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Table 2 Some clinical subgroups are associated with increased or decreased performance of the primary site classifiers PM and PM + CN

From: TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen

  PM PM + CN
Primary site Subgroup Acc. (%) N P Acc. (%) N P
Subtype
Breast ER 64 417 0.064   91 416 0.00033 **
HER2 63 146 0.31   91 138 0.037 *
TNBC 27 98 4.1 × 109 ** 40 97 3.3 × 1018 **
Endometrium MSI 77 71 0.015 * 93 70 3 × 105 **
MSS 54 157 0.17   59 156 0.038 *
Large intestine MSI 97 68 0.091   74 68 8.6 × 105 **
MSS 88 233 0.48   97 230 0.0075 **
Ovary mBRCA1 76 55 0.097   96 55 0.56  
mBRCA2 79 39 0.077   97 38 0.5  
wtBRCA 61 338 0.29   92 333 0.58  
Stage
Breast Stage I 65 129 0.24   82 127 0.6  
Stage II 59 437 0.95   84 432 0.93  
Stage III 57 175 0.55   84 172 1  
Stage IV 47 15 0.43   87 15 1  
Kidney Stage I 80 153 0.8   95 149 1  
Stage II 81 32 1   91 32 0.44  
Stage III 81 78 0.87   97 77 0.39  
Stage IV 88 43 0.39   88 42 0.18  
Large intestine Stage I 89 65 0.82   94 64 1  
Stage II 90 143 0.87   91 141 0.45  
Stage III 89 101 0.85   93 101 1  
Stage IV 94 49 0.6   98 49 0.35  
Lung Stage I 79 261 0.7   82 257 0.53  
Stage II 78 106 0.69   84 105 0.88  
Stage III 87 97 0.16   89 95 0.27  
Stage IV 74 19 0.56   89 18 1  
Grade
Endometrium G1 74 76 0.055   88 76 0.0022 **
G2 73 75 0.073   86 73 0.0088 **
G3 41 92 0.0013 ** 45 92 1.2 × 105 **
Kidney G1 71 7 0.61   100 7 1  
G2 84 128 0.68   93 125 0.66  
G3 80 122 0.68   96 120 0.63  
G4 82 45 1   93 44 0.73  
Ovary G1 0 3 0.056   33 3 0.014 *
G2 60 55 0.77   87 54 0.098  
G3 63 405 0.83   95 394 0.47  
G4 0 1 0.38   100 1 1  
  1. Information on subtype, grade and stage were retrieved from TCGA, and are therefore not available for all tumors in the COSMIC database. ER estrogen receptor positive. HER2 human epidermal growth factor receptor 2 positive. TNBC triple negative breast cancer. MSI microsatellite instability. MSS microsatellite stable. mBRCA1 mutated BRCA1. mBRCA2 mutated BRCA2. wtBRCA wildtype BRCA1 and BRCA2. Acc. accuracy ie. the percentage of tumors correctly classified. N the number of tumors in subgroup. P p-value from Fisher’s exact test comparing accuracy among samples in or not in each subgroup. *p < 0.05. **p < 0.01