Datasets:

electricsheepafrica
/

ssa-breast-disease-progression

sample_id stringlengths 12 12	population stringclasses 7 values	region stringclasses 5 values	is_SSA bool 2 classes	is_reference_panel bool 2 classes	sex stringclasses 2 values	age_years float64 18 90 ⌀	stage_at_diagnosis stringclasses 4 values	tumor_subtype stringclasses 5 values	first_metastasis_site stringclasses 5 values	therapy_class stringclasses 5 values	primary_n_mutations int64 20 145 ⌀	metastasis_n_mutations int64 45 209 ⌀	shared_n_mutations int64 20 126 ⌀	primary_private_n_mutations int64 0 42 ⌀	metastasis_private_n_mutations int64 11 162 ⌀	primary_met_jaccard_index float64 0.13 0.7 ⌀	primary_ESR1_mut bool 2 classes	primary_PIK3CA_mut bool 2 classes	primary_HER2_amp bool 2 classes	primary_TP53_mut bool 2 classes	primary_RB1_loss bool 2 classes	met_ESR1_mut bool 2 classes	met_PIK3CA_mut bool 2 classes	met_HER2_amp bool 2 classes	met_TP53_mut bool 2 classes	met_RB1_loss bool 2 classes	has_clinical_resistance bool 2 classes	resistance_mechanism stringclasses 7 values
DP_PAT_00001	SSA_West	West	true	false	Female	25.6	IV	Basal_like	Brain	Chemo_only	80	148	80	0	68	0.541	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00002	SSA_West	West	true	false	Female	50.3	III	Basal_like	Brain	Chemo_only	92	129	78	14	51	0.545	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00003	SSA_West	West	true	false	Female	44.1	IV	Basal_like	Liver	HER2_targeted	95	124	77	18	47	0.542	false	false	false	true	true	false	false	true	true	true	true	HER2_amp_gain_resistance
DP_PAT_00004	SSA_West	West	true	false	Female	37.6	IV	Luminal_A	Brain	Chemo_only	64	103	64	0	39	0.621	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00005	SSA_West	West	true	false	Female	23.1	III	Basal_like	Lung	Chemo_only	84	130	75	9	55	0.54	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00006	SSA_West	West	true	false	Female	58.4	I	Luminal_A	Bone	CDK4_6_plus_endocrine	79	180	79	0	101	0.439	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00007	SSA_West	West	true	false	Female	41.6	III	Basal_like	Liver	Chemo_only	97	119	76	21	43	0.543	false	true	false	true	false	false	true	false	true	false	false	None
DP_PAT_00008	SSA_West	West	true	false	Female	52.9	IV	Basal_like	Liver	Chemo_only	74	110	65	9	45	0.546	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00009	SSA_West	West	true	false	Female	57.7	III	Basal_like	Brain	Chemo_only	87	151	84	3	67	0.545	false	true	false	true	false	false	true	false	true	false	false	None
DP_PAT_00010	SSA_West	West	true	false	Female	53.2	IV	Basal_like	Bone	Chemo_plus_endocrine	82	146	80	2	66	0.541	false	true	true	true	false	true	true	true	true	false	false	None
DP_PAT_00011	SSA_West	West	true	false	Female	47.8	IV	Basal_like	Lung	HER2_targeted	136	137	96	40	41	0.542	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00012	SSA_West	West	true	false	Female	57.2	III	Basal_like	Brain	Chemo_only	87	121	73	14	48	0.541	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00013	SSA_West	West	true	false	Female	55.7	III	Luminal_A	Other	Endocrine_only	87	172	87	0	85	0.506	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00014	SSA_West	West	true	false	Female	56.6	III	Basal_like	Brain	Chemo_plus_endocrine	82	148	81	1	67	0.544	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00015	SSA_West	West	true	false	Female	31.8	I	Basal_like	Lung	CDK4_6_plus_endocrine	89	110	70	19	40	0.543	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00016	SSA_West	West	true	false	Female	45.7	II	Luminal_A	Lung	CDK4_6_plus_endocrine	65	101	65	0	36	0.644	false	false	false	true	false	false	false	false	true	true	true	RB1_loss_CDK4_6_resistance
DP_PAT_00017	SSA_West	West	true	false	Female	42.5	I	Luminal_A	Bone	Chemo_plus_endocrine	75	109	75	0	34	0.688	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00018	SSA_West	West	true	false	Female	82.3	II	Basal_like	Other	Chemo_only	67	155	67	0	88	0.432	false	true	false	false	false	false	true	false	false	false	false	None
DP_PAT_00019	SSA_West	West	true	false	Female	42.7	II	Basal_like	Brain	Chemo_only	73	74	52	21	22	0.547	false	false	false	false	false	false	false	false	false	true	false	None
DP_PAT_00020	SSA_West	West	true	false	Female	63.8	IV	HER2_enriched	Bone	HER2_targeted	78	104	68	10	36	0.596	false	true	true	false	false	false	true	true	false	false	true	PI3K_pathway_HER2_resistance
DP_PAT_00021	SSA_West	West	true	false	Female	31.5	III	Basal_like	Brain	HER2_targeted	80	136	76	4	60	0.543	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00022	SSA_West	West	true	false	Female	45.6	II	HER2_enriched	Brain	HER2_targeted	89	131	82	7	49	0.594	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00023	SSA_West	West	true	false	Female	34.2	II	Basal_like	Liver	Chemo_only	103	109	75	28	34	0.547	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00024	SSA_West	West	true	false	Female	52.1	IV	Luminal_A	Brain	Endocrine_only	91	112	83	8	29	0.692	false	false	true	false	false	false	false	true	false	false	false	None
DP_PAT_00025	SSA_West	West	true	false	Female	69.9	IV	Luminal_B	Bone	Chemo_only	119	145	106	13	39	0.671	false	false	false	true	true	false	false	false	true	true	false	None
DP_PAT_00026	SSA_West	West	true	false	Female	40.2	IV	Luminal_A	Other	Chemo_only	64	102	64	0	38	0.627	false	true	false	false	false	false	true	false	false	false	false	None
DP_PAT_00027	SSA_West	West	true	false	Female	58.7	III	Luminal_A	Bone	Chemo_plus_endocrine	67	194	67	0	127	0.345	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00028	SSA_West	West	true	false	Female	58.5	IV	Luminal_A	Bone	Chemo_plus_endocrine	80	140	80	0	60	0.571	false	true	false	false	false	false	true	false	false	false	false	None
DP_PAT_00029	SSA_West	West	true	false	Female	57	III	Basal_like	Lung	Chemo_only	81	82	57	24	25	0.538	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00030	SSA_West	West	true	false	Female	47.5	III	Luminal_A	Bone	Endocrine_only	79	117	79	0	38	0.675	false	false	false	false	true	false	false	false	false	true	false	None
DP_PAT_00031	SSA_West	West	true	false	Female	48.3	IV	Basal_like	Lung	CDK4_6_plus_endocrine	77	165	77	0	88	0.467	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00032	SSA_West	West	true	false	Female	51.5	III	Luminal_B	Bone	Endocrine_only	55	92	55	0	37	0.598	false	true	false	false	false	false	true	false	false	false	false	None
DP_PAT_00033	SSA_West	West	true	false	Female	52.3	III	Basal_like	Bone	Chemo_only	109	140	88	21	52	0.547	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00034	SSA_West	West	true	false	Female	51.7	II	Basal_like	Liver	Chemo_only	82	92	61	21	31	0.54	false	false	false	true	true	false	false	false	true	true	false	None
DP_PAT_00035	SSA_West	West	true	false	Female	58.6	III	Luminal_B	Bone	Endocrine_only	71	121	71	0	50	0.587	false	true	false	false	false	false	true	false	false	false	false	None
DP_PAT_00036	SSA_West	West	true	false	Female	48.6	III	Luminal_A	Bone	CDK4_6_plus_endocrine	57	122	57	0	65	0.467	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00037	SSA_West	West	true	false	Female	56	III	Luminal_B	Brain	Chemo_plus_endocrine	62	108	62	0	46	0.574	false	true	false	false	false	false	true	false	false	false	false	None
DP_PAT_00038	SSA_West	West	true	false	Female	53.3	II	Luminal_A	Bone	Chemo_plus_endocrine	93	123	88	5	35	0.688	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00039	SSA_West	West	true	false	Female	37.7	III	Basal_like	Lung	Chemo_only	116	124	85	31	39	0.548	false	false	false	true	true	false	false	false	true	true	false	None
DP_PAT_00040	SSA_West	West	true	false	Female	39.9	III	Luminal_A	Other	Endocrine_only	34	108	34	0	74	0.315	false	false	false	true	false	true	false	false	true	false	true	ESR1_mutation_acquired
DP_PAT_00041	SSA_West	West	true	false	Female	56.2	III	HER2_enriched	Brain	HER2_targeted	111	158	100	11	58	0.592	false	false	true	true	false	false	false	true	true	false	false	None
DP_PAT_00042	SSA_West	West	true	false	Female	55.3	III	Luminal_A	Lung	Chemo_only	56	87	56	0	31	0.644	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00043	SSA_West	West	true	false	Female	61.9	II	Basal_like	Lung	CDK4_6_plus_endocrine	81	82	57	24	25	0.538	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00044	SSA_West	West	true	false	Female	25.4	I	Luminal_A	Bone	CDK4_6_plus_endocrine	118	128	101	17	27	0.697	false	false	true	true	false	false	false	true	true	false	false	None
DP_PAT_00045	SSA_West	West	true	false	Female	56.8	IV	Luminal_A	Liver	Chemo_only	91	129	90	1	39	0.692	false	true	false	false	false	false	true	false	false	false	false	None
DP_PAT_00046	SSA_West	West	true	false	Female	23.5	III	Luminal_B	Bone	Endocrine_only	95	113	84	11	29	0.677	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00047	SSA_West	West	true	false	Female	49.4	III	Basal_like	Other	Chemo_plus_endocrine	71	72	50	21	22	0.538	false	false	false	false	true	false	false	false	false	true	false	None
DP_PAT_00048	SSA_West	West	true	false	Female	22.7	II	Luminal_B	Bone	Endocrine_only	78	113	77	1	36	0.675	false	true	false	false	false	true	true	false	false	false	true	ESR1_mutation_acquired
DP_PAT_00049	SSA_West	West	true	false	Female	64.8	II	Luminal_A	Bone	Endocrine_only	72	112	72	0	40	0.643	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00050	SSA_West	West	true	false	Female	40.6	III	Luminal_A	Bone	Endocrine_only	62	107	62	0	45	0.579	false	true	false	true	false	false	true	false	true	false	false	None
DP_PAT_00051	SSA_West	West	true	false	Female	73.9	III	Basal_like	Liver	Chemo_only	144	145	102	42	43	0.545	false	false	false	false	false	false	false	false	false	true	false	None
DP_PAT_00052	SSA_West	West	true	false	Female	52.3	IV	Luminal_B	Liver	Endocrine_only	93	94	75	18	19	0.67	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00053	SSA_West	West	true	false	Female	59.3	IV	Basal_like	Other	Chemo_only	44	51	33	11	18	0.532	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00054	SSA_West	West	true	false	Female	56.3	III	Luminal_A	Bone	Chemo_plus_endocrine	74	94	69	5	25	0.697	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00055	SSA_West	West	true	false	Female	69.8	II	Basal_like	Bone	Chemo_only	81	150	81	0	69	0.54	false	false	false	true	true	false	false	false	true	true	false	None
DP_PAT_00056	SSA_West	West	true	false	Female	49.7	II	Luminal_A	Other	Endocrine_only	74	119	74	0	45	0.622	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00057	SSA_West	West	true	false	Female	37.4	III	Basal_like	Liver	Chemo_plus_endocrine	71	153	71	0	82	0.464	false	false	false	true	true	false	false	false	true	true	false	None
DP_PAT_00058	SSA_West	West	true	false	Female	37	IV	Luminal_B	Liver	Chemo_only	71	140	71	0	69	0.507	false	true	false	false	false	false	true	false	false	false	false	None
DP_PAT_00059	SSA_West	West	true	false	Female	39.9	III	Basal_like	Other	Chemo_plus_endocrine	59	120	59	0	61	0.492	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00060	SSA_West	West	true	false	Female	50.6	II	Basal_like	Lung	CDK4_6_plus_endocrine	98	99	69	29	30	0.539	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00061	SSA_West	West	true	false	Female	53.9	III	Basal_like	Brain	Chemo_only	89	132	78	11	54	0.545	false	false	false	false	false	false	true	false	false	false	false	None
DP_PAT_00062	SSA_West	West	true	false	Female	47.1	III	Luminal_A	Bone	CDK4_6_plus_endocrine	68	138	68	0	70	0.493	false	false	false	false	true	false	false	false	false	true	true	RB1_loss_CDK4_6_resistance
DP_PAT_00063	SSA_West	West	true	false	Female	51.7	IV	Basal_like	Lung	Chemo_only	83	117	70	13	47	0.538	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00064	SSA_West	West	true	false	Female	67.1	III	Basal_like	Lung	Chemo_plus_endocrine	98	135	82	16	53	0.543	false	false	false	true	false	true	false	false	true	false	false	None
DP_PAT_00065	SSA_West	West	true	false	Female	30.5	III	Basal_like	Brain	Chemo_plus_endocrine	64	118	64	0	54	0.542	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00066	SSA_West	West	true	false	Female	43.9	II	Luminal_B	Bone	CDK4_6_plus_endocrine	108	145	102	6	43	0.675	false	true	false	false	false	false	true	false	false	false	false	None
DP_PAT_00067	SSA_West	West	true	false	Female	61.3	IV	Luminal_B	Liver	Endocrine_only	116	117	94	22	23	0.676	false	true	false	true	false	false	true	false	true	false	false	None
DP_PAT_00068	SSA_West	West	true	false	Female	38.3	III	Basal_like	Liver	Chemo_only	90	145	83	7	62	0.546	false	false	false	true	true	false	false	false	true	true	false	None
DP_PAT_00069	SSA_West	West	true	false	Female	61.4	III	Luminal_B	Other	Chemo_plus_endocrine	83	169	83	0	86	0.491	false	false	true	false	false	true	false	true	false	false	true	ESR1_mutation_acquired
DP_PAT_00070	SSA_West	West	true	false	Female	45.3	III	Luminal_A	Liver	CDK4_6_plus_endocrine	83	173	83	0	90	0.48	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00071	SSA_West	West	true	false	Male	43.6	III	Basal_like	Lung	Chemo_plus_endocrine	50	117	50	0	67	0.427	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00072	SSA_West	West	true	false	Female	47.9	II	Basal_like	Brain	Chemo_only	60	84	51	9	33	0.548	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00073	SSA_West	West	true	false	Female	51.9	II	Luminal_B	Other	Endocrine_only	109	110	88	21	22	0.672	false	false	true	true	false	false	true	true	true	false	true	PIK3CA_mutation_acquired
DP_PAT_00074	SSA_West	West	true	false	Female	46.2	IV	Luminal_A	Bone	Endocrine_only	115	116	95	20	21	0.699	false	true	false	false	false	false	true	false	false	false	false	None
DP_PAT_00075	SSA_West	West	true	false	Female	66.7	III	Basal_like	Liver	Chemo_only	106	114	78	28	36	0.549	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00076	SSA_West	West	true	false	Female	46	III	Luminal_A	Bone	Endocrine_only	111	115	93	18	22	0.699	false	true	false	false	true	false	true	false	false	true	false	None
DP_PAT_00077	SSA_West	West	true	false	Female	63.2	II	HER2_enriched	Bone	HER2_targeted	61	170	61	0	109	0.359	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00078	SSA_West	West	true	false	Female	62.1	II	Luminal_A	Bone	Endocrine_only	55	102	55	0	47	0.539	false	false	false	false	false	true	false	false	false	false	true	ESR1_mutation_acquired
DP_PAT_00079	SSA_West	West	true	false	Female	47.8	IV	Basal_like	Other	Chemo_plus_endocrine	98	157	90	8	67	0.545	false	true	false	false	false	false	true	false	false	false	false	None
DP_PAT_00080	SSA_West	West	true	false	Female	65.4	I	Luminal_A	Bone	Endocrine_only	95	126	91	4	35	0.7	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00081	SSA_West	West	true	false	Female	70.3	IV	Basal_like	Liver	CDK4_6_plus_endocrine	87	141	80	7	61	0.541	false	false	false	true	false	true	false	false	true	false	false	None
DP_PAT_00082	SSA_West	West	true	false	Female	57.3	IV	Luminal_A	Bone	Chemo_plus_endocrine	72	103	72	0	31	0.699	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00083	SSA_West	West	true	false	Female	59.8	III	Basal_like	Lung	Chemo_only	107	120	80	27	40	0.544	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00084	SSA_West	West	true	false	Female	30.9	II	Luminal_B	Bone	Chemo_plus_endocrine	48	145	48	0	97	0.331	false	false	false	false	false	false	false	true	false	false	false	None
DP_PAT_00085	SSA_West	West	true	false	Female	56.7	II	Luminal_A	Bone	CDK4_6_plus_endocrine	107	116	91	16	25	0.689	false	true	false	false	false	false	true	false	true	false	false	None
DP_PAT_00086	SSA_West	West	true	false	Female	62.5	II	HER2_enriched	Liver	HER2_targeted	90	174	90	0	84	0.517	false	false	true	true	false	false	false	true	true	false	false	None
DP_PAT_00087	SSA_West	West	true	false	Female	70.5	III	HER2_enriched	Bone	CDK4_6_plus_endocrine	66	130	66	0	64	0.508	false	false	true	false	false	false	false	true	false	false	false	None
DP_PAT_00088	SSA_West	West	true	false	Female	45.4	III	Luminal_A	Bone	Endocrine_only	102	108	86	16	22	0.694	false	false	true	true	false	false	false	true	true	false	false	None
DP_PAT_00089	SSA_West	West	true	false	Female	52.7	IV	Luminal_A	Bone	CDK4_6_plus_endocrine	123	124	101	22	23	0.692	false	false	false	false	false	false	false	false	false	false	false	None
DP_PAT_00090	SSA_West	West	true	false	Female	63.6	III	Luminal_A	Liver	Endocrine_only	72	133	72	0	61	0.541	false	false	true	true	false	false	false	true	true	false	false	None
DP_PAT_00091	SSA_West	West	true	false	Female	42.7	III	Basal_like	Lung	Chemo_only	55	117	55	0	62	0.47	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00092	SSA_West	West	true	false	Female	57.3	II	Basal_like	Bone	Chemo_plus_endocrine	69	175	69	0	106	0.394	false	false	true	true	true	true	false	true	true	true	false	None
DP_PAT_00093	SSA_West	West	true	false	Female	18.1	II	Luminal_A	Liver	CDK4_6_plus_endocrine	110	111	91	19	20	0.7	false	false	false	true	false	false	false	false	true	true	true	RB1_loss_CDK4_6_resistance
DP_PAT_00094	SSA_West	West	true	false	Female	56.9	III	Basal_like	Liver	Chemo_only	101	158	91	10	67	0.542	false	false	false	false	true	false	false	false	false	true	false	None
DP_PAT_00095	SSA_West	West	true	false	Female	32.3	IV	Basal_like	Other	Chemo_plus_endocrine	93	145	84	9	61	0.545	false	false	false	true	false	false	false	false	true	false	false	None
DP_PAT_00096	SSA_West	West	true	false	Female	31.9	III	Luminal_A	Brain	Chemo_plus_endocrine	94	114	85	9	29	0.691	false	true	false	false	false	false	true	false	false	false	false	None
DP_PAT_00097	SSA_West	West	true	false	Female	46.6	III	Luminal_B	Liver	HER2_targeted	88	179	88	0	91	0.492	false	false	true	false	true	false	false	true	false	true	false	None
DP_PAT_00098	SSA_West	West	true	false	Female	44.6	II	Basal_like	Bone	Chemo_plus_endocrine	84	85	59	25	26	0.536	false	false	false	true	false	true	false	false	true	false	false	None
DP_PAT_00099	SSA_West	West	true	false	Female	50	II	Basal_like	Other	Endocrine_only	59	133	59	0	74	0.444	false	true	false	true	false	true	true	false	true	false	false	None
DP_PAT_00100	SSA_West	West	true	false	Female	22.2	III	HER2_enriched	Other	HER2_targeted	76	156	76	0	80	0.487	false	false	true	false	false	false	false	true	false	false	false	None

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SSA Breast Disease Progression (Tumour Evolution & Resistance, Synthetic)

Dataset summary

This module provides a synthetic tumour evolution dataset focused on:

Primary → metastatic genomic divergence (shared vs private mutations, Jaccard index).
Clonal evolution under systemic therapy (dominant truncal clone, sensitive subclones, resistant clones).
Resistance mechanism development (e.g., ESR1 mutations, PIK3CA mutations, HER2 amplification, RB1 loss).

The design is grounded in large-scale genomic studies of primary and metastatic breast cancer and in conceptual work on clonal evolution and therapy resistance. All records are fully synthetic.

Cohort design

Sample size and populations

Baseline patients: 4,000.
Populations:
- SSA_West: 800
- SSA_East: 800
- SSA_Central: 600
- SSA_Southern: 600
- AAW (African American women): 600
- EUR: 400
- EAS: 200

Key baseline variables

sex: mostly Female (~99%), with a small Male fraction.
age_years: 18–90, with slightly younger ages in SSA cohorts than EUR/EAS.
stage_at_diagnosis: I–IV, with later stages more common in SSA, matching other modules.
tumor_subtype (PAM50-like):
- Luminal_A, Luminal_B, HER2_enriched, Basal_like, Normal_like, with higher basal-like prevalence in SSA and AAW.
first_metastasis_site:
- Bone, Liver, Lung, Brain, Other, with patterns such as bone-dominant metastases in luminal disease and more lung/brain in basal-like disease.
therapy_class:
- Endocrine_only
- Chemo_only
- Chemo_plus_endocrine
- HER2_targeted
- CDK4_6_plus_endocrine

Therapy distributions depend on subtype (e.g., more endocrine and CDK4/6 in luminal, more HER2-targeted in HER2-enriched, chemo-dominant in basal-like).

Primary → metastatic genomic divergence

For each patient, the baseline table includes summary mutation counts and divergence metrics:

primary_n_mutations
metastasis_n_mutations
shared_n_mutations
primary_private_n_mutations
metastasis_private_n_mutations
primary_met_jaccard_index – Jaccard index of the mutation sets.

The generator is tuned so that, on average:

Metastases have higher mutation burden than primaries.
Jaccard indices are high but not perfect (most drivers shared, additional private events in metastasis), with typical mean values by subtype inspired by Yates et al. (Cancer Cell 2017):
- Luminal A/B: ~0.7
- HER2-enriched: ~0.6
- Basal-like: ~0.55

These Jaccard targets are validated in the report.

Driver events and resistance mechanisms

We model a small panel of recurrent driver alterations:

ESR1_mut
PIK3CA_mut
HER2_amp
TP53_mut
RB1_loss

For each gene we provide:

primary_<event> (e.g., primary_ESR1_mut)
met_<event> (e.g., met_ESR1_mut)

Primary prevalences are subtype-specific. Metastatic lesions can gain additional events with probabilities that depend on therapy class, reflecting selection under treatment (e.g., ESR1 and PIK3CA under endocrine therapy, RB1 loss under CDK4/6 inhibition, HER2/PI3K pathway changes under HER2-targeted therapy).

At the patient level we summarise resistance as:

has_clinical_resistance (boolean)
resistance_mechanism – e.g.:
- ESR1_mutation_acquired
- PIK3CA_mutation_acquired
- RB1_loss_CDK4_6_resistance
- HER2_amp_gain_resistance
- PI3K_pathway_HER2_resistance
- TP53_mutation_chemo_resistance
- None

The overall fraction of patients with any annotated resistance falls in a target range (≈30–80%), and among ER+ patients on endocrine-based therapy, ESR1-mediated resistance occurs in ~15–40%, in line with clinical sequencing studies.

Clonal time-series under treatment

The clonal time-series table describes clone-level fractions over time:

Time points: time_months ∈ {0, 6, 12, 24}.
Each patient has:
- A dominant truncal clone (clone_type = "Truncal").
- 0–3 sensitive subclones (clone_type = "Sensitive").
- 0–1 resistant clones (clone_type = "Resistant") when a resistance mechanism is present.

Per row:

sample_id
population
tumor_subtype
therapy_class
resistance_mechanism (patient-level)
clone_id (e.g., C0, S1, R1)
clone_type
clone_resistance_mechanism (for resistant clones)
time_months
clone_fraction (fractions per patient/timepoint sum to ≈1.0)

Trajectories are constructed so that, typically:

Truncal clone: starts dominant (~70%) and gradually declines.
Sensitive subclones: shrink under treatment.
Resistant clones: start at low frequency and expand over time, often becoming dominant by 24 months.

The validator checks that:

Most resistant clones have increasing fractions.
Most sensitive clones have decreasing fractions.

Files and schema

Baseline table

Files:

disease_progression_baseline.parquet
disease_progression_baseline.csv

Columns (per patient):

Identifiers & demographics:
- sample_id, population, region, is_SSA, is_reference_panel, sex, age_years.
Tumour & metastasis context:
- stage_at_diagnosis, tumor_subtype, first_metastasis_site, therapy_class.
Genomics & divergence:
- primary_n_mutations, metastasis_n_mutations, shared_n_mutations,
- primary_private_n_mutations, metastasis_private_n_mutations,
- primary_met_jaccard_index.
Driver events:
- primary_ESR1_mut, met_ESR1_mut,
- primary_PIK3CA_mut, met_PIK3CA_mut,
- primary_HER2_amp, met_HER2_amp,
- primary_TP53_mut, met_TP53_mut,
- primary_RB1_loss, met_RB1_loss.
Resistance summary:
- has_clinical_resistance, resistance_mechanism.

Clonal time-series table

Files:

disease_progression_clones.parquet
disease_progression_clones.csv

Columns (per clone × timepoint):

sample_id, population, tumor_subtype, therapy_class, resistance_mechanism (patient-level).
clone_id, clone_type, clone_resistance_mechanism.
time_months.
clone_fraction.

Generation

The dataset is generated using:

disease_progression/scripts/generate_disease_progression.py

with configuration:

disease_progression/configs/disease_progression_config.yaml

and literature inventory:

disease_progression/docs/LITERATURE_INVENTORY.csv

The generator:

Builds a multi-ancestry baseline cohort with stage, subtype, metastasis site, and therapy.
Simulates primary vs metastatic mutation counts and Jaccard indices by subtype.
Assigns driver events at baseline and in metastasis, with therapy-dependent gain probabilities.
Annotates resistance mechanisms based on acquired events and treatment.
Constructs clone-level trajectories with truncal, sensitive, and resistant clones and normalised fractions over time.

Validation

Validation is performed with:

disease_progression/scripts/validate_disease_progression.py

and summarized in:

disease_progression/output/validation_report.md

Checks include:

C01–C02: Sample size and population counts vs configuration.
C03: Mean primary→metastasis Jaccard index by subtype vs targets.
C04: Metastasis mutation burden greater than primary in most patients.
C05: Overall fraction of patients with any annotated resistance in a plausible range.
C06: ESR1-mediated resistance fraction among ER+ endocrine-treated patients within a literature-informed window.
C07: Clonal dynamics: resistant clones increase, sensitive clones decrease.
C08: Missingness in key baseline and clone-level variables.

Intended use

This dataset is intended for:

Developing and benchmarking tumour evolution and clonal dynamics models.
Exploring primary→metastasis divergence and resistance mechanism inference.
Teaching about clonal evolution, late dissemination, and therapy-driven selection in breast cancer.

It is not intended for:

Estimating true frequencies of specific resistance mechanisms in any real population.
Evaluating particular clinical regimens.
Direct clinical decision-making.

Ethical considerations

All data are synthetic and not derived from individual patients.
Population and subtype distributions are inspired by published cohorts but do not represent any single registry.
Resistance labels and clonal patterns are for methodological exploration only.

License

License: CC BY-NC 4.0.
Free for non-commercial research, method development, and education with attribution.

Citation

If you use this dataset, please cite:

Electric Sheep Africa. "SSA Breast Disease Progression (Tumour Evolution & Resistance, Synthetic)." Hugging Face Datasets.

and foundational work on breast cancer metastasis and clonal evolution (e.g., Yates et al. 2017, Ng et al. 2019, Greaves & Maley 2012, Jeselsohn et al. 2015).

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