Py_Ped_Sim: A Flexible Forward Pedigree and Genetic Simulator for Complex Family Pedigree Analysis

• NCJ Number: 310483
• Journal: Bmc Bioinformatics Volume: 26 Dated: 2025 Pages: 122
• Author(s): Miguel Guardado; Cynthia Perez; Sthen Campana; Berenice Chavez Rojas; Joaquín Magaña; Shalom Jackson; et al
• Date Published: May 2025
• Length: 18 pages
• Grant Number(s): 15PNIJ-23-AG-04262-DNAX; 2019-DU-BX-0028
• Agencies: NIJ-Sponsored
• Publication Type: Research (Applied/Empirical)
• Award: Quantifying the Accuracy of Two Innovative Forensic Genetic Identification Techniques: Genealogical Searching and Low-Template DNA Mixture Analysis; Quantifying the accuracy of low quality DNA sample analysis from genotyping to genealogical searching and integration as a bioinformatic pipeline

Annotation

In this paper, the authors discuss the design, implementation, and results from a project to develop an open-source command line tool in Python that is designed to integrate the simulation of dynamic pedigrees and genomes.

Abstract

Large-scale family pedigrees are commonly used across medical, evolutionary, and forensic genetics. These pedigrees are tools for identifying genetic disorders, tracking evolutionary patterns, and establishing familial relationships via forensic genetic identification. However, there is a lack of software to accurately simulate different pedigree structures along with genomes corresponding to those individuals in a family pedigree. This limits simulation-based evaluations of methods that use pedigrees. The authors have developed a python command-line-based tool called py_ped_sim that facilitates the simulation of pedigree structures and the genomes of individuals in a pedigree. py_ped_sim represents pedigrees as directed acyclic graphs, enabling conversion between standard pedigree formats and integration with the forward population genetic simulator, SLiM. Notably, py_ped_sim allows the simulation of varying numbers of offspring for a set of parents, with the capacity to shift the distribution of sibship sizes over generations. The authors also add simulations for events of misattributed paternity, which offers a way to simulate half-sibling relationships, and simulations to extend the breadth of a family pedigree. They validated the accuracy of both the genome simulator and pedigree simulator. They show that it is possible to simulate genomes onto family pedigrees with levels of expected kinship. py_ped_sim is a user-friendly and open-source solution for simulating pedigree structures and conducting pedigree genome simulations. It empowers medical, forensic, and evolutionary genetics researchers to gain deeper insights into the dynamics of genetic inheritance and relatedness within families. (Published Abstract Provided)