BMC Medical Genomics

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	**
Endometrium	MSS	54	157	0.17		59	156	0.038	*
Large intestine	MSI	97	68	0.091		74	68	8.6 × 10⁵	**
Large intestine	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

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

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