SkyWhal3/STXBP1_Base_Editing_Parameter_Sweep

STXBP1 Base Editing Parameter Sweep

654 million parameter combinations analyzed for 170 pathogenic STXBP1 variants

Overview

This dataset contains exhaustive parameter optimization results for base editing guide design targeting STXBP1 mutations. It identifies which variants can be studied in wild-type mouse models versus those requiring humanized mice.

🏆 Perfect Score Variants (100/100)

Variant	cDNA	Editor	WT Mouse Compatible
E53X	c.157G>T	Prime	✅ YES
A297S	c.889G>T	Prime	✅ YES
E302X	c.904G>T	Prime	✅ YES
M443R	c.1328T>G	Prime	✅ YES
L446F	c.1336C>T	CBE	✅ YES

Dataset Statistics

Metric	Value
Total analyses	654,595,200
Variants	170 SNVs
Parameter combos/variant	3,850,560
Compatible variants	~95
Compute time	35 minutes
Hardware	NVIDIA GH200 (ARM64 + H100)

Files

• stxbp1_ULTIMATE_best.json - Optimal parameters for each variant (recommended)
• stxbp1_ULTIMATE_sweep.csv.gz - All 654M analyses (~5GB compressed)

Parameter Space

Parameter	Range	Values
Scan radius	10-200 bp	191
Context radius	5-100 bp	96
Edit window	(1,1) to (20,20)	210

Scoring System (0-100)

• Context identity (40 pts): Human-mouse sequence conservation
• Guide quality (30 pts): Protospacer mismatch penalty
• Edit window (20 pts): Target base in optimal editing positions
• WT compatible (10 pts): Can use wild-type mouse

Editor Types

Editor	Change	Count	Example
ABE	A→G	32	ABE8e
CBE	C→T	50	BE4max
Prime	Any	82	PE2/PE3

Usage

import json

# Load optimal configurations
with open('stxbp1_ULTIMATE_best.json') as f:
    best = json.load(f)

# Get K196X optimal parameters
k196x = best['K196X']
print(f"Score: {k196x['score']}")
print(f"Editor: {k196x['edit_type']}")
print(f"Compatible: {k196x['compatible']}")

Query the Full CSV

import duckdb

# Find all parameter combos for K196X scoring > 90
results = duckdb.query("""
    SELECT * FROM 'stxbp1_ULTIMATE_sweep.csv.gz'
    WHERE label = 'K196X' AND score > 90
    ORDER BY score DESC
    LIMIT 100
""").df()

Reference Sequences

• Human: NM_001032221.6 (1,785 bp, 594 aa)
• Mouse: NM_009295 (1,785 bp, 594 aa)
• Overall identity: 90.9%

Interactive Tool

Test individual variants: STXBP1 Base Editing Verifier

Citation

@dataset{stxbp1_base_editing_sweep_2026,
  author = {Freygang, Adam},
  title = {STXBP1 Base Editing Mouse Model Compatibility Parameter Sweep},
  year = {2026},
  publisher = {HuggingFace},
  url = {https://huggingface.co/datasets/SkyWhal3/stxbp1-base-editing-sweep}
}

License

MIT

Acknowledgments

• STXBP1 Foundation
• Lambda Cloud (compute)
• STXBP1-ARIA Project

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For research use. Not medical advice.