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Development of a novel five dye insertion/deletion (INDEL) panel for ancestry determination

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Abstract

The use of genetic markers, specifically Short Tandem Repeats (STRs), has been a valuable tool for identifying persons of interest. However, the ability to analyze additional markers including Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletion (INDELs) polymorphisms allows laboratories to explore other investigative leads. INDELs were chosen in this study because large panels can be differentiated by size, allowing them to be genotyped by capillary electrophoresis. Moreover, these markers do not produce stutter and are smaller in size than STRs, facilitating the recovery of genetic information from degraded samples. The INDEL Ancestry Informative Markers (AIMs) in this study were selected from the 1000 Genomes Project based on a fixation index (FST) greater than 0.50, high allele frequency divergence, and genetic distance. A total of 25 INDEL-AIMs were optimized and validated according to SWGDAM guidelines in a five-dye multiplex. To validate the panel, genotyping was performed on 155 unrelated individuals from four ancestral groups (Caucasian, African, Hispanic, and East Asian). Bayesian clustering and principal component analysis (PCA) were performed revealing clear separation among three groups, with some observed overlap within the Hispanic group. Additionally, the PCA results were compared against a training set of 793 samples from the 1000 Genomes Project, demonstrating consistent results. Validation studies showed the assay to be reproducible, tolerant to common inhibitors, robust with challenging casework type samples, and sensitive down to 125 pg. In conclusion, our results demonstrated the robustness and effectiveness of a 25 loci INDEL system for ancestry inference of four ancestries commonly found in the United States.

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Acknowledgements

We would like to acknowledge the Sam Houston State University Department of Forensic Science as well as the Southeast Texas Applied Forensic Science Facility and the donors and their loved ones, without whom this research would not be possible. We would also like to thank Natalia Czado for her helpful edits to this manuscript.

Funding

This study was partially funded by the National Institute of Justice Award #2013-DN-BX-K036. The opinions, findings, conclusions, or recommendations expressed in this presentation are those of the authors and do not necessarily reflect those of the National Institute of Justice.

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Authors and Affiliations

  1. Department of Forensic Science, Sam Houston State University, 1003 Bowers Blvd., Huntsville, TX, 77340, USA

    Lucio L. Avellaneda, Damani T. Johnson, Ryan M. Gutierrez, Rachel M. Houston & Bobby L. LaRue

  2. Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, TX, 76107, USA

    Lindsey Thompson, Sarah A. Sturm, Kelly A. Sage & Bobby L. LaRue

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  1. Lucio L. Avellaneda
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  2. Damani T. Johnson
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Correspondence to Lucio L. Avellaneda.

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Compliance with ethical standards

The hair, blood, and buccal samples used in this study were collected in accordance with Institutional Review Board (IRB) approved protocols (IRB-FY2017-32804). All procedures were in accordance with the 1964 Helsinki Declaration and its later amendments.

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Avellaneda, L.L., Johnson, D.T., Gutierrez, R.M. et al. Development of a novel five dye insertion/deletion (INDEL) panel for ancestry determination. Int J Legal Med (2024). https://doi.org/10.1007/s00414-024-03196-1

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