An open methods and data description for a governed synthetic genetic pool simulated with msprime

This is a methods and data paper accompanying the proof-of-concept implementation of the CORGData governed synthetic genetic pool. Where the original paper reported the scientific rationale and headline results, this document specifies the complete computational pipeline at a level of detail sufficient for independent reproduction, and specifies the planned open data deposit file by file. Founder haplotypes are seeded from the European subgroup of gnomAD v4 genomes for five MC1R variants (rs1805005-rs1805009); inheritance is simulated with msprime's fixed-pedigree ancestry model over the physical MC1R interval (GRCh38 chr16:89,919,436-89,920,138); governance acts through a parameterized parent-selection operator with governance strength lambda >= 0. A planned open deposit will contain simulation histories (neutral and governed), the locus panel definition, the governance-strength sweep, figure sources, and the complete Python source, all under CC-BY 4.0. Data and code follow the FAIR guiding principles. This is a method demonstration, not a clinical predictor or a person-level reconstruction system, and the limits of the demonstration are stated explicitly.

Authors

Publication Details

Journal
Zenodo (CERN European Organization for Nuclear Research)
Published
2026-09-30
DOI
https://doi.org/10.5281/zenodo.23069112
Primary Topic
Genetic Associations and Epidemiology
Type
preprint
Controls
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preprint

An open methods and data description for a governed synthetic genetic pool simulated with msprime

Pavel Zagadailov
Zenodo (CERN European Organization for Nuclear Research)
Genetic Associations and Epidemiology
preprint

An open methods and data description for a governed synthetic genetic pool simulated with msprime

Pavel Zagadailov
preprint en

Abstract

This is a methods and data paper accompanying the proof-of-concept implementation of the CORGData governed synthetic genetic pool. Where the original paper reported the scientific rationale and headline results, this document specifies the complete computational pipeline at a level of detail sufficient for independent reproduction, and specifies the planned open data deposit file by file. Founder haplotypes are seeded from the European subgroup of gnomAD v4 genomes for five MC1R variants (rs1805005-rs1805009); inheritance is simulated with msprime's fixed-pedigree ancestry model over the physical MC1R interval (GRCh38 chr16:89,919,436-89,920,138); governance acts through a parameterized parent-selection operator with governance strength lambda >= 0. A planned open deposit will contain simulation histories (neutral and governed), the locus panel definition, the governance-strength sweep, figure sources, and the complete Python source, all under CC-BY 4.0. Data and code follow the FAIR guiding principles. This is a method demonstration, not a clinical predictor or a person-level reconstruction system, and the limits of the demonstration are stated explicitly.

Zenodo (CERN European Organization for Nuclear Research)
Genetic Associations and Epidemiology
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An open methods and data description for a governed synthetic genetic pool simulated with msprime — Pavel Zagadailov · Zenodo (CERN European Organization for Nuclear Research) (2026) | TGRS Research Map | TGRS