Datasets:

electricsheepafrica
/

ssa-breast-biomarker-trajectories

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	therapy_class stringclasses 5 values	response_class stringclasses 5 values	ca153_baseline_u_per_ml float64 2.81 475 ⌀	ca153_nadir_u_per_ml float64 0.8 353 ⌀	ca153_best_delta_fraction float64 -0.9 0 ⌀	ca2729_baseline_u_per_ml float64 2.98 481 ⌀	ca2729_nadir_u_per_ml float64 0.79 315 ⌀	ca2729_best_delta_fraction float64 -0.91 0 ⌀	ctdna_baseline_copies_per_ml float64 1.41 3.34k ⌀	ctdna_min_copies_per_ml float64 0.13 2.22k ⌀	ctdna_baseline_detectable bool 2 classes	ctdna_cleared_by_6m bool 2 classes
BT_PAT_00001	SSA_West	West	true	false	Female	25.6	III	Basal_like	CDK4_6_plus_endocrine	Late_progression	34.95	18.5	-0.470734	40.1	17.89	-0.553848	37.93	19.64	true	false
BT_PAT_00002	SSA_West	West	true	false	Female	50.3	IV	Basal_like	Chemo_only	Partial_response	97.35	32.97	-0.661285	95.76	28.94	-0.69785	110.67	17.53	true	false
BT_PAT_00003	SSA_West	West	true	false	Female	44.1	II	Luminal_B	CDK4_6_plus_endocrine	Early_progression	20.33	20.33	0	21.7	21.7	0	20.47	20.47	true	false
BT_PAT_00004	SSA_West	West	true	false	Female	37.6	II	HER2_enriched	Chemo_plus_endocrine	Early_progression	31.72	31.72	0	30.86	30.86	0	128.92	88.67	true	false
BT_PAT_00005	SSA_West	West	true	false	Female	23.1	II	Basal_like	Chemo_only	Deep_response	42.89	12.54	-0.707528	37.73	12.85	-0.659464	582.66	48.21	true	false
BT_PAT_00006	SSA_West	West	true	false	Female	58.4	IV	Luminal_A	Endocrine_only	Deep_response	127.59	33.83	-0.734836	133.12	34.14	-0.743524	147.25	14.05	true	false
BT_PAT_00007	SSA_West	West	true	false	Female	41.6	III	Luminal_A	Chemo_plus_endocrine	Partial_response	124.91	41.67	-0.666357	143.19	46.7	-0.673837	37.36	7.62	true	false
BT_PAT_00008	SSA_West	West	true	false	Female	52.9	III	Luminal_A	Endocrine_only	Late_progression	41.86	24.43	-0.416265	40.14	25.48	-0.365212	30.34	16.28	true	false
BT_PAT_00009	SSA_West	West	true	false	Female	57.7	II	Basal_like	Chemo_only	Partial_response	25.86	15.25	-0.410119	21.8	14.46	-0.336762	12.84	4.58	true	false
BT_PAT_00010	SSA_West	West	true	false	Female	53.2	IV	Basal_like	Chemo_only	Stable_disease	80.2	71.41	-0.109527	89.14	65.18	-0.268807	152.8	146.75	true	false
BT_PAT_00011	SSA_West	West	true	false	Female	47.8	III	Basal_like	Chemo_only	Partial_response	65.28	26.4	-0.595565	59.55	28.4	-0.523007	201.51	45.9	true	false
BT_PAT_00012	SSA_West	West	true	false	Female	57.2	II	Basal_like	Chemo_only	Deep_response	26.74	6.92	-0.741437	33.23	6.51	-0.804157	28.06	2.66	true	false
BT_PAT_00013	SSA_West	West	true	false	Female	55.7	III	Luminal_A	CDK4_6_plus_endocrine	Partial_response	35.24	15.6	-0.557285	34.67	15.31	-0.558353	299.68	57.6	true	false
BT_PAT_00014	SSA_West	West	true	false	Female	56.6	III	Luminal_A	Chemo_only	Deep_response	47.66	11.55	-0.757603	49.6	11.19	-0.774453	304.46	19.91	true	false
BT_PAT_00015	SSA_West	West	true	false	Female	31.8	IV	Luminal_B	CDK4_6_plus_endocrine	Early_progression	67.99	58.96	-0.13291	66.88	66.88	0	382.83	382.83	true	false
BT_PAT_00016	SSA_West	West	true	false	Female	45.7	IV	Luminal_B	CDK4_6_plus_endocrine	Deep_response	152.5	39.29	-0.742347	159.77	35.75	-0.776251	298	28.43	true	false
BT_PAT_00017	SSA_West	West	true	false	Female	42.5	IV	Luminal_B	Chemo_plus_endocrine	Deep_response	160.92	36.4	-0.773795	148.59	33.5	-0.774576	256.67	14.13	true	false
BT_PAT_00018	SSA_West	West	true	false	Female	82.3	IV	Luminal_A	Chemo_plus_endocrine	Partial_response	126.39	61.9	-0.510262	136.51	60.36	-0.557854	342.85	72.41	true	false
BT_PAT_00019	SSA_West	West	true	false	Female	42.7	I	HER2_enriched	HER2_targeted	Deep_response	18.56	4.65	-0.749244	16.15	4.75	-0.705945	13.03	1.09	true	true
BT_PAT_00020	SSA_West	West	true	false	Female	63.8	I	Luminal_A	Endocrine_only	Deep_response	7.54	1.92	-0.745755	6.97	1.76	-0.747164	9.23	0.99	true	true
BT_PAT_00021	SSA_West	West	true	false	Female	31.5	III	Luminal_B	Chemo_plus_endocrine	Deep_response	57.83	11.68	-0.797999	57.6	12.42	-0.784402	55.86	5.85	true	false
BT_PAT_00022	SSA_West	West	true	false	Female	45.6	III	HER2_enriched	HER2_targeted	Late_progression	27.04	15.41	-0.430201	27.4	13.12	-0.521109	734.14	307.68	true	false
BT_PAT_00023	SSA_West	West	true	false	Female	34.2	II	Luminal_B	Chemo_plus_endocrine	Deep_response	36.54	6.46	-0.823113	42.41	5.64	-0.866928	71.65	5.26	true	false
BT_PAT_00024	SSA_West	West	true	false	Female	52.1	III	Basal_like	CDK4_6_plus_endocrine	Early_progression	29.35	29.35	0	30.98	30.98	0	43.15	37.09	true	false
BT_PAT_00025	SSA_West	West	true	false	Female	69.9	III	Luminal_A	Chemo_plus_endocrine	Stable_disease	68.71	62.55	-0.089677	59.23	56.69	-0.042779	173.65	146.45	true	false
BT_PAT_00026	SSA_West	West	true	false	Female	40.2	I	Basal_like	Chemo_only	Deep_response	12.49	3.55	-0.716127	11.88	3.38	-0.715424	18.65	1.52	true	true
BT_PAT_00027	SSA_West	West	true	false	Female	58.7	III	Basal_like	Chemo_only	Late_progression	73.27	51.33	-0.299421	76.68	50.51	-0.341204	57.07	25.66	true	false
BT_PAT_00028	SSA_West	West	true	false	Female	58.5	III	Luminal_A	Endocrine_only	Partial_response	52.54	23.76	-0.547689	55.04	25.05	-0.544775	187.05	49.7	true	false
BT_PAT_00029	SSA_West	West	true	false	Female	57	III	Basal_like	Chemo_plus_endocrine	Stable_disease	49.11	47.67	-0.029309	54.63	47.78	-0.125381	84.31	64.21	true	false
BT_PAT_00030	SSA_West	West	true	false	Female	47.5	III	Basal_like	Chemo_plus_endocrine	Early_progression	50.14	48.25	-0.037672	45.58	45.58	0	170.69	126.56	true	false
BT_PAT_00031	SSA_West	West	true	false	Female	48.3	III	Luminal_B	Chemo_plus_endocrine	Partial_response	65.52	26.53	-0.595075	60.11	21.3	-0.645688	149.61	38.79	true	false
BT_PAT_00032	SSA_West	West	true	false	Female	51.5	I	Basal_like	Chemo_only	Partial_response	10.26	4.5	-0.561475	10.53	4.78	-0.546603	7.53	1.09	true	true
BT_PAT_00033	SSA_West	West	true	false	Female	52.3	II	Basal_like	Chemo_only	Late_progression	31.59	15.89	-0.497067	34.97	14.44	-0.587209	13.68	5.66	true	false
BT_PAT_00034	SSA_West	West	true	false	Female	51.7	III	Luminal_B	Endocrine_only	Early_progression	54.27	54.27	0	59.38	56.67	-0.045528	118.09	77.26	true	false
BT_PAT_00035	SSA_West	West	true	false	Female	58.6	II	HER2_enriched	Chemo_only	Deep_response	13.89	3.4	-0.755536	15.19	3.71	-0.755964	64.19	3.4	true	false
BT_PAT_00036	SSA_West	West	true	false	Female	48.6	II	Luminal_B	CDK4_6_plus_endocrine	Partial_response	65.9	25.38	-0.614941	57.95	23.03	-0.602625	41.57	8.58	true	false
BT_PAT_00037	SSA_West	West	true	false	Female	56	III	HER2_enriched	HER2_targeted	Deep_response	36.29	8.9	-0.754774	32.3	8.2	-0.745967	78.97	5.69	true	false
BT_PAT_00038	SSA_West	West	true	false	Female	53.3	III	Basal_like	Chemo_only	Stable_disease	44.87	44.87	0	43.33	43.33	0	227.15	157.54	true	false
BT_PAT_00039	SSA_West	West	true	false	Female	37.7	I	Luminal_A	Endocrine_only	Partial_response	22.43	9.8	-0.563025	22.45	9.11	-0.594167	31.83	10.82	true	false
BT_PAT_00040	SSA_West	West	true	false	Female	39.9	III	Basal_like	Chemo_only	Stable_disease	57.12	57.12	0	58.18	53.63	-0.078144	44.15	35.28	true	false
BT_PAT_00041	SSA_West	West	true	false	Female	56.2	III	Luminal_A	CDK4_6_plus_endocrine	Deep_response	47.06	11.96	-0.745819	46.69	11.6	-0.751559	106.36	6.8	true	false
BT_PAT_00042	SSA_West	West	true	false	Female	55.3	IV	Basal_like	Chemo_plus_endocrine	Stable_disease	163.22	115.99	-0.289352	166.53	124.24	-0.253983	80.68	80.68	true	false
BT_PAT_00043	SSA_West	West	true	false	Female	61.9	III	Basal_like	Chemo_only	Early_progression	40.28	40.28	0	42.2	42.2	0	105.82	54.45	true	false
BT_PAT_00044	SSA_West	West	true	false	Female	25.4	III	Basal_like	Chemo_plus_endocrine	Stable_disease	46.62	34.76	-0.254435	54.44	34.29	-0.370148	53.55	30.37	true	false
BT_PAT_00045	SSA_West	West	true	false	Female	56.8	III	Luminal_A	Chemo_only	Deep_response	46.71	9.27	-0.801491	50.83	8.04	-0.841883	469.18	32.98	true	false
BT_PAT_00046	SSA_West	West	true	false	Female	23.5	IV	Basal_like	HER2_targeted	Partial_response	79.33	30.45	-0.616139	72.35	29.58	-0.591114	66.74	19.41	true	false
BT_PAT_00047	SSA_West	West	true	false	Female	49.4	III	Luminal_A	CDK4_6_plus_endocrine	Late_progression	26.91	25.59	-0.048999	22.4	21.31	-0.04858	91.28	50.25	true	false
BT_PAT_00048	SSA_West	West	true	false	Female	22.7	II	Basal_like	Chemo_only	Partial_response	14.57	5.74	-0.606487	14.22	6.1	-0.571121	31.71	9.88	true	false
BT_PAT_00049	SSA_West	West	true	false	Female	64.8	III	Luminal_A	Endocrine_only	Stable_disease	101.11	76.14	-0.24702	90.06	78.75	-0.125635	127.48	117.6	true	false
BT_PAT_00050	SSA_West	West	true	false	Female	40.6	III	HER2_enriched	HER2_targeted	Late_progression	67.67	54.26	-0.198191	62.64	52.11	-0.168016	67.46	67.46	true	false
BT_PAT_00051	SSA_West	West	true	false	Female	73.9	II	Luminal_A	Endocrine_only	Deep_response	18.93	4.25	-0.775469	16.76	4.1	-0.755467	12.94	1.15	true	true
BT_PAT_00052	SSA_West	West	true	false	Female	52.3	II	Basal_like	CDK4_6_plus_endocrine	Deep_response	20.56	2.86	-0.861045	20.9	3.16	-0.849034	165.59	12.48	true	false
BT_PAT_00053	SSA_West	West	true	false	Female	59.3	IV	Luminal_B	Chemo_plus_endocrine	Early_progression	193.07	193.07	0	213.59	213.59	0	57.53	40.02	true	false
BT_PAT_00054	SSA_West	West	true	false	Female	56.3	II	HER2_enriched	Endocrine_only	Stable_disease	47.03	43.89	-0.06667	43.69	43.69	0	31.96	23.79	true	false
BT_PAT_00055	SSA_West	West	true	false	Female	69.8	I	Basal_like	Chemo_plus_endocrine	Early_progression	17.58	16.12	-0.082989	17.35	16.35	-0.057794	9.87	9.18	true	false
BT_PAT_00056	SSA_West	West	true	false	Female	49.7	II	Basal_like	Chemo_only	Deep_response	30.06	6.02	-0.799672	33.92	5.4	-0.840803	31.91	2.37	true	false
BT_PAT_00057	SSA_West	West	true	false	Female	37.4	II	HER2_enriched	HER2_targeted	Deep_response	18.03	4.23	-0.765692	18.43	3.88	-0.789235	130.28	11.04	true	false
BT_PAT_00058	SSA_West	West	true	false	Female	37	IV	Basal_like	Chemo_plus_endocrine	Late_progression	92.28	56.09	-0.392167	97.03	55.9	-0.423928	262.66	120.83	true	false
BT_PAT_00059	SSA_West	West	true	false	Female	39.9	III	Luminal_B	Chemo_only	Deep_response	35.52	8.21	-0.768925	37.15	8.29	-0.776751	242.06	12.78	true	false
BT_PAT_00060	SSA_West	West	true	false	Female	50.6	I	Luminal_B	Chemo_plus_endocrine	Deep_response	11.94	2.19	-0.816133	11.81	2.02	-0.82897	25.03	2.02	true	false
BT_PAT_00061	SSA_West	West	true	false	Female	53.9	III	Basal_like	Chemo_only	Partial_response	34.39	17.25	-0.498409	30.65	17.14	-0.440922	82.95	16.27	true	false
BT_PAT_00062	SSA_West	West	true	false	Female	47.1	III	Basal_like	Chemo_only	Stable_disease	88.06	88.06	0	73.98	73.98	0	600.67	330.66	true	false
BT_PAT_00063	SSA_West	West	true	false	Female	51.7	IV	HER2_enriched	HER2_targeted	Deep_response	128.62	27.64	-0.785105	108.23	26.74	-0.752892	68.31	9.63	true	false
BT_PAT_00064	SSA_West	West	true	false	Female	67.1	II	Basal_like	Chemo_only	Deep_response	48.63	8.74	-0.820342	49.48	9.54	-0.807275	48.09	4.99	true	false
BT_PAT_00065	SSA_West	West	true	false	Female	30.5	III	HER2_enriched	HER2_targeted	Stable_disease	86.11	57.95	-0.327009	96.34	50.22	-0.478733	199.72	189.8	true	false
BT_PAT_00066	SSA_West	West	true	false	Female	43.9	II	Luminal_A	CDK4_6_plus_endocrine	Partial_response	74.62	32.85	-0.559744	75.1	27.69	-0.631265	29.12	7.38	true	false
BT_PAT_00067	SSA_West	West	true	false	Female	61.3	III	Luminal_B	Chemo_only	Stable_disease	27.11	26.72	-0.014441	28.54	26.99	-0.054543	188.96	137.79	true	false
BT_PAT_00068	SSA_West	West	true	false	Female	38.3	II	HER2_enriched	Chemo_plus_endocrine	Stable_disease	18.44	15.36	-0.167163	20.58	15.97	-0.223771	46.47	33.17	true	false
BT_PAT_00069	SSA_West	West	true	false	Female	61.4	II	Basal_like	Chemo_plus_endocrine	Partial_response	33.58	20.72	-0.382941	38.91	20.89	-0.463263	21.41	4.47	true	false
BT_PAT_00070	SSA_West	West	true	false	Female	45.3	III	Basal_like	Chemo_only	Early_progression	104.9	104.9	0	117.83	117.83	0	190.38	164.6	true	false
BT_PAT_00071	SSA_West	West	true	false	Female	43.6	III	Luminal_B	CDK4_6_plus_endocrine	Early_progression	54.29	54.29	0	53.31	53.31	0	203.7	203.7	true	false
BT_PAT_00072	SSA_West	West	true	false	Female	47.9	IV	Luminal_A	CDK4_6_plus_endocrine	Partial_response	91.77	37.99	-0.585988	87.41	40.27	-0.539327	3,335.17	772.31	true	false
BT_PAT_00073	SSA_West	West	true	false	Female	51.9	III	Basal_like	Chemo_only	Partial_response	47.46	22.98	-0.515711	57.07	19.72	-0.654513	97.24	21.75	true	false
BT_PAT_00074	SSA_West	West	true	false	Female	46.2	II	Luminal_A	Chemo_plus_endocrine	Deep_response	13.88	3.08	-0.778078	13.64	3.15	-0.769265	27.18	2.02	true	false
BT_PAT_00075	SSA_West	West	true	false	Female	66.7	II	Luminal_A	Endocrine_only	Deep_response	54.96	12.59	-0.770844	61.51	12.37	-0.798913	33.69	3.23	true	false
BT_PAT_00076	SSA_West	West	true	false	Female	46	III	Basal_like	Chemo_only	Deep_response	62.39	10.24	-0.835834	57.27	9.6	-0.832328	67.09	5.65	true	false
BT_PAT_00077	SSA_West	West	true	false	Female	63.2	III	Basal_like	Chemo_only	Stable_disease	40.87	32.88	-0.195495	38.43	32.69	-0.149407	280.17	222.52	true	false
BT_PAT_00078	SSA_West	West	true	false	Female	62.1	II	Basal_like	CDK4_6_plus_endocrine	Deep_response	36.99	8.26	-0.776708	39.88	8.24	-0.793281	43.02	4.87	true	false
BT_PAT_00079	SSA_West	West	true	false	Female	47.8	III	Basal_like	Chemo_only	Stable_disease	44.4	38.03	-0.143504	39.07	38.22	-0.021781	42.33	40.49	true	false
BT_PAT_00080	SSA_West	West	true	false	Female	65.4	II	Luminal_A	CDK4_6_plus_endocrine	Partial_response	35.2	12.64	-0.640861	35.05	12.55	-0.642126	64.2	16.23	true	false
BT_PAT_00081	SSA_West	West	true	false	Female	70.3	III	Basal_like	Chemo_only	Deep_response	34.71	8.64	-0.751017	39.59	8.07	-0.796234	528.56	49.22	true	false
BT_PAT_00082	SSA_West	West	true	false	Female	57.3	IV	Luminal_A	HER2_targeted	Stable_disease	132.33	100.59	-0.239846	148.48	96.21	-0.352072	224.29	196.4	true	false
BT_PAT_00083	SSA_West	West	true	false	Female	59.8	III	Basal_like	Chemo_only	Stable_disease	50.72	33.21	-0.345235	49.38	29.5	-0.402634	198.22	182.7	true	false
BT_PAT_00084	SSA_West	West	true	false	Female	30.9	II	Basal_like	Chemo_only	Partial_response	32.1	15.83	-0.506633	31.49	13.69	-0.56525	341.95	94.27	true	false
BT_PAT_00085	SSA_West	West	true	false	Female	56.7	II	Basal_like	HER2_targeted	Deep_response	73.73	16.75	-0.772854	79.36	17	-0.785779	17.8	1.49	true	true
BT_PAT_00086	SSA_West	West	true	false	Female	62.5	I	HER2_enriched	Chemo_only	Partial_response	8.55	2.76	-0.677442	8.34	2.58	-0.690982	60.72	15.89	true	false
BT_PAT_00087	SSA_West	West	true	false	Female	70.5	IV	HER2_enriched	CDK4_6_plus_endocrine	Partial_response	184.8	71.33	-0.614025	191.44	70.42	-0.632164	657.57	175.7	true	false
BT_PAT_00088	SSA_West	West	true	false	Female	45.4	III	Basal_like	Chemo_only	Deep_response	31.68	9.69	-0.69414	29.05	9.62	-0.668951	209.51	24.56	true	false
BT_PAT_00089	SSA_West	West	true	false	Female	52.7	II	Basal_like	Chemo_only	Stable_disease	30.21	24.69	-0.182734	32.81	31.8	-0.030773	37.8	26.66	true	false
BT_PAT_00090	SSA_West	West	true	false	Female	63.6	I	Basal_like	CDK4_6_plus_endocrine	Deep_response	8.35	2.14	-0.743557	7.83	1.87	-0.760812	25.32	1.93	true	false
BT_PAT_00091	SSA_West	West	true	false	Female	42.7	IV	Luminal_A	Endocrine_only	Stable_disease	93.77	90.35	-0.036522	79.57	79.57	0	278.13	166.6	true	false
BT_PAT_00092	SSA_West	West	true	false	Female	57.3	III	HER2_enriched	HER2_targeted	Partial_response	67.88	30.19	-0.555284	83.38	28.67	-0.656143	25.15	6.28	true	false
BT_PAT_00093	SSA_West	West	true	false	Female	18.1	I	Luminal_A	CDK4_6_plus_endocrine	Partial_response	7.53	2.63	-0.65006	7.56	2.92	-0.613689	11.35	1.87	true	true
BT_PAT_00094	SSA_West	West	true	false	Female	56.9	IV	HER2_enriched	HER2_targeted	Stable_disease	135.33	93.59	-0.308429	149.67	85.47	-0.428967	112.55	75.01	true	false
BT_PAT_00095	SSA_West	West	true	false	Female	32.3	III	HER2_enriched	HER2_targeted	Partial_response	55.96	25.64	-0.541831	45.1	21.77	-0.517398	137.18	45.52	true	false
BT_PAT_00096	SSA_West	West	true	false	Female	31.9	II	Luminal_A	Endocrine_only	Deep_response	35.25	6.67	-0.81072	41.05	6.67	-0.837447	7.95	1.01	true	true
BT_PAT_00097	SSA_West	West	true	false	Female	46.6	I	Basal_like	CDK4_6_plus_endocrine	Partial_response	21.48	8.41	-0.608377	19.59	7.89	-0.597132	10.34	2.32	true	false
BT_PAT_00098	SSA_West	West	true	false	Female	44.6	III	Luminal_B	CDK4_6_plus_endocrine	Late_progression	25.43	20.81	-0.181848	26.82	18.91	-0.294832	171.35	108.26	true	false
BT_PAT_00099	SSA_West	West	true	false	Male	50	III	Basal_like	Endocrine_only	Deep_response	45.9	10.25	-0.776712	41.92	9.48	-0.773925	266.59	31.29	true	false
BT_PAT_00100	SSA_West	West	true	false	Female	22.2	I	Basal_like	Chemo_only	Deep_response	4.98	1.12	-0.774601	5.24	1.03	-0.80445	31.27	2.93	true	false

End of preview. Expand in Data Studio

SSA Breast Biomarker Trajectories (Synthetic)

Dataset summary

This module provides a synthetic biomarker trajectory dataset for breast cancer treatment monitoring, focused on:

Serum tumour markers: CA 15-3 and CA 27-29.
Circulating tumour DNA (ctDNA) levels.
Treatment response monitoring over 0–24 months.

It is designed to emulate:

Higher baseline marker levels in advanced-stage disease.
Early declines in CA 15-3 and ctDNA in responders.
Rising or non-clearing ctDNA in early and late progression.

All records are fully synthetic, grounded in clinical literature on serial CA15-3/CA27-29 measurement and ctDNA dynamics in metastatic and early breast cancer.

Cohort design

Sample size and populations

Baseline patients: 6,000.
Populations:
- SSA_West: 1,500
- SSA_East: 1,500
- SSA_Central: 1,000
- SSA_Southern: 1,000
- AAW (African American women): 1,000
- EUR: 600
- EAS: 400

Baseline variables

sex: predominantly Female (~99%).
age_years: 18–90, with slightly younger distribution in SSA vs EUR/EAS.
stage_at_diagnosis: I–IV, with later stages more frequent in SSA.
tumor_subtype:
- Luminal_A, Luminal_B, HER2_enriched, Basal_like, Normal_like, with higher basal-like in SSA and AAW.
therapy_class:
- Endocrine_only
- Chemo_only
- Chemo_plus_endocrine
- HER2_targeted
- CDK4_6_plus_endocrine
response_class (treatment course):
- Deep_response
- Partial_response
- Stable_disease
- Early_progression
- Late_progression

These response classes drive biomarker trajectories.

Time structure

Patients are followed at:

time_months: [0, 3, 6, 9, 12, 18, 24].

At each time point, biomarker levels are simulated conditional on:

stage_at_diagnosis (baseline tumour burden).
response_class (kinetic pattern).

Biomarkers

CA 15-3

Units: U/mL.
Baseline means increase with stage (approximate):
- Stage I: ~15 U/mL
- Stage II: ~30 U/mL
- Stage III: ~60 U/mL
- Stage IV: ~120 U/mL
SD fraction ~0.6 (log-normal variability).

Response-class–specific trajectories (multipliers on baseline):

Deep_response: rapid drop (e.g., ~50% at 3 months, ~75% reduction by 12 months).
Partial_response: moderate drop (~30% at 3 months, ~50% reduction by 12 months).
Stable_disease: flat or slightly drifting around baseline.
Early_progression: early rise (>10% increase by 3 months, continuing upward).
Late_progression: initial drop, followed by rise after ~12 months.

These patterns reflect published CA15-3 kinetics linking rapid declines to radiologic response and surges to progression.

CA 27-29

Units: U/mL.
Modelled as a correlated companion marker to CA 15-3:
- ca2729_u_per_ml is sampled as CA 27-29 ≈ CA 15-3 × log-normal noise.
Captures that CA 27-29 is clinically used in a similar role to CA 15-3 but with independent assay noise.

ctDNA

Units: copies_per_mL.
Baseline log10 means increase with stage:
- Stage I: ~10^1.3
- Stage II: ~10^1.7
- Stage III: ~10^2.1
- Stage IV: ~10^2.5
Detection limit: ~5 copies/mL.

Kinetic patterns by response_class:

Deep_response:
- Rapid and deep ctDNA decline; many become undetectable by 3–6 months.
Partial_response:
- Substantial decline but less complete clearance.
Stable_disease:
- Small changes, often hovering near baseline.
Early_progression:
- Transient modest fall, followed by strong rise (often >2–3× by 12–24 months).
Late_progression:
- Early decline then late rise (mirroring late progression in CA 15-3).

Summary flags:

ctdna_baseline_detectable
ctdna_cleared_by_6m (detectable at baseline and undetectable at all timepoints ≤6 months).

Files and schema

Baseline table

Files:

biomarker_trajectories_baseline.parquet
biomarker_trajectories_baseline.csv

Columns (per patient):

Identifiers & demographics:
- sample_id, population, region, is_SSA, is_reference_panel, sex, age_years.
Tumour & therapy:
- stage_at_diagnosis, tumor_subtype, therapy_class, response_class.
CA 15-3 summary:
- ca153_baseline_u_per_ml
- ca153_nadir_u_per_ml
- ca153_best_delta_fraction (nadir vs baseline, negative values indicate decline).
CA 27-29 summary:
- ca2729_baseline_u_per_ml
- ca2729_nadir_u_per_ml
- ca2729_best_delta_fraction.
ctDNA summary:
- ctdna_baseline_copies_per_ml
- ctdna_min_copies_per_ml
- ctdna_baseline_detectable
- ctdna_cleared_by_6m.

Timeseries table

Files:

biomarker_trajectories_timeseries.parquet
biomarker_trajectories_timeseries.csv

Columns (per patient × timepoint):

sample_id
population
stage_at_diagnosis
tumor_subtype
therapy_class
response_class
time_months
ca153_u_per_ml
ca2729_u_per_ml
ctdna_copies_per_ml
ctdna_detectable

Generation

The dataset is generated using:

biomarker_trajectories/scripts/generate_biomarker_trajectories.py

with configuration:

biomarker_trajectories/configs/biomarker_trajectories_config.yaml

and literature inventory:

biomarker_trajectories/docs/LITERATURE_INVENTORY.csv

Key steps:

Baseline cohort: draw populations, sex, age, stage, subtype, therapy, and response class.
Baseline markers: sample CA 15-3 and ctDNA baseline values by stage using log-normal distributions.
Trajectories: apply response-class–specific multipliers at each timepoint, with log-normal noise, to generate CA 15-3, CA 27-29, and ctDNA levels.
Summaries: compute nadirs, best percentage changes, baseline detectability, and ctDNA clearance.

Validation

Validation is performed with:

biomarker_trajectories/scripts/validate_biomarker_trajectories.py

and summarised in:

biomarker_trajectories/output/validation_report.md

Checks include:

C01–C02: Sample size and population counts vs configuration.
C03: CA 15-3 baseline means increase monotonically with stage.
C04: CA 15-3 kinetics by response class (deep responders show early declines; early progressors show rises).
C05: ctDNA clearance is higher in deep responders and low in progression classes.
C06: Baseline ctDNA detectability is substantially higher in stage IV than in stage I.
C07: Missingness in key baseline and timeseries variables.

Intended use

This dataset is intended for:

Developing and benchmarking models for biomarker-based response assessment.
Exploring surrogate endpoints based on CA 15-3, CA 27-29, and ctDNA dynamics.
Teaching about biomarker kinetics in metastatic and advanced breast cancer.

It is not intended for:

Estimating real-world cutoffs or predictive values.
Guiding individual patient management.

Ethical considerations

All data are synthetically generated from literature-informed parameters.
Population and clinical patterns are inspired by published cohorts but do not represent any specific registry or trial.
The goal is to support method development and education around biomarker trajectories in diverse breast cancer populations, including SSA.