Fifty-SNP Assay for Biogeographic Ancestry and Phenotype Prediction in the U.S. Population

• NCJ Number: 246746
• Journal: Forensic Science International: Genetics Volume: 8 Issue: 1 Dated: January 2014 Pages: 101-108
• Author(s): Katherine B. Gettings; Ronald Lai; Joni L. Johnson; Michelle A. Peck; Jessica A. Hart; Heather Gordish-Dressman; Moses S. Schanfield; Daniele S. Podini
• Date Published: January 2014
• Length: 8 pages
• Publication Format: Article
• Publication Type: Report (Study/Research)
• Language: English
• Country: United States of America

Annotation

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.

Abstract

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. We have 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 American. We have optimized this assay to a sensitivity level comparable to current forensic DNA analyses, and shown robust performance on forensic-type samples. In addition, we 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, we evaluated the biogeographic ancestry prediction model using a test set, and we evaluated an existing model for eye color with our U.S. sample set. Using these models with recommended thresholds, the 50 SNP assay provided accurate ancestry information in 98.6% of the test set samples, and provided accurate eye color information in 61% of the European samples tested 25% were inconclusive and 14% 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.