Datasets:

electricsheepafrica
/

colorectal-genomic-ssa

sample_id stringlengths 16 16	region stringclasses 4 values	age float64 25 90	sex stringclasses 2 values	tumor_location stringclasses 3 values	stage stringclasses 4 values	MSI_status stringclasses 3 values	Lynch_syndrome_status stringclasses 2 values	tmb_mut_per_mb float64 0.1 64.9	KRAS_mut bool 2 classes	BRAF_mut bool 2 classes
CRC_SAMPLE_00000	Southern_Africa	39.1	Male	Rectum	III	MSS	Non_Lynch	3.938814	false	false
CRC_SAMPLE_00001	East_Africa	50.7	Female	Right_colon	III	MSS	Non_Lynch	6.567425	false	false
CRC_SAMPLE_00002	Central_Africa	49.1	Male	Left_colon	IV	MSI-H	Non_Lynch	31.267474	true	false
CRC_SAMPLE_00003	Southern_Africa	52.6	Male	Right_colon	IV	MSS	Non_Lynch	7.121601	false	false
CRC_SAMPLE_00004	West_Africa	63.3	Female	Rectum	I	MSS	Non_Lynch	1.106597	false	false
CRC_SAMPLE_00005	Central_Africa	66	Male	Rectum	III	MSS	Non_Lynch	4.060211	false	false
CRC_SAMPLE_00006	Southern_Africa	48.9	Female	Rectum	I	MSS	Non_Lynch	2.608497	false	false
CRC_SAMPLE_00007	Southern_Africa	51.3	Female	Left_colon	IV	MSS	Non_Lynch	2.695306	false	false
CRC_SAMPLE_00008	West_Africa	71.9	Male	Right_colon	II	MSS	Non_Lynch	7.012657	false	false
CRC_SAMPLE_00009	East_Africa	78.8	Male	Right_colon	IV	MSS	Non_Lynch	5.172282	true	false
CRC_SAMPLE_00010	East_Africa	73.8	Male	Rectum	III	MSS	Non_Lynch	7.211125	false	false
CRC_SAMPLE_00011	Central_Africa	41.9	Female	Right_colon	III	MSS	Non_Lynch	6.558717	false	false
CRC_SAMPLE_00012	Southern_Africa	73.1	Male	Right_colon	IV	MSI-H	Non_Lynch	27.031844	false	false
CRC_SAMPLE_00013	Southern_Africa	80.4	Female	Right_colon	II	MSS	Non_Lynch	3.392014	false	false
CRC_SAMPLE_00014	East_Africa	41.3	Female	Right_colon	III	MSS	Non_Lynch	3.555844	false	false
CRC_SAMPLE_00015	West_Africa	71.9	Female	Right_colon	I	MSS	Non_Lynch	9.000249	false	false
CRC_SAMPLE_00016	East_Africa	62.5	Female	Right_colon	IV	MSS	Non_Lynch	6.364327	false	false
CRC_SAMPLE_00017	West_Africa	56.4	Male	Right_colon	II	MSS	Non_Lynch	2.382076	false	false
CRC_SAMPLE_00018	Southern_Africa	61.2	Male	Rectum	I	MSS	Non_Lynch	6.076917	false	false
CRC_SAMPLE_00019	Southern_Africa	64.9	Male	Rectum	II	MSS	Non_Lynch	3.913351	false	false
CRC_SAMPLE_00020	Southern_Africa	72.7	Male	Right_colon	IV	MSS	Non_Lynch	8.005745	false	false
CRC_SAMPLE_00021	East_Africa	72.2	Female	Left_colon	I	MSI-H	Non_Lynch	23.374211	false	false
CRC_SAMPLE_00022	Central_Africa	43.4	Female	Left_colon	I	MSI-H	Non_Lynch	21.119132	true	true
CRC_SAMPLE_00023	Central_Africa	52.9	Male	Left_colon	III	MSS	Non_Lynch	3.217804	true	false
CRC_SAMPLE_00024	Southern_Africa	61	Male	Rectum	III	MSS	Non_Lynch	3.98902	true	false
CRC_SAMPLE_00025	West_Africa	77.3	Male	Rectum	III	MSS	Non_Lynch	7.31718	false	false
CRC_SAMPLE_00026	East_Africa	30	Male	Right_colon	I	MSS	Non_Lynch	3.138172	true	false
CRC_SAMPLE_00027	West_Africa	53.3	Male	Rectum	III	MSI-H	Non_Lynch	29.088445	false	false
CRC_SAMPLE_00028	West_Africa	43.2	Female	Right_colon	III	MSS	Non_Lynch	0.627478	false	false
CRC_SAMPLE_00029	Southern_Africa	44.9	Male	Left_colon	II	MSS	Non_Lynch	9.402248	false	false
CRC_SAMPLE_00030	Southern_Africa	70.8	Female	Right_colon	IV	MSS	Non_Lynch	8.831576	false	false
CRC_SAMPLE_00031	Central_Africa	54.1	Male	Left_colon	I	MSS	Non_Lynch	3.158033	false	false
CRC_SAMPLE_00032	East_Africa	34.3	Male	Left_colon	IV	MSS	Non_Lynch	5.104087	false	false
CRC_SAMPLE_00033	East_Africa	58.3	Male	Right_colon	III	MSS	Non_Lynch	7.521009	false	false
CRC_SAMPLE_00034	East_Africa	82.4	Male	Right_colon	I	MSS	Non_Lynch	4.997024	true	false
CRC_SAMPLE_00035	West_Africa	40.1	Male	Right_colon	III	MSS	Non_Lynch	1.163919	false	false
CRC_SAMPLE_00036	West_Africa	65.9	Female	Left_colon	III	MSS	Non_Lynch	1.807605	false	false
CRC_SAMPLE_00037	East_Africa	77.2	Female	Left_colon	II	MSS	Non_Lynch	6.679779	true	false
CRC_SAMPLE_00038	West_Africa	59.5	Female	Left_colon	III	MSI-L	Non_Lynch	12.040959	true	false
CRC_SAMPLE_00039	Southern_Africa	81.2	Female	Rectum	III	MSS	Non_Lynch	2.713868	false	false
CRC_SAMPLE_00040	East_Africa	52.7	Female	Right_colon	IV	MSS	Non_Lynch	4.436078	false	false
CRC_SAMPLE_00041	Southern_Africa	75.9	Female	Left_colon	IV	MSS	Non_Lynch	3.967711	false	false
CRC_SAMPLE_00042	Southern_Africa	73.3	Male	Left_colon	IV	MSS	Non_Lynch	4.293087	false	false
CRC_SAMPLE_00043	East_Africa	59.6	Male	Left_colon	III	MSS	Non_Lynch	8.208001	false	false
CRC_SAMPLE_00044	Southern_Africa	43.6	Female	Rectum	II	MSS	Non_Lynch	4.873406	true	false
CRC_SAMPLE_00045	Southern_Africa	49	Female	Right_colon	III	MSS	Non_Lynch	4.271999	true	false
CRC_SAMPLE_00046	East_Africa	34.2	Female	Rectum	I	MSS	Non_Lynch	4.194748	true	true
CRC_SAMPLE_00047	West_Africa	66.5	Female	Right_colon	IV	MSS	Non_Lynch	3.877719	false	false
CRC_SAMPLE_00048	Southern_Africa	65.2	Female	Right_colon	III	MSS	Non_Lynch	5.605933	false	false
CRC_SAMPLE_00049	West_Africa	60.9	Male	Right_colon	IV	MSS	Non_Lynch	0.1	false	false
CRC_SAMPLE_00050	West_Africa	58.7	Male	Right_colon	II	MSS	Non_Lynch	4.80225	false	false
CRC_SAMPLE_00051	West_Africa	74.9	Male	Left_colon	I	MSI-H	Lynch	17.925679	false	false
CRC_SAMPLE_00052	Southern_Africa	63.3	Male	Left_colon	I	MSI-H	Non_Lynch	20.682065	true	false
CRC_SAMPLE_00053	Southern_Africa	53.9	Female	Right_colon	III	MSS	Non_Lynch	3.370026	true	false
CRC_SAMPLE_00054	Southern_Africa	61.6	Male	Right_colon	IV	MSS	Non_Lynch	5.761249	true	false
CRC_SAMPLE_00055	Southern_Africa	82.5	Female	Right_colon	IV	MSI-H	Non_Lynch	23.838067	false	false
CRC_SAMPLE_00056	East_Africa	66.8	Female	Rectum	III	MSS	Non_Lynch	4.821618	false	false
CRC_SAMPLE_00057	East_Africa	55.7	Female	Rectum	III	MSS	Non_Lynch	3.006398	true	false
CRC_SAMPLE_00058	West_Africa	59.5	Female	Right_colon	II	MSS	Non_Lynch	3.303462	false	false
CRC_SAMPLE_00059	West_Africa	65.1	Female	Rectum	II	MSS	Non_Lynch	4.29654	false	false
CRC_SAMPLE_00060	Southern_Africa	55.4	Female	Right_colon	III	MSS	Non_Lynch	2.879439	false	false
CRC_SAMPLE_00061	East_Africa	54.4	Female	Left_colon	IV	MSS	Non_Lynch	4.952718	true	false
CRC_SAMPLE_00062	East_Africa	59.9	Male	Rectum	II	MSS	Non_Lynch	4.566347	false	true
CRC_SAMPLE_00063	Southern_Africa	76.7	Female	Left_colon	I	MSS	Non_Lynch	5.082322	false	false
CRC_SAMPLE_00064	Southern_Africa	68.7	Female	Right_colon	III	MSS	Non_Lynch	1.870263	false	false
CRC_SAMPLE_00065	East_Africa	55.5	Male	Rectum	III	MSS	Non_Lynch	5.643626	false	false
CRC_SAMPLE_00066	East_Africa	69.6	Male	Rectum	I	MSS	Non_Lynch	1.25135	false	false
CRC_SAMPLE_00067	East_Africa	60.1	Male	Right_colon	II	MSS	Non_Lynch	6.500004	false	false
CRC_SAMPLE_00068	West_Africa	63.8	Male	Right_colon	II	MSS	Non_Lynch	3.193797	false	false
CRC_SAMPLE_00069	East_Africa	62.8	Female	Rectum	III	MSS	Non_Lynch	5.613487	false	false
CRC_SAMPLE_00070	West_Africa	36.8	Female	Right_colon	IV	MSS	Non_Lynch	3.611661	false	false
CRC_SAMPLE_00071	East_Africa	26.5	Male	Right_colon	III	MSS	Non_Lynch	5.074147	false	false
CRC_SAMPLE_00072	Central_Africa	62.5	Male	Left_colon	IV	MSS	Non_Lynch	5.305675	true	false
CRC_SAMPLE_00073	West_Africa	50.6	Female	Left_colon	IV	MSS	Non_Lynch	3.646955	false	false
CRC_SAMPLE_00074	West_Africa	42	Female	Left_colon	I	MSI-L	Non_Lynch	6.029996	true	false
CRC_SAMPLE_00075	West_Africa	51	Male	Right_colon	III	MSS	Non_Lynch	9.166636	false	false
CRC_SAMPLE_00076	West_Africa	70.2	Male	Right_colon	II	MSS	Non_Lynch	2.813294	false	false
CRC_SAMPLE_00077	Southern_Africa	63.9	Male	Rectum	III	MSS	Non_Lynch	3.42583	true	false
CRC_SAMPLE_00078	East_Africa	68.5	Male	Rectum	IV	MSI-H	Non_Lynch	26.763315	false	false
CRC_SAMPLE_00079	Southern_Africa	65	Male	Right_colon	II	MSS	Non_Lynch	5.542066	true	false
CRC_SAMPLE_00080	Southern_Africa	49.9	Male	Rectum	IV	MSI-H	Non_Lynch	37.896929	false	false
CRC_SAMPLE_00081	East_Africa	68.5	Male	Left_colon	IV	MSS	Non_Lynch	2.382992	false	false
CRC_SAMPLE_00082	Southern_Africa	66.4	Male	Right_colon	IV	MSS	Non_Lynch	3.060682	false	false
CRC_SAMPLE_00083	West_Africa	58.7	Male	Rectum	IV	MSS	Non_Lynch	4.950517	false	false
CRC_SAMPLE_00084	West_Africa	60.6	Female	Right_colon	I	MSS	Non_Lynch	7.529602	false	false
CRC_SAMPLE_00085	West_Africa	68.7	Female	Right_colon	II	MSS	Non_Lynch	2.506609	true	false
CRC_SAMPLE_00086	Southern_Africa	51.8	Female	Right_colon	I	MSS	Non_Lynch	4.436032	false	false
CRC_SAMPLE_00087	East_Africa	72	Male	Rectum	IV	MSI-H	Lynch	17.117221	true	false
CRC_SAMPLE_00088	West_Africa	66.2	Male	Rectum	II	MSS	Non_Lynch	6.405442	false	false
CRC_SAMPLE_00089	East_Africa	60	Male	Rectum	IV	MSS	Non_Lynch	3.527754	false	false
CRC_SAMPLE_00090	West_Africa	76.8	Male	Left_colon	III	MSS	Non_Lynch	0.80115	false	false
CRC_SAMPLE_00091	Southern_Africa	45.8	Female	Left_colon	IV	MSS	Non_Lynch	3.92342	true	false
CRC_SAMPLE_00092	East_Africa	54.9	Female	Left_colon	II	MSS	Non_Lynch	4.845716	true	false
CRC_SAMPLE_00093	East_Africa	52.5	Male	Right_colon	I	MSS	Non_Lynch	4.478325	true	false
CRC_SAMPLE_00094	East_Africa	63.9	Male	Rectum	I	MSS	Non_Lynch	2.18928	false	false
CRC_SAMPLE_00095	Southern_Africa	73	Female	Rectum	III	MSS	Non_Lynch	8.882097	true	false
CRC_SAMPLE_00096	East_Africa	49.2	Female	Right_colon	III	MSS	Non_Lynch	4.57073	false	false
CRC_SAMPLE_00097	West_Africa	90	Female	Rectum	II	MSS	Non_Lynch	3.728699	false	false
CRC_SAMPLE_00098	West_Africa	52.7	Male	Left_colon	III	MSS	Non_Lynch	3.800389	false	false
CRC_SAMPLE_00099	Central_Africa	64	Female	Right_colon	II	MSS	Non_Lynch	3.466137	true	false

End of preview. Expand in Data Studio

Colorectal Cancer Genomic Profiles (SSA, Synthetic)

Dataset owner: Electric Sheep Africa
Dataset type: Synthetic colorectal cancer genomic profiles (KRAS/BRAF, MSI, Lynch, TMB)
Populations: Colorectal cancer patients from sub-Saharan Africa (modeled cohorts)
Version: 1.0.0
License: CC-BY-NC-4.0

1. Dataset Description

This dataset provides synthetic genomic profiles for 30,000 colorectal tumors from sub-Saharan Africa (SSA).

The dataset encodes:

Per-sample KRAS and BRAF mutation status
Microsatellite instability (MSI) status and a derived Lynch_syndrome_status label
Tumor mutational burden (TMB) in mutations per megabase
Basic clinical context: region, age, sex, tumor_location, and stage

All records are fully synthetic and parameterized using SSA-focused colorectal genomics literature plus global MSI/TMB reviews. No real patient-level data are used.

Important: This dataset contains no real patient data. It is derived entirely from literature-based distributions and internal coherence rules.

2. Intended Use

This dataset is intended for:

Method development for somatic mutation–based risk models and MSI/Lynch detection
Benchmarking algorithms for TMB-aware modeling and biomarker discovery
Educational use in colorectal cancer genomics and precision oncology in SSA

Not intended for clinical decision-making or individual patient stratification.

3. Cohort Design

3.1 Regions

West_Africa
East_Africa
Southern_Africa
Central_Africa

3.2 Sample Size & Demographics

Total samples: 30,000 synthetic colorectal tumors
Age range: 25–90 years, centered around ~60
Sex distribution: ~55% Male, 45% Female

3.3 Tumor Location

Right_colon
Left_colon
Rectum

3.4 Stage

stage ∈ {I, II, III, IV} (enriched for stage II–III)

4. Genomic Features

4.1 KRAS and BRAF

Per-sample boolean flags indicate mutation status:

KRAS_mut
BRAF_mut

Regional targets are informed by SSA literature:

West_Africa (e.g., Nigerian cohorts): KRAS ~20–25%; BRAF ~5%
East_Africa (e.g., Kenyan cohorts): KRAS ~45–50%; BRAF ~5%
Southern/Central Africa: intermediate values, guided by global CRC ranges

4.2 Microsatellite Instability (MSI) and Lynch Syndrome

MSI_status ∈ {MSS, MSI-L, MSI-H}
Lynch_syndrome_status ∈ {Lynch, Non_Lynch}

Approximate targets:

MSI-H ≈ 15–16% of all CRC
~20% of MSI-H tumors are labeled Lynch (≈3% of all CRC), the rest Non_Lynch (sporadic MSI-H)

4.3 Tumor Mutational Burden (TMB)

tmb_mut_per_mb – Tumor mutational burden (mutations per megabase)

Distributions by MSI class:

MSS: mean ~4 mut/Mb (low TMB)
MSI-L: modestly elevated TMB
MSI-H: mean ~25 mut/Mb (hypermutated), with a wide tail

The validator checks that TMB in MSI-H tumors is several-fold higher than in MSS tumors.

5. Main File Schema

5.1 `colorectal_genomic_data.csv`

Rows: 30,000 samples
Columns:

Clinical & context:

sample_id – Synthetic ID (CRC_SAMPLE_00000 ...)
region – {West_Africa, East_Africa, Southern_Africa, Central_Africa}
age – Age in years
sex – {Male, Female}
tumor_location – {Right_colon, Left_colon, Rectum}
stage – {I, II, III, IV}

Genomic features:

MSI_status – {MSS, MSI-L, MSI-H}
Lynch_syndrome_status – {Lynch, Non_Lynch}
tmb_mut_per_mb – Tumor mutational burden (mut/Mb)
KRAS_mut – Boolean, KRAS mutated
BRAF_mut – Boolean, BRAF (primarily V600E) mutated

6. Data Access & Files

Main Dataset (root)

colorectal_genomic_data.csv – 30,000 × 11 variables (main table, CSV)
colorectal_genomic_data.parquet – Same table in Parquet format for efficient loading

No auxiliary long-format variant or CNV tables are provided for this dataset; it focuses on per-sample biomarker status and TMB.

7. Generation & Validation (Summary)

The dataset was generated using the GENOMICS Synthetic Data Playbook:

Domain specification – Identify key colorectal biomarkers (KRAS, BRAF, MSI, Lynch, TMB) relevant for SSA cohorts.
Literature-informed parameters – Extract KRAS/BRAF frequencies from Nigerian and Kenyan cohorts, MSI-H and Lynch fractions from South African and global CRC studies, and TMB distributions from MSI/TMB reviews (see local docs/LITERATURE_INVENTORY.csv).
Configuration – Encode parameters in colorectal_genomic/configs/colorectal_genomic_config.yaml.
Generation – Use scripts/generate_colorectal_genomic.py to simulate 30,000 tumors.
Validation – Use scripts/validate_colorectal_genomic.py to check distributions, MSI/Lynch prevalence, TMB patterns, and missingness.

7.1 Validation Status

Validation run on: colorectal_genomic/output/colorectal_genomic_data.csv
Checks include:
- Region distribution vs config
- KRAS/BRAF prevalences (overall and by region) vs config
- MSI and Lynch prevalence vs config
- TMB shift in MSI-H vs MSS
- Missingness in key variables

The current validation report indicates Overall Status: PASS (all checks PASS).

8. Example Usage

8.1 Load with pandas

import pandas as pd

df = pd.read_csv("colorectal_genomic_data.csv")
print(df.shape)
print(df.head())

8.2 Load with `datasets` (Hugging Face)

from datasets import load_dataset

crc = load_dataset("electricsheepafrica/colorectal-genomic-ssa")
df = crc["train"].to_pandas()

print(f"Samples: {len(df)}")
print(f"Columns: {len(df.columns)}")

8.3 TMB vs MSI status

summary = df.groupby("MSI_status")["tmb_mut_per_mb"].describe()
print(summary)

8.4 KRAS/BRAF by region

region_mut = df.groupby("region")["KRAS_mut", "BRAF_mut"].mean()
print(region_mut)

9. Ethical & Appropriate Use

9.1 Appropriate Uses ✅

Method development and benchmarking in CRC biomarker modeling
Educational use in colorectal cancer genomics and TMB/MSI modeling
Health equity and disparity analysis using synthetic data

9.2 Inappropriate Uses ❌

Clinical decision-making for individual patients
Real-world prognosis or treatment selection
Insurance, employment, or financial decisions

This dataset is synthetic and must not be used as a substitute for real clinical or genomic data in patient care.

10. License

License: CC-BY-NC-4.0
Commercial use: Not permitted without explicit permission.

11. Citation

Electric Sheep Africa (2025).
Colorectal Cancer Genomic Profiles (SSA, Synthetic Dataset).
Generated using literature-informed synthetic data methods.
Hugging Face Datasets. Version 1.0.0.