Development of a SNP panel for predicting biogeographical ancestry and phenotype using massively parallel sequencing

Area of Science:

• Forensic Genetics
• Human Population Genetics
• Genomic Analysis

Background:

• Accurate inference of ancestry and physical characteristics is crucial for investigations involving unidentified individuals.
• Current methods require refinement for diverse populations and complex forensic scenarios.

Purpose of the Study:

• To develop and validate a custom SNP panel for massively parallel sequencing (MPS) to predict biogeographic ancestry and phenotype.
• To enhance ancestry prediction using a two-tier approach integrating ancestry-informative SNPs (AISNPs) and phenotype-informative SNPs.

Main Methods:

• A custom panel of 156 SNPs was designed, incorporating AISNP panels (Kidd 55 and SWA) and phenotype-informative SNPs.
• The panel was evaluated for sensitivity, genotype concordance, mixture analysis, ancestry assignment, and phenotype prediction (eye, hair, skin color).
• One SNP (rs6599400) was removed due to poor performance; extreme mixtures (1:10) presented interpretation challenges.

Main Results:

• The developed SNP panel demonstrated accurate ancestry assignment and phenotype predictions for individuals from intermediate population regions.
• High coverage data was achieved, enabling reliable inference of biogeographic ancestry.
• Phenotype predictions for eye, hair, and skin color were accurate based on the samples' population origins.

Conclusions:

• The custom 156 SNP panel is effective for inferring biogeographic ancestry and predicting key physical characteristics using MPS.
• This tool has significant potential for forensic applications, including cold cases and disaster victim identification.
• The panel's accuracy in intermediate populations enhances its utility for global forensic genetics.