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MHappaMundi: A custom AmpliSeq microhaplotype panel for ancestry inference
Pedro Rodrigues1, Nádia Pinto2, Maria João Prata3
1Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen DK-2100, Denmark; Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal; Institute of Molecular Pathology and Immunology, University of Porto (IPATIMUP), Porto, Portugal; Faculty of Sciences of the University of Porto (FCUP), Porto, Portugal.
A new microhaplotype (MH) panel, MHappaMundi, effectively differentiates major continental ancestries, including challenging European and South Asian groups. This tool aids forensic genetics by accurately estimating ancestry in admixed individuals.
Area of Science:
- Forensic genetics
- Population genetics
- Human ancestry inference
Background:
- Microhaplotypes (MHs) are emerging genetic markers with potential in forensics, offering alternatives to STRs and SNPs.
- Existing MH panels for ancestry inference are limited, hindering widespread adoption.
- A novel panel is needed to accurately differentiate diverse continental populations and aid forensic applications.
Purpose of the Study:
- To develop and validate a novel microhaplotype panel, MHappaMundi, for accurate ancestry inference.
- To differentiate between five major continental ancestries: Sub-Saharan African, European, South Asian, East Asian, and Native American.
- To assess the panel's performance in forensic and population genetics contexts, including admixed individuals.
Main Methods:
- Developed MHappaMundi by selecting 100 MHs based on pairwise FST values from the MicroHapDB database and 1000 Genomes Project (1kGP) data.
- Sequenced 368 individuals from European, East Asian, and Native American populations using the Ion GeneStudio™ S5 System.
- Evaluated population genetic clustering using STRUCTURE, Principal Component Analysis (PCA), and Multidimensional Scaling (MDS) with existing 1kGP and Middle Eastern population data.
Main Results:
- The final MHappaMundi panel comprises 92 MHs and 466 allele-defining SNPs after excluding 8 loci.
- The panel effectively distinguished the five continental groups, notably resolving challenges in separating Europeans and South Asians.
- MHappaMundi demonstrated accurate estimation of ancestry proportions in admixed individuals.
Conclusions:
- MHappaMundi is a valuable tool for accurate ancestry inference in forensic investigations and population genetics studies.
- The panel's ability to differentiate closely related populations enhances its utility in diverse forensic scenarios.
- MHappaMundi shows promise for broader community acceptance and application in human identification and biogeographic ancestry estimation.
