SNP-Based Microarray Technology for Use in Forensic Applications' Final Technical Report

• NCJ Number: 223977
• Author(s): Giulia C. Kennedy
• Date Published: 2008
• Length: 43 pages
• Grant Number(s): 2005-DA-BX-K101
• Agencies: NIJ-Sponsored
• Publication Type: Report (Study/Research)

Annotation

This project enabled the detection and analysis of forensically relevant single-nucleotide polymorphisms (SNPs), which will enhance and complement the genomic information currently being used for forensic DNA identification.

Abstract

Using Affymetrix 500K nuclear SNP genotyping arrays, the project demonstrated that preamplification using whole genome amplification (WGA) on low template samples yields successful genotyping for 80-90 percent of the markers on the 500K arrays. These results represent approximately 5-10 percent lower call rates than the non-preamplifier standard assay. Degraded samples prepared by DNase I digestion provide genotype data on many thousands of SNPs in the 500K assay. Using the standard assay, researchers detected mixed samples composed of two, three, or four components. In mixtures with two components, researchers detected as low as a 5-percent contribution from the minor component. The project ran the 500K SNP assay on all samples and analyzed the data using the standard algorithm. The results show that all samples, except for hair shaft (no root) yielded useable genotype data; genders were correctly assigned in all cases; mixtures were detected, and the two components of the mixture were identified; semen and buccal samples yielded high call rates comparable to control samples; vaginal samples had 5-10 percent lower call rates than semen and buccal samples; WGA samples yielded 5-10 percent lower call rates than unamplified genomic DNA; and all ethnicities were correctly identified, including a sample with ancestry from a Taiwanese aborigine. The project focused on developing an accurate, affordable micro array-based forensic DNA analysis assay capable of rapid, simultaneous, SNP genotyping for human identification testing for three forensic sample types. These were characterized by low template single-donor samples; degraded samples; and mixtures that contained two or more DNA sources. 9 tables, 14 figures, and 39 references