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SNP Genotype Imputation in Forensics-A Performance Study
Linköping University, Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology. Linköping University, Faculty of Medicine and Health Sciences. Natl Board Forens Med, Dept Forens Genet & Forens Toxicol, SE-58758 Linkoping, Sweden.
Natl Board Forens Med, Dept Forens Genet & Forens Toxicol, SE-58758 Linkoping, Sweden; Oslo Univ Hosp, Norway.
2024 (English)In: Genes, E-ISSN 2073-4425, Vol. 15, no 11, article id 1386Article in journal (Refereed) Published
Abstract [en]

Background/Objectives: Emerging forensic genetic applications, such as forensic investigative genetic genealogy (FIGG), advanced DNA phenotyping, and distant kinship inference, increasingly require dense SNP genotype datasets. However, forensic-grade DNA often contains missing genotypes due to its quality and quantity limitations, potentially hindering these applications. Genotype imputation, a method that predicts missing genotypes, is widely used in population and medical genetics, but its utility in forensic genetics has not been thoroughly explored. This study aims to assess the performance of genotype imputation in forensic contexts and determine the conditions under which it can be effectively applied. Methods: We employed a simulation-based approach to generate realistic forensic SNP genotype datasets with varying numbers, densities, and qualities of observed genotypes. Genotype imputation was performed using Beagle software, and the performance was evaluated based on the call rate and imputation accuracy across different datasets and imputation settings. Results: The results demonstrate that genotype imputation can significantly increase the number of SNP genotypes. However, imputation accuracy was dependent on factors such as the quality of the original genotype data and the characteristics of the reference population. Higher SNP density and fewer genotype errors generally resulted in improved imputation accuracy. Conclusions: This study highlights the potential of genotype imputation to enhance forensic SNP datasets but underscores the importance of optimizing imputation parameters and understanding the limitations of the original data. These findings will inform the future application of imputation in forensic genetics, supporting its integration into forensic workflows.

Place, publisher, year, edition, pages
MDPI , 2024. Vol. 15, no 11, article id 1386
Keywords [en]
forensic genetics; forensic investigative genetic genealogy; kinship analysis
National Category
Endocrinology and Diabetes
Identifiers
URN: urn:nbn:se:liu:diva-210334DOI: 10.3390/genes15111386ISI: 001364979000001PubMedID: 39596586OAI: oai:DiVA.org:liu-210334DiVA, id: diva2:1919967
Note

Funding Agencies|Strategic Research Area in Forensic Science, Linkoping University

Available from: 2024-12-10 Created: 2024-12-10 Last updated: 2024-12-10

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