README.md

---
license: cc-by-nc-4.0
language:
- en
tags:
- synthetic
- healthcare
- rare-disease
- pediatrics
- diagnostic-odyssey
- orphan-drug
- genomics
- health-economics
pretty_name: "Rare Pediatric Disorders: Diagnostic Odyssey, Multi-System Phenotype, Orphan-Drug Access & Outcomes (Sample)"
size_categories:
- n<1K
---

# HC-GEN-005 — Rare Pediatric Disorders: Diagnostic Odyssey, Multi-System Phenotype, Orphan-Drug Access & Outcomes (Sample)

Synthetic patient-level dataset spanning **40 rare pediatric disorders across 10 clinical classes** — lysosomal storage, organic acidemias, urea-cycle defects, mitochondrial, neuromuscular, leukodystrophy, skeletal dysplasia, immune deficiency, dermatologic, and syndromic disorders. The dataset models the diagnostic odyssey, multi-system phenotype, genetic testing cascade, orphan-drug access and health economics, clinical outcomes, caregiver burden, and social determinants of health.

This is a **500-patient sample** of the full HC-GEN-005 product. It is **synthetic** — generated by a calibrated simulation engine. It contains **no real patient data**.

> **Not for clinical use.** This dataset is for ML development, benchmarking, schema prototyping, and education only. It must not be used to inform real patient care, diagnosis, or treatment decisions.

## Calibration anchors

Sample-level observed values (seed 42, n=500):

| Metric | Observed | Target | Anchor |
|---|---|---|---|
| Diagnostic delay (median, non-NBS) | 3.53 yr | 2.8–4.6 | NORD Diagnostic Delay Survey (4.8y) |
| Specialists seen (median) | 7.0 | 6.0–9.0 | Shire Rare Disease Impact Report (~7.3) |
| Pathogenic variant confirmed | 0.78 | 0.72–0.84 | IRDiRC molecular-confirmation yield |
| Orphan cohort on DMT | 0.785 | 0.68–0.88 | orphan-drug-eligible treatment uptake |
| Overall by-18 mortality | 0.316 | 0.24–0.36 | severity-mixed rare-disease cohort |
| Newborn-screening capture | 0.302 | 0.22–0.36 | NBS-eligible capture fraction |
| PedsQL total (mean) | 52.5 | 48–58 | severity-mixed pediatric QoL |
| Caregiver Zarit burden (mean) | 46.9 | 42–52 | rare pediatric caregiver burden |
| NBS delay reduction | 4.84 yr | ≥3.0 (floor) | NBS collapses diagnostic delay |
| Severity → cognitive deficit | 34.8 pts | ≥15 (floor) | severity-graded impairment |
| MPS urine-GAG separation | 0.983 | ≥0.80 (floor) | GAG elevation specific to MPS |
| OA/UCD amino-acid separation | 0.814 | ≥0.55 (floor) | metabolic class abnormality |
| Respiratory FVC deficit | 34.2 pp | ≥20 (floor) | FVC reduction with respiratory involvement |
| Supportive-only DMT-cost violations | 0 | =0 (floor) | cost-integrity check |

Validation: **Grade A+ (10.00/10)** across all six canonical seeds (42, 7, 123, 2024, 99, 1), deterministic. The engine additionally passes its own internal 4/4 Grade A+ benchmark suite on every seed.

## Schema highlights by module

149 columns, single table. Module groups:

- **Demographics & access** — sex (inheritance-aware X-linked skew), race/ethnicity, region, residence, SES, language, insurance.
- **Disease taxonomy** — `primary_disease_category` (40 disorders), `disease_class` (10 classes), Orpha & OMIM codes, inheritance pattern, `disease_severity_index`, untreated by-18 mortality prior.
- **Diagnostic odyssey** — symptom onset, age at diagnosis, diagnostic delay, prior misdiagnoses, specialists/PCP/ER visits, newborn-screening eligibility & capture, genetic-test modality/cost/denial, pathogenic confirmation, diagnosis source, odyssey cost, parent advocacy.
- **Clinical presentation** — developmental milestones, motor/language/cognitive quotients, autism/ADHD, seizures, cardiac (LVH severity), respiratory (FVC, NIV, trach), GI/G-tube, hepatic/renal/ophtho/hearing/skeletal involvement, growth z-scores.
- **Metabolic & biomarkers** — amino acids, organic acids, acylcarnitine, urine GAG, chitotriosidase, lyso-Gb1/Gb3, GAA/GLA activity, ammonia, lactate/pyruvate, CK, LDH, AST, ferritin, sIL-2R.
- **Treatment & health economics** — therapy class (ERT/SRT/chaperone/gene-therapy/ASO/small-molecule/HSCT), specific products, treatment start/delay/cost, payer coverage, appeals, PAP enrollment, copay, ICER value, QALY, adherence, infusion/ADA reactions, efficacy, HSCT details.
- **Outcomes & function at 18** — progression velocity, hospitalizations, metabolic crises, ICU, respiratory failure, ambulation/communication/G-tube/vent status, schooling, mortality (flag/age/cause), hospice.
- **Caregiver & QoL** — Zarit, PHQ-9, GAD-7, employment disruption, lost income, sleep, OOP cost, PedsQL subscales, sibling impact, marital strain, advocacy/registry/trial engagement.
- **Social determinants** — distance to specialty center, travel burden, telehealth, language barrier, immigration concern, food/housing insecurity, transport barrier, missed appointments, SDOH composite.

## Files

- `hc_gen_005_sample.csv` — 500 synthetic patients, 149 columns.
- `README.md` — this file.

## Loading

```python
import pandas as pd
df = pd.read_csv("hc_gen_005_sample.csv")
print(df.shape)  # (500, 149)

# Diagnostic delay by newborn-screening capture
print(df.groupby("newborn_screening_caught")["diagnostic_delay_years"].median())
```

```python
from datasets import load_dataset
ds = load_dataset("xpertsystems/hc-gen-005-sample")
```

## Use cases

- Diagnostic-odyssey and time-to-diagnosis modeling across heterogeneous rare disorders.
- Orphan-drug access, payer-coverage, and health-economic (ICER/QALY) analysis.
- Newborn-screening impact simulation (delay collapse, mortality reduction).
- Multi-class rare-disease classification and severity stratification.
- Caregiver-burden and social-determinant modeling.
- Synthetic-data methodology benchmarking and schema/ETL prototyping (FHIR R4 export available in the engine).

## Limitations (honestly disclosed)

- **Synthetic, cross-sectional snapshot.** Each row is one patient with onset/diagnosis ages, status-at-18 projections, and annualized rates; there is no visit-level longitudinal table.
- **Diagnostic-delay median runs slightly below the NORD 4.8y anchor.** The engine's observed non-NBS median is ~3.5y, within its own ±1.5y tolerance of the NORD figure; the scorecard ranges the metric on the observed value and notes the anchor. Real-world delay varies widely by disorder.
- **Relative, not absolute, disease prevalence.** Category weights are *relative* within the represented rare-pediatric cohort, not population incidence; the 40-disorder mix is illustrative.
- **Marginal calibration, not full joint fidelity.** Univariate prevalences and the engineered structural separations (NBS delay collapse, severity-cognitive gradient, MPS-GAG and OA/UCD metabolic specificity, respiratory FVC deficit) are anchored; higher-order correlations beyond those engineered are not independently validated.
- **Therapy/economic parameters are illustrative.** Treatment products, costs, ICER/QALY values, and access pathways represent plausible ranges rather than payer-specific real-world data.
- **No engine defects identified.** The HC-GEN-005 engine passes its own internal 4/4 Grade A+ benchmark suite across all six canonical seeds with a stable 149-column schema; all sampling uses the seeded generator (no global-RNG issue); the Weibull sampler uses the accepted bare `lam*rng.weibull(k,n)` form. No defects were observed or suppressed.
- **Small-sample variance.** At n=500 some rates carry sampling variance; scorecard ranges accommodate this without masking real misses, and structural floors are weighted to dominate.

## Commercial / full version

| | Sample (this) | Full (commercial) |
|---|---|---|
| Patients | 500 | 20,000+ (configurable) |
| Columns | 149 | 149 |
| Disorders | 40 categories / 10 classes | 40 categories / 10 classes |
| Formats | CSV | CSV / JSON / Parquet / FHIR R4 bundle |
| Seeds / reproducibility | 6 canonical | Unlimited |
| License | CC-BY-NC-4.0 | Commercial |
| Support | — | SLA, custom calibration, vertical extensions |

Contact **pradeep@xpertsystems.ai** · https://xpertsystems.ai

## Citation

```bibtex
@dataset{xpertsystems_hcgen005_2026,
  title  = {HC-GEN-005: Synthetic Rare Pediatric Disorders Dataset ---
            Diagnostic Odyssey, Multi-System Phenotype, Orphan-Drug Access
            & Outcomes (Sample)},
  author = {XpertSystems.ai},
  year   = {2026},
  publisher = {Hugging Face},
  note   = {Synthetic data. Not for clinical use. Calibration anchors:
            NORD Diagnostic Delay Survey; IRDiRC diagnostic-odyssey data;
            Shire Rare Disease Impact Report; EURORDIS Rare Barometer;
            Orphanet prevalence; disease-specific trials (ENDEAR, STR1VE,
            CHERISH, ENGAGE) and ICER value assessments.},
  url    = {https://huggingface.co/datasets/xpertsystems/hc-gen-005-sample}
}
```