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A 50-SNP assay for biogeographic ancestry and phenotype prediction in the U.S. population

NCJ Number
Forensic Science International: Genetics Volume: 8 Dated: 2014 Pages: 101-108
Date Published
8 pages

This article reports on a project that used single base primer extension (SBE) technology to develop a 50 SNP assay (composed of three multiplexes) designed to predict ancestry among the primary U.S. populations (African American, East Asian, European American, and Hispanic American/Native American), as well as pigmentation phenotype (eye, hair, and skin color) among European Americans.


When an STR DNA profile obtained from crime scene evidence does not match identified suspects or profiles from available databases, further DNA analyses targeted at inferring the possible ancestral origin and phenotypic characteristics of the perpetrator could yield valuable information. Single Nucleotide Polymorphisms (SNPs), the most common form of genetic polymorphisms, have alleles associated with specific populations and/or correlated to physical characteristics. The current study optimized the assay used to a sensitivity level comparable to current forensic DNA analyses, and showed robust performance on forensic-type samples. In addition, it developed a prediction model for ancestry in the U.S. population, based on the random match probability and likelihood ratio formulas already used in forensic laboratories. Lastly, researchers evaluated the biogeographic ancestry prediction model using a test set and evaluated an existing model for eye color with the U.S. sample set. Using these models with recommended thresholds, the 50 SNP assay provided accurate ancestry information in 98.6 percent of the test set samples and provided accurate eye color information in 61 percent of the European samples tested (25 percent were inconclusive and 14 percent were incorrect). This method, which uses equipment already available in forensic DNA laboratories, is recommended for use in U.S. forensic casework to provide additional information about the donor of a DNA sample when the STR profile has not been linked to an individual. (publisher abstract modified)

Date Published: January 1, 2014