer revealed in urinary cfDNA
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 |
